Rubidium in PDB 1w5u: Gramicidin D From Bacillus Brevis (Ethanol Solvate)
Protein crystallography data
The structure of Gramicidin D From Bacillus Brevis (Ethanol Solvate), PDB code: 1w5u
was solved by
M.L.Glowka,
A.Olczak,
J.Bojarska,
M.Szczesio,
W.L.Duax,
B.M.Burkhart,
W.A.Pangborn,
D.A.Langs,
Z.Wawrzak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
20.00 /
1.14
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
30.060,
31.300,
51.691,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.1 /
21.5
|
Other elements in 1w5u:
The structure of Gramicidin D From Bacillus Brevis (Ethanol Solvate) also contains other interesting chemical elements:
Rubidium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Rubidium atom in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
(pdb code 1w5u). This binding sites where shown within
5.0 Angstroms radius around Rubidium atom.
In total 14 binding sites of Rubidium where determined in the
Gramicidin D From Bacillus Brevis (Ethanol Solvate), PDB code: 1w5u:
Jump to Rubidium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Rubidium binding site 1 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 1 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 1 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb1017
b:17.4
occ:0.26
|
RB
|
C:RB1021
|
1.2
|
9.9
|
0.3
|
|
RB
|
A:RB1018
|
1.5
|
21.3
|
0.2
|
|
O
|
A:HOH2002
|
2.1
|
14.1
|
0.3
|
|
O
|
A:HOH2004
|
2.6
|
19.2
|
0.2
|
|
O
|
B:DLE12
|
3.1
|
15.8
|
1.0
|
|
O
|
A:DLE4
|
3.4
|
22.6
|
1.0
|
|
O
|
A:ALA5
|
3.4
|
13.2
|
1.0
|
|
O
|
A:GLY2
|
3.5
|
21.9
|
1.0
|
|
N
|
A:DLE4
|
3.5
|
10.7
|
1.0
|
|
C
|
A:DLE4
|
3.6
|
12.1
|
1.0
|
|
O
|
B:TRP15
|
3.6
|
16.0
|
1.0
|
|
N
|
B:DLE14
|
3.7
|
9.9
|
1.0
|
|
O
|
B:HOH2007
|
3.7
|
16.8
|
0.7
|
|
C
|
A:ALA5
|
3.8
|
9.8
|
1.0
|
|
C
|
B:DLE14
|
3.9
|
10.7
|
1.0
|
|
O
|
B:DLE14
|
3.9
|
14.5
|
1.0
|
|
C
|
A:ALA3
|
3.9
|
11.4
|
1.0
|
|
C
|
B:DLE12
|
4.0
|
10.3
|
1.0
|
|
C
|
B:TRP15
|
4.0
|
13.2
|
1.0
|
|
CA
|
A:DLE4
|
4.1
|
11.0
|
1.0
|
|
N
|
B:TRP15
|
4.1
|
9.3
|
1.0
|
|
N
|
A:ALA5
|
4.1
|
11.0
|
1.0
|
|
C
|
B:TRP13
|
4.2
|
9.2
|
1.0
|
|
C
|
A:GLY2
|
4.2
|
12.2
|
1.0
|
|
CA
|
A:ALA3
|
4.2
|
11.5
|
1.0
|
|
N
|
A:DVA6
|
4.3
|
9.3
|
1.0
|
|
CA
|
B:DLE14
|
4.3
|
11.0
|
1.0
|
|
O
|
B:HOH2008
|
4.4
|
18.0
|
0.5
|
|
CA
|
B:TRP13
|
4.4
|
9.5
|
1.0
|
|
O
|
A:VAL7
|
4.4
|
12.3
|
1.0
|
|
CA
|
A:ALA5
|
4.5
|
11.8
|
1.0
|
|
N
|
B:TRP13
|
4.5
|
9.3
|
1.0
|
|
N
|
A:ALA3
|
4.5
|
11.1
|
1.0
|
|
N
|
B:ETA16
|
4.6
|
16.2
|
1.0
|
|
O
|
A:ALA3
|
4.6
|
14.3
|
1.0
|
|
CA
|
A:DVA6
|
4.6
|
9.6
|
1.0
|
|
CA
|
B:TRP15
|
4.6
|
11.4
|
1.0
|
|
N
|
B:DLE12
|
4.8
|
9.2
|
1.0
|
|
N
|
A:VAL7
|
4.8
|
8.4
|
1.0
|
|
CA
|
B:ETA16
|
4.9
|
19.7
|
1.0
|
|
Rubidium binding site 2 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 2 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 2 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb1018
b:21.3
occ:0.17
|
RB
|
A:RB1017
|
1.5
|
17.4
|
0.3
|
|
O
|
A:HOH2004
|
1.6
|
19.2
|
0.2
|
|
RB
|
C:RB1021
|
2.5
|
9.9
|
0.3
|
|
O
|
A:ALA5
|
3.3
|
13.2
|
1.0
|
|
C
|
B:TRP15
|
3.4
|
13.2
|
1.0
|
|
O
|
B:TRP15
|
3.4
|
16.0
|
1.0
|
|
O
|
B:DLE14
|
3.5
|
14.5
|
1.0
|
|
O
|
A:GLY2
|
3.5
|
21.9
|
1.0
|
|
N
|
B:ETA16
|
3.6
|
16.2
|
1.0
|
|
O
|
A:HOH2002
|
3.6
|
14.1
|
0.3
|
|
N
|
A:DLE4
|
3.9
|
10.7
|
1.0
|
|
C
|
B:DLE14
|
3.9
|
10.7
|
1.0
|
|
CA
|
B:ETA16
|
3.9
|
19.7
|
1.0
|
|
C
|
A:GLY2
|
3.9
|
12.2
|
1.0
|
|
C
|
A:ALA3
|
3.9
|
11.4
|
1.0
|
|
N
|
B:TRP15
|
4.1
|
9.3
|
1.0
|
|
C
|
A:ALA5
|
4.2
|
9.8
|
1.0
|
|
CA
|
B:TRP15
|
4.2
|
11.4
|
1.0
|
|
O
|
A:ALA3
|
4.2
|
14.3
|
1.0
|
|
C
|
A:DLE4
|
4.2
|
12.1
|
1.0
|
|
N
|
A:ALA3
|
4.2
|
11.1
|
1.0
|
|
O
|
B:DLE12
|
4.3
|
15.8
|
1.0
|
|
CA
|
A:DLE4
|
4.3
|
11.0
|
1.0
|
|
CA
|
A:ALA3
|
4.3
|
11.5
|
1.0
|
|
CB
|
B:ETA16
|
4.3
|
28.2
|
1.0
|
|
N
|
A:GLY2
|
4.3
|
11.6
|
1.0
|
|
N
|
B:DLE14
|
4.4
|
9.9
|
1.0
|
|
O
|
A:DLE4
|
4.4
|
22.6
|
1.0
|
|
N
|
A:ALA5
|
4.5
|
11.0
|
1.0
|
|
CA
|
A:GLY2
|
4.7
|
12.5
|
1.0
|
|
CA
|
B:DLE14
|
4.8
|
11.0
|
1.0
|
|
N
|
A:DVA6
|
4.9
|
9.3
|
1.0
|
|
O
|
A:HOH2001
|
5.0
|
39.7
|
1.0
|
|
O1
|
A:FVA1
|
5.0
|
18.2
|
1.0
|
|
CA
|
A:ALA5
|
5.0
|
11.8
|
1.0
|
|
Rubidium binding site 3 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 3 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 3 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Rb1016
b:26.5
occ:0.21
|
RB
|
C:RB1016
|
2.5
|
14.3
|
0.2
|
|
O
|
B:GLY2
|
3.3
|
10.5
|
1.0
|
|
N
|
A:ETA16
|
3.4
|
18.5
|
1.0
|
|
O
|
A:DLE14
|
3.7
|
13.2
|
1.0
|
|
C
|
A:TRP15
|
3.7
|
15.7
|
1.0
|
|
CB
|
A:ETA16
|
3.8
|
21.6
|
0.5
|
|
O1
|
B:FVA1
|
3.8
|
19.3
|
1.0
|
|
C
|
B:GLY2
|
3.8
|
8.8
|
1.0
|
|
CA
|
A:ETA16
|
3.9
|
20.9
|
0.5
|
|
O
|
B:ALA5
|
3.9
|
16.9
|
1.0
|
|
O
|
A:HOH2006
|
3.9
|
16.8
|
0.6
|
|
O
|
B:ALA3
|
4.0
|
10.9
|
1.0
|
|
C
|
B:ALA3
|
4.0
|
8.9
|
1.0
|
|
N
|
B:GLY2
|
4.1
|
9.8
|
1.0
|
|
CA
|
A:ETA16
|
4.1
|
21.0
|
0.5
|
|
C
|
A:DLE14
|
4.1
|
10.7
|
1.0
|
|
CA
|
A:TRP15
|
4.2
|
13.8
|
1.0
|
|
N
|
B:DLE4
|
4.2
|
8.9
|
1.0
|
|
O
|
A:TRP15
|
4.3
|
16.4
|
1.0
|
|
N
|
A:TRP15
|
4.3
|
11.2
|
1.0
|
|
N
|
B:ALA3
|
4.3
|
9.2
|
1.0
|
|
CA
|
B:GLY2
|
4.5
|
9.6
|
1.0
|
|
N
|
B:ALA5
|
4.6
|
10.0
|
1.0
|
|
CA
|
B:ALA3
|
4.6
|
9.3
|
1.0
|
|
C
|
B:DLE4
|
4.6
|
9.9
|
1.0
|
|
CA
|
B:DLE4
|
4.6
|
9.8
|
1.0
|
|
CN
|
B:FVA1
|
4.6
|
16.5
|
1.0
|
|
C
|
B:ALA5
|
4.6
|
11.8
|
1.0
|
|
O
|
B:HOH2002
|
4.7
|
16.1
|
0.6
|
|
C
|
B:FVA1
|
4.8
|
11.3
|
1.0
|
|
N
|
A:DLE14
|
4.8
|
8.7
|
1.0
|
|
O
|
B:HOH2001
|
4.9
|
40.3
|
0.6
|
|
CA
|
B:FVA1
|
4.9
|
11.6
|
1.0
|
|
O
|
A:ETA16
|
4.9
|
23.0
|
0.5
|
|
Rubidium binding site 4 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 4 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 4 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Rb1017
b:16.0
occ:0.19
|
O
|
B:HOH2005
|
0.9
|
15.5
|
0.3
|
|
O
|
B:HOH2003
|
1.4
|
17.9
|
0.6
|
|
O
|
A:HOH2005
|
1.9
|
17.7
|
0.5
|
|
RB
|
B:RB1018
|
2.2
|
12.0
|
0.2
|
|
O
|
B:HOH2002
|
2.7
|
16.1
|
0.6
|
|
O
|
B:HOH2004
|
3.1
|
14.2
|
0.6
|
|
N
|
B:DVA8
|
3.2
|
8.9
|
1.0
|
|
O
|
A:HOH2006
|
3.5
|
16.8
|
0.6
|
|
O
|
B:DVA6
|
3.5
|
12.2
|
1.0
|
|
O
|
A:DVA8
|
3.5
|
10.2
|
1.0
|
|
C
|
B:VAL7
|
3.6
|
9.8
|
1.0
|
|
O
|
A:DLE10
|
3.6
|
13.0
|
1.0
|
|
C
|
B:DVA8
|
3.6
|
8.1
|
1.0
|
|
O
|
B:DVA8
|
3.6
|
9.6
|
1.0
|
|
C
|
A:DLE10
|
3.8
|
9.2
|
1.0
|
|
CA
|
B:DVA8
|
3.8
|
9.3
|
1.0
|
|
CA
|
B:VAL7
|
3.9
|
10.7
|
1.0
|
|
C
|
B:DVA6
|
3.9
|
11.0
|
1.0
|
|
N
|
A:DLE10
|
3.9
|
9.2
|
1.0
|
|
O
|
B:TRP9
|
4.0
|
10.0
|
1.0
|
|
N
|
B:VAL7
|
4.0
|
10.6
|
1.0
|
|
N
|
B:TRP9
|
4.1
|
7.8
|
1.0
|
|
N
|
A:TRP11
|
4.1
|
8.0
|
1.0
|
|
C
|
A:TRP11
|
4.2
|
7.9
|
1.0
|
|
C
|
B:TRP9
|
4.2
|
8.2
|
1.0
|
|
N
|
A:DLE12
|
4.2
|
7.8
|
1.0
|
|
O
|
B:VAL7
|
4.3
|
11.5
|
1.0
|
|
O
|
A:TRP11
|
4.4
|
8.9
|
1.0
|
|
CA
|
A:DLE10
|
4.4
|
10.7
|
1.0
|
|
C
|
A:DVA8
|
4.4
|
8.3
|
1.0
|
|
CA
|
A:TRP11
|
4.5
|
7.8
|
1.0
|
|
C
|
A:TRP9
|
4.5
|
9.4
|
1.0
|
|
N
|
B:DVA6
|
4.7
|
10.0
|
1.0
|
|
CA
|
B:TRP9
|
4.7
|
8.0
|
1.0
|
|
O
|
A:TRP13
|
4.7
|
8.1
|
1.0
|
|
CA
|
A:DLE12
|
4.7
|
8.1
|
1.0
|
|
N
|
B:DLE10
|
4.8
|
7.6
|
1.0
|
|
N
|
A:TRP13
|
4.8
|
7.1
|
1.0
|
|
CA
|
A:TRP9
|
4.8
|
9.2
|
1.0
|
|
O
|
B:HOH2008
|
4.8
|
18.0
|
0.5
|
|
C
|
A:DLE12
|
4.8
|
7.9
|
1.0
|
|
CA
|
B:DVA6
|
4.9
|
11.5
|
1.0
|
|
N
|
A:TRP9
|
4.9
|
8.5
|
1.0
|
|
RB
|
C:RB1016
|
4.9
|
14.3
|
0.2
|
|
Rubidium binding site 5 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 5 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 5 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Rb1018
b:12.0
occ:0.20
|
O
|
B:HOH2004
|
1.2
|
14.2
|
0.6
|
|
O
|
B:HOH2005
|
1.5
|
15.5
|
0.3
|
|
RB
|
B:RB1017
|
2.2
|
16.0
|
0.2
|
|
O
|
B:HOH2008
|
2.8
|
18.0
|
0.5
|
|
O
|
B:HOH2003
|
3.3
|
17.9
|
0.6
|
|
O
|
B:HOH2007
|
3.5
|
16.8
|
0.7
|
|
O
|
B:DVA8
|
3.6
|
9.6
|
1.0
|
|
O
|
A:DVA8
|
3.6
|
10.2
|
1.0
|
|
O
|
B:TYR11
|
3.7
|
12.1
|
0.5
|
|
N
|
A:DLE10
|
3.7
|
9.2
|
1.0
|
|
N
|
A:TRP11
|
3.7
|
8.0
|
1.0
|
|
N
|
B:DLE10
|
3.7
|
7.6
|
1.0
|
|
N
|
B:TYR11
|
3.8
|
7.8
|
0.2
|
|
C
|
A:DLE10
|
3.8
|
9.2
|
1.0
|
|
O
|
A:HOH2005
|
3.8
|
17.7
|
0.5
|
|
N
|
B:TYR11
|
3.8
|
7.1
|
0.8
|
|
C
|
B:DLE10
|
3.8
|
8.1
|
1.0
|
|
O
|
A:TRP11
|
3.8
|
8.9
|
1.0
|
|
C
|
B:TRP9
|
3.8
|
8.2
|
1.0
|
|
O
|
B:TYR11
|
3.8
|
8.8
|
0.2
|
|
C
|
A:TRP9
|
3.9
|
9.4
|
1.0
|
|
CA
|
B:DLE10
|
4.0
|
9.2
|
1.0
|
|
CA
|
A:DLE10
|
4.0
|
10.7
|
1.0
|
|
C
|
A:DVA8
|
4.0
|
8.3
|
1.0
|
|
C
|
B:TYR11
|
4.0
|
9.5
|
0.5
|
|
O
|
B:TRP9
|
4.1
|
10.0
|
1.0
|
|
C
|
B:DVA8
|
4.1
|
8.1
|
1.0
|
|
C
|
A:TRP11
|
4.2
|
7.9
|
1.0
|
|
C
|
B:TYR11
|
4.2
|
8.7
|
0.2
|
|
O
|
A:DLE10
|
4.3
|
13.0
|
1.0
|
|
O
|
A:TRP9
|
4.3
|
11.9
|
0.5
|
|
O
|
A:TRP9
|
4.3
|
8.8
|
0.5
|
|
O
|
B:DLE10
|
4.3
|
11.8
|
1.0
|
|
N
|
A:TRP9
|
4.3
|
8.5
|
1.0
|
|
N
|
A:DVA8
|
4.4
|
8.6
|
1.0
|
|
CA
|
A:TRP9
|
4.5
|
9.2
|
1.0
|
|
CA
|
B:TYR11
|
4.5
|
8.2
|
0.8
|
|
N
|
B:DVA8
|
4.5
|
8.9
|
1.0
|
|
N
|
B:TRP9
|
4.5
|
7.8
|
1.0
|
|
CA
|
A:TRP11
|
4.5
|
7.8
|
1.0
|
|
CA
|
B:TRP9
|
4.6
|
8.0
|
1.0
|
|
CA
|
B:TYR11
|
4.6
|
8.0
|
0.2
|
|
N
|
B:DLE12
|
4.7
|
9.2
|
1.0
|
|
O
|
B:DVA6
|
4.7
|
12.2
|
1.0
|
|
O
|
B:HOH2002
|
4.8
|
16.1
|
0.6
|
|
N
|
A:DLE12
|
4.8
|
7.8
|
1.0
|
|
CA
|
A:DVA8
|
4.9
|
8.9
|
1.0
|
|
O
|
A:HOH2002
|
4.9
|
14.1
|
0.3
|
|
CA
|
B:DVA8
|
5.0
|
9.3
|
1.0
|
|
Rubidium binding site 6 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 6 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 6 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb1016
b:14.3
occ:0.21
|
O
|
A:HOH2006
|
1.6
|
16.8
|
0.6
|
|
O
|
B:HOH2002
|
2.3
|
16.1
|
0.6
|
|
RB
|
B:RB1016
|
2.5
|
26.5
|
0.2
|
|
O
|
B:GLY2
|
3.1
|
10.5
|
1.0
|
|
O
|
A:HOH2005
|
3.3
|
17.7
|
0.5
|
|
O
|
A:DLE12
|
3.4
|
11.3
|
1.0
|
|
N
|
A:DLE14
|
3.5
|
8.7
|
1.0
|
|
O
|
B:DLE4
|
3.6
|
11.7
|
1.0
|
|
C
|
B:DLE4
|
3.7
|
9.9
|
1.0
|
|
N
|
B:DLE4
|
3.7
|
8.9
|
1.0
|
|
O
|
B:HOH2003
|
3.8
|
17.9
|
0.6
|
|
C
|
A:DLE14
|
3.8
|
10.7
|
1.0
|
|
O
|
B:ALA5
|
3.9
|
16.9
|
1.0
|
|
C
|
B:ALA5
|
3.9
|
11.8
|
1.0
|
|
C
|
A:TRP13
|
4.0
|
7.8
|
1.0
|
|
O
|
A:DLE14
|
4.0
|
13.2
|
1.0
|
|
N
|
A:TRP15
|
4.0
|
11.2
|
1.0
|
|
C
|
A:DLE12
|
4.0
|
7.9
|
1.0
|
|
N
|
B:ALA5
|
4.0
|
10.0
|
1.0
|
|
C
|
B:ALA3
|
4.0
|
8.9
|
1.0
|
|
CA
|
A:DLE14
|
4.1
|
10.2
|
1.0
|
|
CA
|
A:TRP13
|
4.2
|
7.4
|
1.0
|
|
C
|
B:GLY2
|
4.2
|
8.8
|
1.0
|
|
N
|
B:DVA6
|
4.2
|
10.0
|
1.0
|
|
O
|
A:TRP15
|
4.2
|
16.4
|
1.0
|
|
CA
|
B:DLE4
|
4.2
|
9.8
|
1.0
|
|
C
|
A:TRP15
|
4.3
|
15.7
|
1.0
|
|
N
|
A:TRP13
|
4.3
|
7.1
|
1.0
|
|
CA
|
B:ALA3
|
4.4
|
9.3
|
1.0
|
|
CA
|
B:ALA5
|
4.4
|
10.6
|
1.0
|
|
CA
|
B:DVA6
|
4.6
|
11.5
|
1.0
|
|
CA
|
A:TRP15
|
4.7
|
13.8
|
1.0
|
|
N
|
B:ALA3
|
4.7
|
9.2
|
1.0
|
|
O
|
B:ALA3
|
4.7
|
10.9
|
1.0
|
|
N
|
A:ETA16
|
4.7
|
18.5
|
1.0
|
|
O
|
B:VAL7
|
4.7
|
11.5
|
1.0
|
|
N
|
A:DLE12
|
4.8
|
7.8
|
1.0
|
|
O
|
A:TRP13
|
4.8
|
8.1
|
1.0
|
|
N
|
B:VAL7
|
4.9
|
10.6
|
1.0
|
|
C
|
B:DVA6
|
4.9
|
11.0
|
1.0
|
|
RB
|
B:RB1017
|
4.9
|
16.0
|
0.2
|
|
Rubidium binding site 7 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 7 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 7 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb1018
b:13.3
occ:0.17
|
O
|
D:HOH2006
|
1.6
|
21.5
|
0.4
|
|
RB
|
D:RB1016
|
2.4
|
16.3
|
0.2
|
|
O
|
C:HOH2003
|
3.1
|
16.9
|
0.6
|
|
N
|
C:ETA16
|
3.2
|
17.1
|
1.0
|
|
O
|
D:ALA5
|
3.4
|
17.8
|
1.0
|
|
O
|
C:DLE14
|
3.5
|
18.6
|
1.0
|
|
C
|
C:TRP15
|
3.5
|
12.9
|
1.0
|
|
CA
|
C:ETA16
|
3.5
|
20.3
|
1.0
|
|
O
|
D:GLY2
|
3.6
|
12.4
|
1.0
|
|
O1
|
D:FVA1
|
3.7
|
21.2
|
1.0
|
|
C
|
C:DLE14
|
3.9
|
12.9
|
1.0
|
|
O
|
D:HOH2001
|
3.9
|
75.5
|
1.0
|
|
CA
|
C:TRP15
|
4.0
|
11.3
|
1.0
|
|
N
|
C:TRP15
|
4.0
|
11.3
|
1.0
|
|
O
|
C:TRP15
|
4.1
|
15.8
|
1.0
|
|
C
|
D:GLY2
|
4.1
|
9.8
|
1.0
|
|
C
|
D:ALA5
|
4.2
|
11.7
|
1.0
|
|
O
|
D:ALA3
|
4.3
|
13.0
|
1.0
|
|
C
|
D:ALA3
|
4.3
|
11.9
|
1.0
|
|
N
|
D:GLY2
|
4.3
|
11.2
|
1.0
|
|
O
|
D:HOH2002
|
4.3
|
16.4
|
0.7
|
|
N
|
D:DLE4
|
4.5
|
12.1
|
1.0
|
|
N
|
D:ALA5
|
4.5
|
12.9
|
1.0
|
|
CN
|
D:FVA1
|
4.6
|
19.1
|
1.0
|
|
C
|
D:DLE4
|
4.6
|
13.1
|
1.0
|
|
N
|
C:DLE14
|
4.7
|
10.2
|
1.0
|
|
N
|
D:ALA3
|
4.7
|
10.9
|
1.0
|
|
CA
|
D:GLY2
|
4.8
|
10.8
|
1.0
|
|
CA
|
D:DLE4
|
4.8
|
13.2
|
1.0
|
|
CA
|
C:DLE14
|
4.9
|
11.7
|
1.0
|
|
CB
|
C:ETA16
|
4.9
|
26.1
|
1.0
|
|
CA
|
D:ALA3
|
4.9
|
10.7
|
1.0
|
|
N
|
D:DVA6
|
4.9
|
10.7
|
1.0
|
|
Rubidium binding site 8 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 8 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 8 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb1019
b:18.6
occ:0.11
|
O
|
D:HOH2011
|
1.1
|
17.8
|
0.5
|
|
O
|
D:HOH2010
|
1.6
|
16.9
|
0.8
|
|
O
|
D:HOH2009
|
2.2
|
18.7
|
0.7
|
|
RB
|
C:RB1020
|
2.4
|
14.9
|
0.1
|
|
O
|
D:HOH2004
|
2.9
|
20.7
|
0.8
|
|
RB
|
C:RB1022
|
3.3
|
13.7
|
0.3
|
|
O
|
C:VAL7
|
3.4
|
10.2
|
1.0
|
|
N
|
D:DLE14
|
3.4
|
9.0
|
1.0
|
|
C
|
D:DLE14
|
3.4
|
10.7
|
1.0
|
|
CA
|
D:DLE14
|
3.5
|
10.3
|
1.0
|
|
N
|
C:VAL7
|
3.5
|
9.5
|
1.0
|
|
O
|
D:TRP15
|
3.5
|
14.3
|
1.0
|
|
N
|
D:TRP15
|
3.6
|
9.7
|
1.0
|
|
N
|
C:DVA6
|
3.7
|
10.9
|
1.0
|
|
C
|
D:TRP13
|
3.7
|
9.0
|
1.0
|
|
O
|
C:ALA5
|
3.7
|
15.6
|
1.0
|
|
C
|
C:DVA6
|
3.7
|
9.5
|
1.0
|
|
C
|
C:ALA5
|
3.7
|
12.5
|
1.0
|
|
CA
|
C:DVA6
|
3.8
|
10.9
|
1.0
|
|
C
|
C:VAL7
|
3.8
|
8.4
|
1.0
|
|
O
|
D:DLE14
|
3.9
|
12.4
|
1.0
|
|
O
|
D:TRP13
|
4.0
|
10.1
|
1.0
|
|
O
|
D:DLE12
|
4.0
|
11.8
|
1.0
|
|
C
|
D:TRP15
|
4.0
|
11.6
|
1.0
|
|
CA
|
C:VAL7
|
4.2
|
9.6
|
1.0
|
|
C
|
D:DLE12
|
4.3
|
9.3
|
1.0
|
|
CA
|
D:TRP13
|
4.4
|
9.5
|
1.0
|
|
CA
|
D:TRP15
|
4.4
|
10.4
|
1.0
|
|
O
|
D:HOH2007
|
4.4
|
15.2
|
0.5
|
|
O
|
C:DVA6
|
4.5
|
10.6
|
1.0
|
|
N
|
D:TRP13
|
4.5
|
9.6
|
1.0
|
|
CA
|
C:ALA5
|
4.5
|
14.6
|
1.0
|
|
O
|
C:GLY2
|
4.5
|
19.3
|
1.0
|
|
N
|
C:DVA8
|
4.6
|
7.8
|
1.0
|
|
O
|
D:DLE10
|
4.7
|
10.7
|
1.0
|
|
N
|
C:ALA5
|
4.7
|
14.1
|
1.0
|
|
O
|
C:DLE4
|
4.8
|
17.9
|
1.0
|
|
C
|
C:DLE4
|
4.8
|
12.3
|
1.0
|
|
N
|
D:ETA16
|
4.9
|
14.7
|
1.0
|
|
CA
|
C:DVA8
|
5.0
|
8.8
|
1.0
|
|
CB
|
D:DLE14
|
5.0
|
15.0
|
1.0
|
|
N
|
D:DLE12
|
5.0
|
9.4
|
1.0
|
|
Rubidium binding site 9 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 9 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 9 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb1020
b:14.9
occ:0.15
|
O
|
D:HOH2010
|
1.1
|
16.9
|
0.8
|
|
RB
|
C:RB1022
|
1.3
|
13.7
|
0.3
|
|
RB
|
C:RB1019
|
2.4
|
18.6
|
0.1
|
|
O
|
D:HOH2011
|
2.6
|
17.8
|
0.5
|
|
O
|
C:GLY2
|
3.2
|
19.3
|
1.0
|
|
O
|
C:ALA5
|
3.3
|
15.6
|
1.0
|
|
O
|
D:DLE14
|
3.4
|
12.4
|
1.0
|
|
N
|
C:DLE4
|
3.5
|
12.0
|
1.0
|
|
C
|
D:DLE14
|
3.7
|
10.7
|
1.0
|
|
C
|
C:ALA3
|
3.7
|
11.8
|
1.0
|
|
O
|
D:DLE12
|
3.7
|
11.8
|
1.0
|
|
N
|
D:DLE14
|
3.8
|
9.0
|
1.0
|
|
C
|
C:GLY2
|
3.9
|
11.3
|
1.0
|
|
C
|
C:ALA5
|
3.9
|
12.5
|
1.0
|
|
N
|
C:ALA5
|
3.9
|
14.1
|
1.0
|
|
C
|
C:DLE4
|
3.9
|
12.3
|
1.0
|
|
CA
|
C:DLE4
|
4.0
|
13.2
|
1.0
|
|
O
|
C:EOH1017
|
4.1
|
32.8
|
1.0
|
|
CA
|
C:ALA3
|
4.1
|
11.8
|
1.0
|
|
O
|
D:HOH2009
|
4.1
|
18.7
|
0.7
|
|
O
|
C:ALA3
|
4.1
|
17.5
|
1.0
|
|
N
|
D:TRP15
|
4.2
|
9.7
|
1.0
|
|
N
|
C:ALA3
|
4.2
|
12.0
|
1.0
|
|
C
|
D:TRP15
|
4.3
|
11.6
|
1.0
|
|
CA
|
D:DLE14
|
4.3
|
10.3
|
1.0
|
|
O
|
D:TRP15
|
4.3
|
14.3
|
1.0
|
|
O
|
C:DLE4
|
4.4
|
17.9
|
1.0
|
|
CA
|
C:ALA5
|
4.4
|
14.6
|
1.0
|
|
C
|
D:TRP13
|
4.5
|
9.0
|
1.0
|
|
N
|
D:ETA16
|
4.5
|
14.7
|
1.0
|
|
N
|
C:DVA6
|
4.6
|
10.9
|
1.0
|
|
N
|
C:GLY2
|
4.6
|
9.4
|
1.0
|
|
C
|
D:DLE12
|
4.6
|
9.3
|
1.0
|
|
CA
|
D:TRP13
|
4.7
|
9.5
|
1.0
|
|
CA
|
D:TRP15
|
4.7
|
10.4
|
1.0
|
|
CB
|
D:ETA16
|
4.7
|
26.7
|
1.0
|
|
CA
|
C:GLY2
|
4.9
|
11.2
|
1.0
|
|
CA
|
D:ETA16
|
4.9
|
22.8
|
1.0
|
|
CA
|
C:DVA6
|
4.9
|
10.9
|
1.0
|
|
O
|
D:HOH2004
|
4.9
|
20.7
|
0.8
|
|
Rubidium binding site 10 out
of 14 in 1w5u
Go back to
Rubidium Binding Sites List in 1w5u
Rubidium binding site 10 out
of 14 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)
 Mono view
 Stereo pair view
|
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 10 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb1021
b:9.9
occ:0.35
|
RB
|
A:RB1017
|
1.2
|
17.4
|
0.3
|
|
O
|
A:HOH2002
|
1.2
|
14.1
|
0.3
|
|
RB
|
A:RB1018
|
2.5
|
21.3
|
0.2
|
|
O
|
B:HOH2007
|
2.7
|
16.8
|
0.7
|
|
O
|
B:TRP15
|
3.2
|
16.0
|
1.0
|
|
O
|
B:DLE12
|
3.4
|
15.8
|
1.0
|
|
O
|
B:HOH2008
|
3.4
|
18.0
|
0.5
|
|
O
|
A:VAL7
|
3.4
|
12.3
|
1.0
|
|
O
|
A:ALA5
|
3.5
|
13.2
|
1.0
|
|
O
|
A:HOH2004
|
3.6
|
19.2
|
0.2
|
|
O
|
A:DLE4
|
3.6
|
22.6
|
1.0
|
|
N
|
B:DLE14
|
3.6
|
9.9
|
1.0
|
|
C
|
A:ALA5
|
3.7
|
9.8
|
1.0
|
|
C
|
B:DLE14
|
3.7
|
10.7
|
1.0
|
|
N
|
B:TRP15
|
3.8
|
9.3
|
1.0
|
|
N
|
A:VAL7
|
3.8
|
8.4
|
1.0
|
|
N
|
A:DVA6
|
3.8
|
9.3
|
1.0
|
|
C
|
B:TRP15
|
3.9
|
13.2
|
1.0
|
|
C
|
B:TRP13
|
4.0
|
9.2
|
1.0
|
|
CA
|
A:DVA6
|
4.0
|
9.6
|
1.0
|
|
C
|
B:DLE12
|
4.0
|
10.3
|
1.0
|
|
CA
|
B:DLE14
|
4.0
|
11.0
|
1.0
|
|
C
|
A:VAL7
|
4.1
|
9.7
|
1.0
|
|
C
|
A:DVA6
|
4.1
|
8.5
|
1.0
|
|
C
|
A:DLE4
|
4.1
|
12.1
|
1.0
|
|
O
|
B:DLE14
|
4.1
|
14.5
|
1.0
|
|
O
|
A:GLY2
|
4.2
|
21.9
|
1.0
|
|
N
|
B:TRP13
|
4.4
|
9.3
|
1.0
|
|
CA
|
B:TRP13
|
4.4
|
9.5
|
1.0
|
|
CA
|
B:TRP15
|
4.4
|
11.4
|
1.0
|
|
N
|
A:DLE4
|
4.4
|
10.7
|
1.0
|
|
CA
|
A:ALA5
|
4.5
|
11.8
|
1.0
|
|
O
|
B:TRP13
|
4.5
|
10.4
|
1.0
|
|
CA
|
A:VAL7
|
4.5
|
8.5
|
1.0
|
|
N
|
A:ALA5
|
4.6
|
11.0
|
1.0
|
|
N
|
B:DLE12
|
4.7
|
9.2
|
1.0
|
|
N
|
B:ETA16
|
4.7
|
16.2
|
1.0
|
|
O
|
B:DLE10
|
4.8
|
11.8
|
1.0
|
|
CA
|
A:DLE4
|
4.9
|
11.0
|
1.0
|
|
O
|
A:DVA6
|
4.9
|
9.8
|
1.0
|
|
N
|
A:DVA8
|
5.0
|
8.6
|
1.0
|
|
CA
|
B:DLE12
|
5.0
|
11.6
|
1.0
|
|
Reference:
M.L.Glowka,
A.Olczak,
J.Bojarska,
M.Szczesio,
W.L.Duax,
B.M.Burkhart,
W.A.Pangborn,
D.A.Langs,
Z.Wawrzak.
Structure of Gramicidin D-Rbcl Complex at Atomic Resolution From Low-Temperature Synchrotron Data: Interactions of Double-Stranded Gramicidin Channel Contents and Cations with Channel Wall Acta Crystallogr.,Sect.D V. 61 433 2005.
ISSN: ISSN 0907-4449
PubMed: 15805598
DOI: 10.1107/S0907444905000399
Page generated: Wed Dec 16 02:06:44 2020
|
