Rubidium in PDB 5aw6: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min
Protein crystallography data
The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min, PDB code: 5aw6
was solved by
H.Ogawa,
F.Cornelius,
A.Hirata,
C.Toyoshima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.98 /
2.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
220.606,
50.591,
163.163,
90.00,
104.60,
90.00
|
R / Rfree (%)
|
28 /
27.1
|
Other elements in 5aw6:
The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min also contains other interesting chemical elements:
Rubidium Binding Sites:
The binding sites of Rubidium atom in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min
(pdb code 5aw6). This binding sites where shown within
5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the
Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min, PDB code: 5aw6:
Jump to Rubidium binding site number:
1;
2;
3;
Rubidium binding site 1 out
of 3 in 5aw6
Go back to
Rubidium Binding Sites List in 5aw6
Rubidium binding site 1 out
of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_01.jpg) Mono view
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 1 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb2004
b:81.7
occ:0.76
|
K
|
A:K2003
|
0.0
|
81.7
|
0.2
|
OD2
|
A:ASP811
|
2.7
|
79.0
|
1.0
|
OG
|
A:SER782
|
2.7
|
78.5
|
1.0
|
O
|
A:THR779
|
2.7
|
74.2
|
1.0
|
O
|
A:HOH2101
|
2.7
|
83.9
|
1.0
|
OD1
|
A:ASN783
|
2.8
|
76.5
|
1.0
|
OD1
|
A:ASP811
|
3.2
|
80.0
|
1.0
|
CG
|
A:ASP811
|
3.2
|
78.5
|
1.0
|
N
|
A:ASN783
|
3.8
|
78.4
|
1.0
|
OE2
|
A:GLU786
|
3.8
|
83.8
|
1.0
|
C
|
A:SER782
|
3.8
|
78.0
|
1.0
|
CG
|
A:ASN783
|
3.8
|
77.7
|
1.0
|
CB
|
A:SER782
|
3.9
|
77.7
|
1.0
|
C
|
A:THR779
|
3.9
|
74.1
|
1.0
|
K
|
A:K2005
|
4.1
|
81.6
|
0.1
|
RB
|
A:RB2006
|
4.1
|
81.6
|
0.9
|
OE1
|
A:GLU786
|
4.2
|
84.5
|
1.0
|
O
|
A:SER782
|
4.2
|
78.3
|
1.0
|
CA
|
A:ASN783
|
4.2
|
78.5
|
1.0
|
CA
|
A:SER782
|
4.3
|
77.7
|
1.0
|
CG2
|
A:THR779
|
4.3
|
73.4
|
1.0
|
CD
|
A:GLU786
|
4.3
|
84.2
|
1.0
|
OD2
|
A:ASP815
|
4.4
|
78.7
|
1.0
|
CB
|
A:ASP811
|
4.5
|
77.7
|
1.0
|
N
|
A:SER782
|
4.5
|
77.2
|
1.0
|
CB
|
A:ASN783
|
4.6
|
78.4
|
1.0
|
CA
|
A:THR779
|
4.7
|
73.6
|
1.0
|
ND2
|
A:ASN783
|
4.7
|
77.1
|
1.0
|
N
|
A:LEU780
|
4.8
|
74.7
|
1.0
|
CB
|
A:PRO333
|
4.8
|
78.5
|
1.0
|
O
|
A:LEU780
|
4.8
|
75.6
|
1.0
|
CA
|
A:PRO333
|
4.9
|
78.3
|
1.0
|
CA
|
A:LEU780
|
4.9
|
75.2
|
1.0
|
C
|
A:LEU780
|
5.0
|
75.5
|
1.0
|
|
Rubidium binding site 2 out
of 3 in 5aw6
Go back to
Rubidium Binding Sites List in 5aw6
Rubidium binding site 2 out
of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_02.jpg) Mono view
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 2 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb2006
b:81.6
occ:0.95
|
K
|
A:K2005
|
0.0
|
81.6
|
0.1
|
O
|
A:VAL332
|
2.8
|
78.7
|
1.0
|
OD2
|
A:ASP811
|
2.9
|
79.0
|
1.0
|
OE2
|
A:GLU786
|
2.9
|
83.8
|
1.0
|
O
|
A:VAL329
|
2.9
|
82.6
|
1.0
|
O
|
A:ALA330
|
3.0
|
81.0
|
1.0
|
OD1
|
A:ASN783
|
3.0
|
76.5
|
1.0
|
OE1
|
A:GLU334
|
3.2
|
77.7
|
1.0
|
CG
|
A:ASP811
|
3.5
|
78.5
|
1.0
|
C
|
A:ALA330
|
3.6
|
81.3
|
1.0
|
OD1
|
A:ASP811
|
3.6
|
80.0
|
1.0
|
C
|
A:VAL332
|
3.7
|
78.8
|
1.0
|
CG2
|
A:ILE807
|
3.9
|
79.1
|
1.0
|
CG
|
A:ASN783
|
4.0
|
77.7
|
1.0
|
CA
|
A:ALA330
|
4.0
|
81.6
|
1.0
|
CD
|
A:GLU334
|
4.1
|
77.5
|
1.0
|
CD
|
A:GLU786
|
4.1
|
84.2
|
1.0
|
C
|
A:VAL329
|
4.1
|
83.0
|
1.0
|
K
|
A:K2003
|
4.1
|
81.7
|
0.2
|
RB
|
A:RB2004
|
4.1
|
81.7
|
0.8
|
CA
|
A:PRO333
|
4.1
|
78.3
|
1.0
|
OE2
|
A:GLU334
|
4.1
|
78.6
|
1.0
|
N
|
A:PRO333
|
4.2
|
78.6
|
1.0
|
N
|
A:ALA330
|
4.5
|
82.1
|
1.0
|
N
|
A:VAL332
|
4.5
|
79.4
|
1.0
|
ND2
|
A:ASN783
|
4.6
|
77.1
|
1.0
|
N
|
A:ASN331
|
4.6
|
80.7
|
1.0
|
CB
|
A:ASP811
|
4.6
|
77.7
|
1.0
|
N
|
A:GLU334
|
4.6
|
77.8
|
1.0
|
OE1
|
A:GLU786
|
4.6
|
84.5
|
1.0
|
C
|
A:ASN331
|
4.7
|
80.0
|
1.0
|
CA
|
A:VAL332
|
4.8
|
79.1
|
1.0
|
C
|
A:PRO333
|
4.9
|
78.1
|
1.0
|
CA
|
A:ASN783
|
4.9
|
78.5
|
1.0
|
CB
|
A:ASN783
|
5.0
|
78.4
|
1.0
|
|
Rubidium binding site 3 out
of 3 in 5aw6
Go back to
Rubidium Binding Sites List in 5aw6
Rubidium binding site 3 out
of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_03.jpg) Mono view
![](/pictures/RB/pdb/aw/5aw6-RB-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 3 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb2008
b:77.2
occ:0.73
|
K
|
A:K2007
|
0.0
|
77.2
|
0.3
|
O
|
A:ALA728
|
2.7
|
63.9
|
1.0
|
O
|
A:LYS726
|
2.8
|
64.9
|
1.0
|
OD2
|
A:ASP747
|
3.0
|
72.5
|
1.0
|
O
|
A:LEU725
|
3.0
|
62.6
|
1.0
|
C
|
A:LYS726
|
3.6
|
64.5
|
1.0
|
C
|
A:ALA728
|
3.8
|
63.9
|
1.0
|
CG
|
A:ASP747
|
3.8
|
70.9
|
1.0
|
OD1
|
A:ASP747
|
3.9
|
71.9
|
1.0
|
CA
|
A:LYS726
|
4.0
|
64.3
|
1.0
|
N
|
A:GLY731
|
4.0
|
62.2
|
1.0
|
C
|
A:LEU725
|
4.1
|
62.9
|
1.0
|
N
|
A:ALA728
|
4.3
|
64.0
|
1.0
|
O
|
A:ASP729
|
4.4
|
64.1
|
1.0
|
C
|
A:ASP729
|
4.4
|
63.8
|
1.0
|
CA
|
A:ALA728
|
4.4
|
64.1
|
1.0
|
N
|
A:LYS726
|
4.5
|
63.6
|
1.0
|
O
|
A:ALA745
|
4.5
|
69.3
|
1.0
|
CA
|
A:ILE730
|
4.5
|
63.2
|
1.0
|
N
|
A:ILE730
|
4.5
|
63.3
|
1.0
|
N
|
A:LYS727
|
4.6
|
64.3
|
1.0
|
C
|
A:LYS727
|
4.6
|
64.2
|
1.0
|
C
|
A:ILE730
|
4.6
|
62.7
|
1.0
|
CB
|
A:ALA728
|
4.6
|
63.8
|
1.0
|
CA
|
A:GLY731
|
4.8
|
62.0
|
1.0
|
N
|
A:ASP729
|
4.8
|
63.9
|
1.0
|
O
|
A:LYS727
|
5.0
|
64.2
|
1.0
|
CA
|
A:ASP729
|
5.0
|
64.0
|
1.0
|
|
Reference:
H.Ogawa,
F.Cornelius,
A.Hirata,
C.Toyoshima.
Sequential Substitution of K(+) Bound to Na(+),K(+)-Atpase Visualized By X-Ray Crystallography. Nat Commun V. 6 8004 2015.
ISSN: ESSN 2041-1723
PubMed: 26258479
DOI: 10.1038/NCOMMS9004
Page generated: Wed Dec 16 02:07:05 2020
|