Rubidium in PDB 2gj9: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
Protein crystallography data
The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+, PDB code: 2gj9
was solved by
A.Scrima,
A.Wittinghofer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.240,
70.100,
90.210,
90.00,
95.76,
90.00
|
R / Rfree (%)
|
25 /
29.9
|
Other elements in 2gj9:
The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ also contains other interesting chemical elements:
Rubidium Binding Sites:
The binding sites of Rubidium atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
(pdb code 2gj9). This binding sites where shown within
5.0 Angstroms radius around Rubidium atom.
In total 4 binding sites of Rubidium where determined in the
Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+, PDB code: 2gj9:
Jump to Rubidium binding site number:
1;
2;
3;
4;
Rubidium binding site 1 out
of 4 in 2gj9
Go back to
Rubidium Binding Sites List in 2gj9
Rubidium binding site 1 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
Mono view
Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 1 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Rb403
b:18.5
occ:1.00
|
OD1
|
A:ASN226
|
2.6
|
12.9
|
1.0
|
F2
|
A:ALF401
|
2.8
|
13.4
|
1.0
|
O
|
A:ILE247
|
2.9
|
10.4
|
1.0
|
O2A
|
A:GDP400
|
2.9
|
9.6
|
1.0
|
O
|
A:THR245
|
3.0
|
10.7
|
1.0
|
O2B
|
A:GDP400
|
3.0
|
9.0
|
1.0
|
OG1
|
A:THR250
|
3.3
|
14.6
|
1.0
|
O
|
A:HOH11
|
3.6
|
7.7
|
1.0
|
O3A
|
A:GDP400
|
3.6
|
10.2
|
1.0
|
F4
|
A:ALF401
|
3.7
|
11.7
|
1.0
|
C5'
|
A:GDP400
|
3.7
|
13.8
|
1.0
|
C
|
A:ILE247
|
3.8
|
11.1
|
1.0
|
CB
|
A:THR250
|
3.8
|
12.0
|
1.0
|
AL
|
A:ALF401
|
3.8
|
15.1
|
1.0
|
PA
|
A:GDP400
|
3.8
|
12.8
|
1.0
|
CG
|
A:ASN226
|
3.9
|
13.8
|
1.0
|
PB
|
A:GDP400
|
3.9
|
9.8
|
1.0
|
C
|
A:THR245
|
4.0
|
11.5
|
1.0
|
OG1
|
A:THR245
|
4.2
|
14.0
|
1.0
|
O5'
|
A:GDP400
|
4.2
|
11.3
|
1.0
|
N
|
A:ILE247
|
4.3
|
12.4
|
1.0
|
N
|
A:THR245
|
4.3
|
12.7
|
1.0
|
CA
|
A:ASN226
|
4.4
|
13.1
|
1.0
|
CA
|
A:ALA248
|
4.4
|
11.4
|
1.0
|
N
|
A:ALA248
|
4.4
|
10.4
|
1.0
|
N
|
A:THR250
|
4.5
|
12.9
|
1.0
|
N
|
A:ASN226
|
4.5
|
12.3
|
1.0
|
F3
|
A:ALF401
|
4.5
|
13.2
|
1.0
|
O3B
|
A:GDP400
|
4.6
|
10.8
|
1.0
|
CA
|
A:ILE247
|
4.6
|
11.7
|
1.0
|
C
|
A:ASP246
|
4.7
|
13.2
|
1.0
|
CA
|
A:THR245
|
4.7
|
11.2
|
1.0
|
ND2
|
A:ASN226
|
4.7
|
15.4
|
1.0
|
CB
|
A:ASN226
|
4.8
|
13.4
|
1.0
|
CA
|
A:THR250
|
4.8
|
12.8
|
1.0
|
N
|
A:GLY249
|
4.8
|
12.8
|
1.0
|
C4'
|
A:GDP400
|
4.9
|
14.0
|
1.0
|
CG2
|
A:THR250
|
4.9
|
11.2
|
1.0
|
C
|
A:ALA248
|
4.9
|
12.7
|
1.0
|
MG
|
A:MG402
|
4.9
|
13.7
|
1.0
|
N
|
A:ASP246
|
5.0
|
12.0
|
1.0
|
|
Rubidium binding site 2 out
of 4 in 2gj9
Go back to
Rubidium Binding Sites List in 2gj9
Rubidium binding site 2 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
Mono view
Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 2 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Rb503
b:25.8
occ:1.00
|
F4
|
B:ALF501
|
2.6
|
13.9
|
1.0
|
OD1
|
B:ASN226
|
2.7
|
22.8
|
1.0
|
O
|
B:THR245
|
2.8
|
21.2
|
1.0
|
O
|
B:ILE247
|
2.9
|
19.8
|
1.0
|
O2B
|
B:GDP500
|
2.9
|
18.2
|
1.0
|
OG1
|
B:THR250
|
3.3
|
15.9
|
1.0
|
O2A
|
B:GDP500
|
3.4
|
14.2
|
1.0
|
O3A
|
B:GDP500
|
3.6
|
20.7
|
1.0
|
AL
|
B:ALF501
|
3.6
|
15.2
|
1.0
|
CB
|
B:THR250
|
3.7
|
15.2
|
1.0
|
F2
|
B:ALF501
|
3.7
|
16.6
|
1.0
|
C
|
B:ILE247
|
3.8
|
20.1
|
1.0
|
PB
|
B:GDP500
|
3.8
|
16.7
|
1.0
|
C
|
B:THR245
|
3.8
|
23.0
|
1.0
|
C5'
|
B:GDP500
|
3.9
|
15.8
|
1.0
|
CG
|
B:ASN226
|
3.9
|
19.7
|
1.0
|
PA
|
B:GDP500
|
4.0
|
14.0
|
1.0
|
O5'
|
B:GDP500
|
4.3
|
17.2
|
1.0
|
N
|
B:ILE247
|
4.3
|
22.6
|
1.0
|
OG1
|
B:THR245
|
4.3
|
20.5
|
1.0
|
N
|
B:THR250
|
4.4
|
17.0
|
1.0
|
N
|
B:THR245
|
4.4
|
22.0
|
1.0
|
F1
|
B:ALF501
|
4.4
|
12.6
|
1.0
|
N
|
B:ALA248
|
4.4
|
18.1
|
1.0
|
CA
|
B:ASN226
|
4.4
|
20.1
|
1.0
|
CA
|
B:ALA248
|
4.4
|
16.9
|
1.0
|
N
|
B:ASN226
|
4.5
|
18.9
|
1.0
|
C
|
B:ASP246
|
4.5
|
23.6
|
1.0
|
O3B
|
B:GDP500
|
4.6
|
19.4
|
1.0
|
CA
|
B:THR250
|
4.6
|
15.2
|
1.0
|
N
|
B:ASP246
|
4.7
|
22.8
|
1.0
|
CA
|
B:THR245
|
4.7
|
22.1
|
1.0
|
CA
|
B:ASP246
|
4.7
|
23.5
|
1.0
|
CA
|
B:ILE247
|
4.7
|
21.9
|
1.0
|
ND2
|
B:ASN226
|
4.8
|
18.4
|
1.0
|
CG2
|
B:THR250
|
4.8
|
11.5
|
1.0
|
N
|
B:GLY249
|
4.8
|
14.4
|
1.0
|
CB
|
B:ASN226
|
4.8
|
20.6
|
1.0
|
C
|
B:ALA248
|
5.0
|
15.9
|
1.0
|
O
|
B:ASP246
|
5.0
|
21.9
|
1.0
|
|
Rubidium binding site 3 out
of 4 in 2gj9
Go back to
Rubidium Binding Sites List in 2gj9
Rubidium binding site 3 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
Mono view
Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 3 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Rb603
b:19.7
occ:1.00
|
OD1
|
C:ASN226
|
2.6
|
15.1
|
1.0
|
O
|
C:THR245
|
2.6
|
15.6
|
1.0
|
F2
|
C:ALF601
|
2.7
|
20.4
|
1.0
|
O
|
C:ILE247
|
2.9
|
14.8
|
1.0
|
O2A
|
C:GDP600
|
2.9
|
8.9
|
1.0
|
O2B
|
C:GDP600
|
3.1
|
13.1
|
1.0
|
OG1
|
C:THR250
|
3.5
|
16.5
|
1.0
|
F4
|
C:ALF601
|
3.6
|
12.3
|
1.0
|
O
|
C:HOH4
|
3.6
|
9.9
|
1.0
|
O3A
|
C:GDP600
|
3.7
|
11.2
|
1.0
|
C
|
C:ILE247
|
3.7
|
16.7
|
1.0
|
AL
|
C:ALF601
|
3.7
|
15.0
|
1.0
|
CB
|
C:THR250
|
3.7
|
16.2
|
1.0
|
C
|
C:THR245
|
3.8
|
16.7
|
1.0
|
CG
|
C:ASN226
|
3.8
|
15.3
|
1.0
|
C5'
|
C:GDP600
|
3.8
|
11.4
|
1.0
|
PA
|
C:GDP600
|
3.8
|
13.8
|
1.0
|
PB
|
C:GDP600
|
4.0
|
11.4
|
1.0
|
N
|
C:ILE247
|
4.2
|
17.7
|
1.0
|
CA
|
C:ASN226
|
4.3
|
14.5
|
1.0
|
N
|
C:THR245
|
4.3
|
14.6
|
1.0
|
N
|
C:ALA248
|
4.4
|
15.9
|
1.0
|
O5'
|
C:GDP600
|
4.4
|
11.4
|
1.0
|
N
|
C:ASN226
|
4.4
|
15.4
|
1.0
|
N
|
C:THR250
|
4.4
|
15.9
|
1.0
|
CA
|
C:ALA248
|
4.4
|
16.4
|
1.0
|
C
|
C:ASP246
|
4.5
|
17.8
|
1.0
|
CA
|
C:ILE247
|
4.6
|
17.6
|
1.0
|
OG1
|
C:THR245
|
4.6
|
18.4
|
1.0
|
CA
|
C:THR245
|
4.6
|
16.2
|
1.0
|
O3B
|
C:GDP600
|
4.6
|
15.7
|
1.0
|
CB
|
C:ASN226
|
4.6
|
17.0
|
1.0
|
N
|
C:ASP246
|
4.7
|
17.4
|
1.0
|
ND2
|
C:ASN226
|
4.7
|
16.4
|
1.0
|
F3
|
C:ALF601
|
4.7
|
15.8
|
1.0
|
CA
|
C:ASP246
|
4.7
|
18.0
|
1.0
|
CG2
|
C:THR250
|
4.7
|
17.2
|
1.0
|
CA
|
C:THR250
|
4.7
|
16.4
|
1.0
|
N
|
C:GLY249
|
4.7
|
14.6
|
1.0
|
MG
|
C:MG602
|
4.9
|
15.6
|
1.0
|
C
|
C:ALA248
|
4.9
|
17.2
|
1.0
|
C4'
|
C:GDP600
|
4.9
|
14.6
|
1.0
|
|
Rubidium binding site 4 out
of 4 in 2gj9
Go back to
Rubidium Binding Sites List in 2gj9
Rubidium binding site 4 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+
Mono view
Stereo pair view
|
A full contact list of Rubidium with other atoms in the Rb binding
site number 4 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Rb703
b:25.3
occ:1.00
|
OD1
|
D:ASN226
|
2.5
|
21.4
|
1.0
|
O
|
D:ILE247
|
2.8
|
19.6
|
1.0
|
O
|
D:THR245
|
2.8
|
22.4
|
1.0
|
F4
|
D:ALF701
|
2.8
|
19.3
|
1.0
|
O2A
|
D:GDP700
|
3.0
|
15.6
|
1.0
|
O2B
|
D:GDP700
|
3.2
|
19.6
|
1.0
|
OG1
|
D:THR250
|
3.4
|
15.1
|
1.0
|
C
|
D:ILE247
|
3.7
|
20.1
|
1.0
|
CG
|
D:ASN226
|
3.7
|
21.7
|
1.0
|
O3A
|
D:GDP700
|
3.7
|
17.1
|
1.0
|
F2
|
D:ALF701
|
3.8
|
17.9
|
1.0
|
AL
|
D:ALF701
|
3.8
|
17.0
|
1.0
|
CB
|
D:THR250
|
3.8
|
14.0
|
1.0
|
C5'
|
D:GDP700
|
3.8
|
25.9
|
1.0
|
PA
|
D:GDP700
|
3.9
|
20.2
|
1.0
|
C
|
D:THR245
|
3.9
|
23.1
|
1.0
|
PB
|
D:GDP700
|
4.0
|
20.6
|
1.0
|
N
|
D:ILE247
|
4.3
|
21.9
|
1.0
|
OG1
|
D:THR245
|
4.3
|
23.0
|
1.0
|
CA
|
D:ASN226
|
4.3
|
20.1
|
1.0
|
N
|
D:ALA248
|
4.3
|
18.6
|
1.0
|
CA
|
D:ALA248
|
4.4
|
17.6
|
1.0
|
O5'
|
D:GDP700
|
4.4
|
20.7
|
1.0
|
N
|
D:THR245
|
4.4
|
22.1
|
1.0
|
N
|
D:THR250
|
4.4
|
14.8
|
1.0
|
N
|
D:ASN226
|
4.5
|
20.4
|
1.0
|
C
|
D:ASP246
|
4.5
|
23.0
|
1.0
|
CA
|
D:ILE247
|
4.6
|
20.5
|
1.0
|
F1
|
D:ALF701
|
4.6
|
12.9
|
1.0
|
ND2
|
D:ASN226
|
4.6
|
23.6
|
1.0
|
O3B
|
D:GDP700
|
4.6
|
16.1
|
1.0
|
CB
|
D:ASN226
|
4.6
|
21.3
|
1.0
|
CA
|
D:ASP246
|
4.7
|
23.6
|
1.0
|
N
|
D:ASP246
|
4.7
|
23.4
|
1.0
|
CG2
|
D:THR250
|
4.8
|
14.4
|
1.0
|
CA
|
D:THR250
|
4.8
|
14.5
|
1.0
|
CA
|
D:THR245
|
4.8
|
23.0
|
1.0
|
N
|
D:GLY249
|
4.8
|
15.2
|
1.0
|
C4'
|
D:GDP700
|
4.9
|
23.9
|
1.0
|
MG
|
D:MG702
|
4.9
|
23.6
|
1.0
|
C
|
D:ALA248
|
4.9
|
17.8
|
1.0
|
|
Reference:
A.Scrima,
A.Wittinghofer.
Dimerisation-Dependent Gtpase Reaction of Mnme: How Potassium Acts As Gtpase-Activating Element. Embo J. V. 25 2940 2006.
ISSN: ISSN 0261-4189
PubMed: 16763562
DOI: 10.1038/SJ.EMBOJ.7601171
Page generated: Thu Oct 10 11:58:13 2024
|