Potassium in PDB 2gj8: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
Protein crystallography data
The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+, PDB code: 2gj8
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 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.540,
70.227,
91.300,
90.00,
95.51,
90.00
|
R / Rfree (%)
|
20.5 /
25.6
|
Other elements in 2gj8:
The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
(pdb code 2gj8). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+, PDB code: 2gj8:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 2gj8
Go back to
Potassium Binding Sites List in 2gj8
Potassium binding site 1 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:10.8
occ:1.00
|
F2
|
A:ALF601
|
2.6
|
12.0
|
1.0
|
OD1
|
A:ASN226
|
2.7
|
11.7
|
1.0
|
O
|
A:ILE247
|
2.8
|
10.8
|
1.0
|
O2A
|
A:GDP650
|
2.8
|
11.1
|
1.0
|
O
|
A:THR245
|
2.9
|
8.3
|
1.0
|
O2B
|
A:GDP650
|
3.0
|
9.0
|
1.0
|
OG1
|
A:THR250
|
3.3
|
13.1
|
1.0
|
O
|
A:HOH654
|
3.6
|
10.5
|
1.0
|
AL
|
A:ALF601
|
3.7
|
13.0
|
1.0
|
C
|
A:ILE247
|
3.7
|
10.7
|
1.0
|
CB
|
A:THR250
|
3.7
|
10.9
|
1.0
|
O3A
|
A:GDP650
|
3.7
|
7.9
|
1.0
|
PA
|
A:GDP650
|
3.8
|
8.4
|
1.0
|
F4
|
A:ALF601
|
3.8
|
13.2
|
1.0
|
C5'
|
A:GDP650
|
3.8
|
10.7
|
1.0
|
CG
|
A:ASN226
|
3.9
|
11.6
|
1.0
|
PB
|
A:GDP650
|
3.9
|
9.8
|
1.0
|
C
|
A:THR245
|
4.0
|
10.2
|
1.0
|
O5'
|
A:GDP650
|
4.3
|
9.2
|
1.0
|
N
|
A:THR245
|
4.3
|
9.3
|
1.0
|
N
|
A:ILE247
|
4.4
|
9.9
|
1.0
|
CA
|
A:ASN226
|
4.4
|
10.6
|
1.0
|
F3
|
A:ALF601
|
4.4
|
12.5
|
1.0
|
N
|
A:THR250
|
4.4
|
10.7
|
1.0
|
OG1
|
A:THR245
|
4.4
|
9.9
|
1.0
|
N
|
A:ALA248
|
4.4
|
12.4
|
1.0
|
CA
|
A:ALA248
|
4.5
|
12.1
|
1.0
|
O3B
|
A:GDP650
|
4.5
|
7.0
|
1.0
|
N
|
A:ASN226
|
4.6
|
10.7
|
1.0
|
CA
|
A:ILE247
|
4.6
|
11.7
|
1.0
|
C
|
A:ASP246
|
4.7
|
11.0
|
1.0
|
CA
|
A:THR250
|
4.7
|
11.7
|
1.0
|
ND2
|
A:ASN226
|
4.7
|
11.8
|
1.0
|
CB
|
A:ASN226
|
4.7
|
10.5
|
1.0
|
CA
|
A:THR245
|
4.7
|
9.3
|
1.0
|
N
|
A:GLY249
|
4.8
|
10.5
|
1.0
|
CG2
|
A:THR250
|
4.8
|
11.0
|
1.0
|
C
|
A:ALA248
|
4.9
|
11.8
|
1.0
|
N
|
A:ASP246
|
4.9
|
9.9
|
1.0
|
MG
|
A:MG602
|
5.0
|
11.7
|
1.0
|
|
Potassium binding site 2 out
of 4 in 2gj8
Go back to
Potassium Binding Sites List in 2gj8
Potassium binding site 2 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K613
b:16.5
occ:1.00
|
F4
|
B:ALF611
|
2.5
|
16.2
|
1.0
|
OD1
|
B:ASN226
|
2.7
|
16.7
|
1.0
|
O2A
|
B:GDP651
|
2.7
|
18.3
|
1.0
|
O
|
B:THR245
|
2.8
|
18.9
|
1.0
|
O
|
B:ILE247
|
2.9
|
17.5
|
1.0
|
O2B
|
B:GDP651
|
2.9
|
14.7
|
1.0
|
OG1
|
B:THR250
|
3.4
|
18.2
|
1.0
|
O3A
|
B:GDP651
|
3.6
|
16.3
|
1.0
|
AL
|
B:ALF611
|
3.6
|
15.1
|
1.0
|
F2
|
B:ALF611
|
3.6
|
14.9
|
1.0
|
CB
|
B:THR250
|
3.6
|
14.5
|
1.0
|
O
|
B:HOH655
|
3.7
|
11.8
|
1.0
|
PA
|
B:GDP651
|
3.7
|
16.5
|
1.0
|
C
|
B:ILE247
|
3.7
|
16.3
|
1.0
|
PB
|
B:GDP651
|
3.8
|
17.3
|
1.0
|
C5'
|
B:GDP651
|
3.8
|
13.6
|
1.0
|
CG
|
B:ASN226
|
3.8
|
17.2
|
1.0
|
C
|
B:THR245
|
3.9
|
20.2
|
1.0
|
N
|
B:ILE247
|
4.2
|
19.7
|
1.0
|
O5'
|
B:GDP651
|
4.3
|
17.8
|
1.0
|
CA
|
B:ASN226
|
4.3
|
16.0
|
1.0
|
N
|
B:THR250
|
4.4
|
14.1
|
1.0
|
F1
|
B:ALF611
|
4.4
|
17.0
|
1.0
|
N
|
B:THR245
|
4.4
|
19.4
|
1.0
|
N
|
B:ALA248
|
4.4
|
17.0
|
1.0
|
N
|
B:ASN226
|
4.4
|
14.6
|
1.0
|
CA
|
B:ALA248
|
4.5
|
15.6
|
1.0
|
OG1
|
B:THR245
|
4.5
|
19.9
|
1.0
|
O3B
|
B:GDP651
|
4.5
|
13.7
|
1.0
|
C
|
B:ASP246
|
4.6
|
20.9
|
1.0
|
CA
|
B:THR250
|
4.6
|
14.7
|
1.0
|
CA
|
B:ILE247
|
4.6
|
19.1
|
1.0
|
CB
|
B:ASN226
|
4.7
|
15.4
|
1.0
|
CG2
|
B:THR250
|
4.7
|
14.0
|
1.0
|
CA
|
B:THR245
|
4.7
|
19.8
|
1.0
|
ND2
|
B:ASN226
|
4.7
|
14.8
|
1.0
|
N
|
B:ASP246
|
4.8
|
20.4
|
1.0
|
MG
|
B:MG612
|
4.8
|
17.1
|
1.0
|
CA
|
B:ASP246
|
4.8
|
21.2
|
1.0
|
N
|
B:GLY249
|
4.8
|
13.3
|
1.0
|
C
|
B:ALA248
|
5.0
|
14.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 2gj8
Go back to
Potassium Binding Sites List in 2gj8
Potassium binding site 3 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K623
b:11.8
occ:1.00
|
F4
|
C:ALF621
|
2.6
|
12.7
|
1.0
|
OD1
|
C:ASN226
|
2.7
|
13.1
|
1.0
|
O
|
C:THR245
|
2.8
|
12.0
|
1.0
|
O
|
C:ILE247
|
2.9
|
13.5
|
1.0
|
O2A
|
C:GDP652
|
2.9
|
11.6
|
1.0
|
O3B
|
C:GDP652
|
3.0
|
15.8
|
1.0
|
OG1
|
C:THR250
|
3.3
|
13.7
|
1.0
|
AL
|
C:ALF621
|
3.6
|
11.4
|
1.0
|
F2
|
C:ALF621
|
3.7
|
11.0
|
1.0
|
CB
|
C:THR250
|
3.7
|
12.0
|
1.0
|
O3A
|
C:GDP652
|
3.7
|
10.4
|
1.0
|
C
|
C:ILE247
|
3.7
|
13.4
|
1.0
|
O
|
C:HOH654
|
3.8
|
10.6
|
1.0
|
PA
|
C:GDP652
|
3.8
|
10.8
|
1.0
|
CG
|
C:ASN226
|
3.9
|
14.7
|
1.0
|
PB
|
C:GDP652
|
3.9
|
11.0
|
1.0
|
C
|
C:THR245
|
3.9
|
12.5
|
1.0
|
C5'
|
C:GDP652
|
4.0
|
11.5
|
1.0
|
N
|
C:ILE247
|
4.2
|
14.0
|
1.0
|
F1
|
C:ALF621
|
4.3
|
11.7
|
1.0
|
O5'
|
C:GDP652
|
4.4
|
10.5
|
1.0
|
N
|
C:THR245
|
4.4
|
11.1
|
1.0
|
N
|
C:ALA248
|
4.4
|
13.1
|
1.0
|
N
|
C:THR250
|
4.4
|
12.9
|
1.0
|
CA
|
C:ASN226
|
4.4
|
11.6
|
1.0
|
OG1
|
C:THR245
|
4.4
|
11.0
|
1.0
|
CA
|
C:ALA248
|
4.5
|
13.0
|
1.0
|
N
|
C:ASN226
|
4.5
|
11.7
|
1.0
|
C
|
C:ASP246
|
4.5
|
14.2
|
1.0
|
O1B
|
C:GDP652
|
4.5
|
9.2
|
1.0
|
CA
|
C:ILE247
|
4.6
|
13.6
|
1.0
|
CA
|
C:THR250
|
4.7
|
11.9
|
1.0
|
CA
|
C:THR245
|
4.7
|
12.0
|
1.0
|
ND2
|
C:ASN226
|
4.7
|
13.9
|
1.0
|
N
|
C:GLY249
|
4.7
|
11.8
|
1.0
|
CG2
|
C:THR250
|
4.8
|
12.0
|
1.0
|
CB
|
C:ASN226
|
4.8
|
11.3
|
1.0
|
N
|
C:ASP246
|
4.8
|
12.8
|
1.0
|
CA
|
C:ASP246
|
4.8
|
14.0
|
1.0
|
C
|
C:ALA248
|
4.9
|
12.7
|
1.0
|
MG
|
C:MG622
|
5.0
|
9.9
|
1.0
|
|
Potassium binding site 4 out
of 4 in 2gj8
Go back to
Potassium Binding Sites List in 2gj8
Potassium binding site 4 out
of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K633
b:13.5
occ:1.00
|
F2
|
D:ALF631
|
2.6
|
13.1
|
1.0
|
OD1
|
D:ASN226
|
2.7
|
15.7
|
1.0
|
O
|
D:THR245
|
2.8
|
14.0
|
1.0
|
O
|
D:ILE247
|
2.8
|
14.5
|
1.0
|
O2B
|
D:GDP653
|
2.9
|
12.4
|
1.0
|
O2A
|
D:GDP653
|
2.9
|
12.6
|
1.0
|
OG1
|
D:THR250
|
3.3
|
13.2
|
1.0
|
AL
|
D:ALF631
|
3.6
|
13.6
|
1.0
|
O3A
|
D:GDP653
|
3.6
|
13.1
|
1.0
|
C
|
D:ILE247
|
3.7
|
14.2
|
1.0
|
O
|
D:HOH658
|
3.7
|
11.6
|
1.0
|
F4
|
D:ALF631
|
3.8
|
14.0
|
1.0
|
PA
|
D:GDP653
|
3.8
|
13.0
|
1.0
|
CB
|
D:THR250
|
3.8
|
11.3
|
1.0
|
CG
|
D:ASN226
|
3.8
|
16.3
|
1.0
|
C5'
|
D:GDP653
|
3.9
|
13.3
|
1.0
|
PB
|
D:GDP653
|
3.9
|
12.3
|
1.0
|
C
|
D:THR245
|
3.9
|
15.5
|
1.0
|
N
|
D:ILE247
|
4.2
|
13.8
|
1.0
|
F3
|
D:ALF631
|
4.3
|
12.4
|
1.0
|
O5'
|
D:GDP653
|
4.4
|
11.1
|
1.0
|
CA
|
D:ASN226
|
4.4
|
14.6
|
1.0
|
N
|
D:ALA248
|
4.4
|
13.6
|
1.0
|
N
|
D:THR250
|
4.4
|
11.4
|
1.0
|
N
|
D:THR245
|
4.4
|
14.5
|
1.0
|
N
|
D:ASN226
|
4.5
|
14.0
|
1.0
|
OG1
|
D:THR245
|
4.5
|
15.2
|
1.0
|
O3B
|
D:GDP653
|
4.5
|
12.0
|
1.0
|
CA
|
D:ALA248
|
4.5
|
13.9
|
1.0
|
C
|
D:ASP246
|
4.5
|
15.4
|
1.0
|
CA
|
D:ILE247
|
4.6
|
14.3
|
1.0
|
ND2
|
D:ASN226
|
4.7
|
17.4
|
1.0
|
CA
|
D:ASP246
|
4.7
|
16.5
|
1.0
|
CA
|
D:THR245
|
4.8
|
15.2
|
1.0
|
CB
|
D:ASN226
|
4.8
|
14.4
|
1.0
|
CA
|
D:THR250
|
4.8
|
11.6
|
1.0
|
N
|
D:GLY249
|
4.8
|
12.7
|
1.0
|
N
|
D:ASP246
|
4.8
|
15.4
|
1.0
|
CG2
|
D:THR250
|
4.8
|
9.5
|
1.0
|
MG
|
D:MG632
|
5.0
|
13.0
|
1.0
|
C4'
|
D:GDP653
|
5.0
|
16.0
|
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: Mon Aug 12 06:28:30 2024
|