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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:

Fluorine (F) 16 atoms
Magnesium (Mg) 4 atoms
Aluminium (Al) 4 atoms

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: Sun Dec 13 23:10:02 2020

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