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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:

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

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: Wed Dec 16 02:06:45 2020

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