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Aluminium 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
Rubidium (Rb) 4 atoms
Magnesium (Mg) 4 atoms

Aluminium Binding Sites:

The binding sites of Aluminium 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 Aluminium atom.
In total 4 binding sites of Aluminium where determined in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and Rb+, PDB code: 2gj9:
Jump to Aluminium binding site number: 1; 2; 3; 4;

Aluminium binding site 1 out of 4 in 2gj9

Go back to Aluminium Binding Sites List in 2gj9
Aluminium 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 Aluminium with other atoms in the Al 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:Al401

b:15.1
occ:1.00
AL A:ALF401 0.0 15.1 1.0
F4 A:ALF401 1.7 11.7 1.0
F1 A:ALF401 1.8 13.2 1.0
F3 A:ALF401 1.8 13.2 1.0
F2 A:ALF401 1.8 13.4 1.0
O A:HOH9 2.0 7.8 1.0
O2B A:GDP400 2.0 9.0 1.0
PB A:GDP400 3.2 9.8 1.0
MG A:MG402 3.5 13.7 1.0
O3B A:GDP400 3.6 10.8 1.0
RB A:RB403 3.8 18.5 1.0
O1B A:GDP400 3.8 11.2 1.0
N A:ASN226 3.9 12.3 1.0
N A:GLY249 3.9 12.8 1.0
N A:THR250 4.0 12.9 1.0
N A:GLY273 4.1 13.5 1.0
CA A:PRO225 4.1 12.6 1.0
NZ A:LYS229 4.1 9.2 1.0
O A:HOH8 4.2 10.5 1.0
N A:THR251 4.2 13.0 1.0
O A:HOH11 4.2 7.7 1.0
O A:HOH12 4.3 8.0 1.0
OG1 A:THR251 4.4 13.0 1.0
O3A A:GDP400 4.4 10.2 1.0
CB A:THR251 4.4 14.7 1.0
CA A:GLY249 4.5 13.4 1.0
C A:PRO225 4.6 13.2 1.0
CB A:PRO225 4.6 13.5 1.0
O A:THR251 4.6 15.4 1.0
CA A:GLY273 4.7 14.2 1.0
C A:GLY249 4.7 14.4 1.0
CB A:THR250 4.8 12.0 1.0
CA A:THR250 4.8 12.8 1.0
CA A:ASN226 4.9 13.1 1.0
CA A:THR251 4.9 13.4 1.0
C A:ALA248 4.9 12.7 1.0
OD1 A:ASN226 5.0 12.9 1.0

Aluminium binding site 2 out of 4 in 2gj9

Go back to Aluminium Binding Sites List in 2gj9
Aluminium 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 Aluminium with other atoms in the Al 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:Al501

b:15.2
occ:1.00
AL B:ALF501 0.0 15.2 1.0
F2 B:ALF501 1.7 16.6 1.0
F1 B:ALF501 1.7 12.6 1.0
F4 B:ALF501 1.8 13.9 1.0
F3 B:ALF501 1.8 16.1 1.0
O B:HOH14 1.9 12.7 1.0
O2B B:GDP500 1.9 18.2 1.0
PB B:GDP500 3.1 16.7 1.0
O3B B:GDP500 3.6 19.4 1.0
MG B:MG502 3.6 14.4 1.0
RB B:RB503 3.6 25.8 1.0
O1B B:GDP500 3.9 15.0 1.0
N B:THR250 4.0 17.0 1.0
N B:ASN226 4.0 18.9 1.0
N B:GLY249 4.0 14.4 1.0
N B:THR251 4.1 15.8 1.0
NZ B:LYS229 4.1 12.0 1.0
N B:GLY273 4.1 14.5 1.0
CA B:PRO225 4.3 18.1 1.0
O B:HOH13 4.4 13.3 1.0
O3A B:GDP500 4.4 20.7 1.0
OG1 B:THR251 4.5 16.0 1.0
CA B:GLY249 4.5 16.4 1.0
CB B:THR251 4.6 14.9 1.0
CA B:GLY273 4.6 13.8 1.0
O B:THR251 4.6 13.8 1.0
C B:PRO225 4.7 19.3 1.0
C B:GLY249 4.7 16.8 1.0
CB B:THR250 4.7 15.2 1.0
CA B:THR250 4.7 15.2 1.0
CB B:PRO225 4.7 17.4 1.0
CE B:LYS229 4.8 10.9 1.0
CA B:THR251 4.8 15.6 1.0
C B:THR250 4.9 16.6 1.0
OD1 B:ASN226 4.9 22.8 1.0
CA B:ASN226 5.0 20.1 1.0

Aluminium binding site 3 out of 4 in 2gj9

Go back to Aluminium Binding Sites List in 2gj9
Aluminium 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 Aluminium with other atoms in the Al 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:Al601

b:15.0
occ:1.00
AL C:ALF601 0.0 15.0 1.0
F3 C:ALF601 1.8 15.8 1.0
F2 C:ALF601 1.8 20.4 1.0
F4 C:ALF601 1.8 12.3 1.0
F1 C:ALF601 1.8 15.6 1.0
O2B C:GDP600 1.9 13.1 1.0
O C:HOH2 2.0 14.8 1.0
PB C:GDP600 3.3 11.4 1.0
MG C:MG602 3.3 15.6 1.0
O3B C:GDP600 3.6 15.7 1.0
RB C:RB603 3.7 19.7 1.0
N C:GLY249 3.9 14.6 1.0
O C:HOH4 3.9 9.9 1.0
O1B C:GDP600 3.9 12.7 1.0
N C:ASN226 3.9 15.4 1.0
N C:THR251 4.0 15.0 1.0
N C:THR250 4.1 15.9 1.0
N C:GLY273 4.1 14.9 1.0
O C:HOH5 4.1 15.5 1.0
NZ C:LYS229 4.2 6.8 1.0
CA C:PRO225 4.2 15.9 1.0
OG1 C:THR251 4.3 19.3 1.0
O C:HOH1 4.3 11.9 1.0
CA C:GLY249 4.4 14.8 1.0
CB C:THR251 4.4 14.9 1.0
O C:THR251 4.5 15.5 1.0
O3A C:GDP600 4.5 11.2 1.0
C C:PRO225 4.6 14.8 1.0
CA C:GLY273 4.6 15.3 1.0
CB C:PRO225 4.6 14.4 1.0
C C:GLY249 4.7 15.9 1.0
CB C:THR250 4.7 16.2 1.0
CA C:THR251 4.8 15.5 1.0
CA C:THR250 4.8 16.4 1.0
C C:ALA248 4.9 17.2 1.0
C C:THR250 4.9 14.7 1.0
O2A C:GDP600 5.0 8.9 1.0
CA C:ASN226 5.0 14.5 1.0
O C:ILE247 5.0 14.8 1.0

Aluminium binding site 4 out of 4 in 2gj9

Go back to Aluminium Binding Sites List in 2gj9
Aluminium 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 Aluminium with other atoms in the Al 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:Al701

b:17.0
occ:1.00
AL D:ALF701 0.0 17.0 1.0
F2 D:ALF701 1.7 17.9 1.0
F4 D:ALF701 1.8 19.3 1.0
F3 D:ALF701 1.8 16.7 1.0
F1 D:ALF701 1.8 12.9 1.0
O D:HOH7 2.0 14.0 1.0
O2B D:GDP700 2.0 19.6 1.0
PB D:GDP700 3.3 20.6 1.0
MG D:MG702 3.5 23.6 1.0
O3B D:GDP700 3.7 16.1 1.0
RB D:RB703 3.8 25.3 1.0
N D:GLY249 3.9 15.2 1.0
N D:ASN226 4.0 20.4 1.0
O1B D:GDP700 4.1 18.9 1.0
N D:GLY273 4.1 17.8 1.0
N D:THR251 4.1 14.1 1.0
N D:THR250 4.1 14.8 1.0
NZ D:LYS229 4.2 15.6 1.0
OG1 D:THR251 4.3 14.0 1.0
CA D:PRO225 4.3 21.1 1.0
O D:HOH6 4.3 23.6 1.0
CA D:GLY249 4.4 15.7 1.0
CB D:THR251 4.4 13.8 1.0
O3A D:GDP700 4.5 17.1 1.0
O D:THR251 4.6 12.1 1.0
CB D:PRO225 4.6 21.4 1.0
CA D:GLY273 4.6 17.1 1.0
C D:GLY249 4.7 15.4 1.0
C D:PRO225 4.8 21.3 1.0
CB D:THR250 4.8 14.0 1.0
CE D:LYS229 4.8 22.7 1.0
CA D:THR251 4.8 13.1 1.0
CA D:THR250 4.9 14.5 1.0
C D:ALA248 4.9 17.8 1.0
CA D:ASN226 4.9 20.1 1.0
O D:ILE247 4.9 19.6 1.0
C D:THR250 5.0 13.9 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: Sat Dec 12 01:31:41 2020

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