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Magnesium 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
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 2gj9

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402

b:13.7
occ:1.00
OG A:SER230 1.9 14.5 1.0
O3B A:GDP400 1.9 10.8 1.0
F3 A:ALF401 2.0 13.2 1.0
OG1 A:THR251 2.2 13.0 1.0
O A:HOH12 2.3 8.0 1.0
O A:HOH11 2.4 7.7 1.0
CB A:SER230 3.1 11.8 1.0
CB A:THR251 3.1 14.7 1.0
PB A:GDP400 3.2 9.8 1.0
O2B A:GDP400 3.5 9.0 1.0
AL A:ALF401 3.5 15.1 1.0
N A:SER230 3.6 11.2 1.0
F2 A:ALF401 3.8 13.4 1.0
CA A:SER230 3.9 10.7 1.0
OD2 A:ASP270 4.0 18.0 1.0
CG2 A:THR251 4.0 10.8 1.0
O2A A:GDP400 4.1 9.6 1.0
OD1 A:ASP270 4.1 12.6 1.0
N A:THR251 4.1 13.0 1.0
O A:HOH10 4.1 12.0 1.0
O1B A:GDP400 4.1 11.2 1.0
F1 A:ALF401 4.2 13.2 1.0
O3A A:GDP400 4.2 10.2 1.0
CA A:THR251 4.3 13.4 1.0
O A:HOH9 4.5 7.8 1.0
CG A:ASP270 4.5 15.2 1.0
O A:THR271 4.5 14.6 1.0
PA A:GDP400 4.5 12.8 1.0
O A:ILE243 4.6 12.6 1.0
C A:LYS229 4.7 12.2 1.0
O1A A:GDP400 4.8 10.1 1.0
CB A:LYS229 4.8 12.0 1.0
RB A:RB403 4.9 18.5 1.0
NZ A:LYS229 5.0 9.2 1.0

Magnesium binding site 2 out of 4 in 2gj9

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502

b:14.4
occ:1.00
OG B:SER230 2.0 18.5 1.0
O3B B:GDP500 2.1 19.4 1.0
F1 B:ALF501 2.1 12.6 1.0
OG1 B:THR251 2.2 16.0 1.0
CB B:SER230 3.0 17.4 1.0
CB B:THR251 3.3 14.9 1.0
PB B:GDP500 3.3 16.7 1.0
AL B:ALF501 3.6 15.2 1.0
O2B B:GDP500 3.6 18.2 1.0
F4 B:ALF501 3.7 13.9 1.0
N B:SER230 3.8 16.6 1.0
OD1 B:ASP270 3.9 18.7 1.0
CA B:SER230 3.9 17.9 1.0
O2A B:GDP500 4.0 14.2 1.0
N B:THR251 4.1 15.8 1.0
OD2 B:ASP270 4.2 20.6 1.0
CG2 B:THR251 4.2 16.0 1.0
O1B B:GDP500 4.2 15.0 1.0
CA B:THR251 4.3 15.6 1.0
F3 B:ALF501 4.3 16.1 1.0
O3A B:GDP500 4.3 20.7 1.0
O B:ILE243 4.5 16.6 1.0
CG B:ASP270 4.5 19.9 1.0
O B:HOH14 4.5 12.7 1.0
PA B:GDP500 4.5 14.0 1.0
O1A B:GDP500 4.6 16.4 1.0
O B:THR271 4.7 19.0 1.0
C B:LYS229 4.7 15.7 1.0
CB B:LYS229 4.7 15.9 1.0

Magnesium binding site 3 out of 4 in 2gj9

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602

b:15.6
occ:1.00
O3B C:GDP600 1.9 15.7 1.0
F3 C:ALF601 1.9 15.8 1.0
OG1 C:THR251 2.1 19.3 1.0
O C:HOH4 2.1 9.9 1.0
OG C:SER230 2.2 10.1 1.0
O C:HOH5 2.2 15.5 1.0
CB C:SER230 3.1 12.9 1.0
PB C:GDP600 3.1 11.4 1.0
O2B C:GDP600 3.2 13.1 1.0
CB C:THR251 3.2 14.9 1.0
AL C:ALF601 3.3 15.0 1.0
F2 C:ALF601 3.5 20.4 1.0
N C:SER230 3.8 12.5 1.0
CA C:SER230 4.0 12.1 1.0
N C:THR251 4.0 15.0 1.0
OD2 C:ASP270 4.1 15.3 1.0
O2A C:GDP600 4.1 8.9 1.0
O1B C:GDP600 4.1 12.7 1.0
F1 C:ALF601 4.2 15.6 1.0
CG2 C:THR251 4.2 17.6 1.0
O D:HOH3 4.2 14.0 1.0
CA C:THR251 4.2 15.5 1.0
O3A C:GDP600 4.3 11.2 1.0
OD1 C:ASP270 4.4 18.6 1.0
O C:HOH2 4.5 14.8 1.0
O1A C:GDP600 4.5 13.1 1.0
PA C:GDP600 4.5 13.8 1.0
O C:ILE243 4.6 17.6 1.0
CG C:ASP270 4.6 13.2 1.0
O C:THR271 4.7 15.2 1.0
C C:LYS229 4.8 12.2 1.0
RB C:RB603 4.9 19.7 1.0
CB C:LYS229 4.9 10.8 1.0

Magnesium binding site 4 out of 4 in 2gj9

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg702

b:23.6
occ:1.00
OG1 D:THR251 1.9 14.0 1.0
F1 D:ALF701 1.9 12.9 1.0
OG D:SER230 2.1 19.0 1.0
O3B D:GDP700 2.2 16.1 1.0
CB D:THR251 3.1 13.8 1.0
CB D:SER230 3.3 19.5 1.0
PB D:GDP700 3.3 20.6 1.0
O2B D:GDP700 3.4 19.6 1.0
AL D:ALF701 3.5 17.0 1.0
F4 D:ALF701 3.6 19.3 1.0
N D:SER230 3.9 19.4 1.0
N D:THR251 3.9 14.1 1.0
OD1 D:ASP270 4.1 21.1 1.0
CA D:THR251 4.1 13.1 1.0
CG2 D:THR251 4.1 13.1 1.0
CA D:SER230 4.1 20.2 1.0
O2A D:GDP700 4.2 15.6 1.0
F3 D:ALF701 4.2 16.7 1.0
O1B D:GDP700 4.3 18.9 1.0
OD2 D:ASP270 4.4 17.7 1.0
O3A D:GDP700 4.4 17.1 1.0
O D:ILE243 4.5 20.0 1.0
PA D:GDP700 4.6 20.2 1.0
O D:HOH7 4.6 14.0 1.0
O D:THR271 4.6 18.0 1.0
CG D:ASP270 4.6 18.5 1.0
O1A D:GDP700 4.7 17.1 1.0
RB D:RB703 4.9 25.3 1.0
C D:LYS229 4.9 19.2 1.0
CB D:THR250 4.9 14.0 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 Dec 14 07:24:34 2020

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