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Magnesium in PDB 4fmb: Vira-RAB1 Complex Structure

Protein crystallography data

The structure of Vira-RAB1 Complex Structure, PDB code: 4fmb was solved by F.Shao, Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 186.118, 127.311, 107.325, 90.00, 94.45, 90.00
R / Rfree (%) 22.8 / 24.7

Other elements in 4fmb:

The structure of Vira-RAB1 Complex Structure also contains other interesting chemical elements:

Aluminium (Al) 3 atoms
Fluorine (F) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Vira-RAB1 Complex Structure (pdb code 4fmb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Vira-RAB1 Complex Structure, PDB code: 4fmb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4fmb

Go back to Magnesium Binding Sites List in 4fmb
Magnesium binding site 1 out of 3 in the Vira-RAB1 Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vira-RAB1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:0.2
occ:1.00
O B:HOH303 1.8 37.2 1.0
O B:HOH302 2.1 49.0 1.0
OG B:SER25 2.2 89.1 1.0
O3B B:GDP202 2.3 73.0 1.0
OG1 B:THR43 2.5 0.7 1.0
F2 B:AF3201 2.5 73.0 1.0
CB B:THR43 3.1 0.0 1.0
O1B B:GDP202 3.2 73.0 1.0
CB B:SER25 3.2 89.1 1.0
PB B:GDP202 3.4 73.0 1.0
AL B:AF3201 3.6 73.0 1.0
F1 B:AF3201 3.8 73.0 1.0
OD1 B:ASP66 4.0 0.4 1.0
N B:THR43 4.0 0.1 1.0
N B:SER25 4.1 91.3 1.0
CA B:THR43 4.1 0.0 1.0
CG2 B:THR43 4.2 0.5 1.0
O2A B:GDP202 4.2 73.0 1.0
CA B:SER25 4.3 91.8 1.0
O3A B:GDP202 4.4 73.0 1.0
OD2 B:ASP66 4.4 0.7 1.0
CG B:ASP66 4.4 0.7 1.0
O B:THR67 4.5 0.7 1.0
O2B B:GDP202 4.6 73.0 1.0
PA B:GDP202 4.7 73.0 1.0
NH1 A:ARG188 4.7 1.0 1.0
C B:SER42 4.9 0.4 1.0
O B:HOH301 5.0 73.0 1.0

Magnesium binding site 2 out of 3 in 4fmb

Go back to Magnesium Binding Sites List in 4fmb
Magnesium binding site 2 out of 3 in the Vira-RAB1 Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vira-RAB1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:0.2
occ:1.00
O D:HOH302 1.9 37.2 1.0
O D:HOH301 2.0 49.0 1.0
OG D:SER25 2.2 89.6 1.0
OG1 D:THR43 2.4 99.5 1.0
O3B D:GDP202 2.5 89.9 1.0
F2 D:AF3201 2.6 89.9 1.0
CB D:THR43 3.1 0.8 1.0
O1B D:GDP202 3.1 89.9 1.0
CB D:SER25 3.3 89.6 1.0
PB D:GDP202 3.4 89.9 1.0
AL D:AF3201 3.6 89.9 1.0
F1 D:AF3201 3.8 89.9 1.0
OD1 D:ASP66 3.9 0.2 1.0
N D:THR43 4.1 0.4 1.0
CG2 D:THR43 4.1 0.3 1.0
CA D:THR43 4.1 0.3 1.0
N D:SER25 4.1 92.1 1.0
CA D:SER25 4.3 92.5 1.0
CG D:ASP66 4.3 0.5 1.0
OD2 D:ASP66 4.3 0.5 1.0
O D:THR67 4.4 0.8 1.0
O3A D:GDP202 4.5 89.9 1.0
O2A D:GDP202 4.6 89.9 1.0
O2B D:GDP202 4.6 89.9 1.0
PA D:GDP202 4.9 89.9 1.0
C D:SER42 4.9 0.4 1.0
CB D:LYS24 5.0 90.7 1.0
NH1 C:ARG188 5.0 0.8 1.0

Magnesium binding site 3 out of 3 in 4fmb

Go back to Magnesium Binding Sites List in 4fmb
Magnesium binding site 3 out of 3 in the Vira-RAB1 Complex Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vira-RAB1 Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg203

b:0.2
occ:1.00
O F:HOH302 2.0 37.2 1.0
O F:HOH301 2.0 49.0 1.0
OG F:SER25 2.2 92.2 1.0
OG1 F:THR43 2.4 0.6 1.0
F2 F:AF3201 2.8 0.8 1.0
O3B F:GDP202 2.8 0.8 1.0
O1B F:GDP202 3.0 0.8 1.0
CB F:THR43 3.0 0.9 1.0
CB F:SER25 3.3 92.2 1.0
PB F:GDP202 3.5 0.8 1.0
AL F:AF3201 3.7 0.8 1.0
OD1 F:ASP66 3.9 0.5 1.0
N F:THR43 4.0 0.6 1.0
CG2 F:THR43 4.1 0.3 1.0
CA F:THR43 4.1 0.5 1.0
N F:SER25 4.2 95.7 1.0
F1 F:AF3201 4.2 0.8 1.0
O2A F:GDP202 4.3 0.8 1.0
CA F:SER25 4.3 96.1 1.0
CG F:ASP66 4.3 0.8 1.0
OD2 F:ASP66 4.3 0.8 1.0
O F:THR67 4.4 0.4 1.0
O3A F:GDP202 4.5 0.8 1.0
PA F:GDP202 4.7 0.8 1.0
O2B F:GDP202 4.7 0.8 1.0
O1A F:GDP202 4.8 0.8 1.0
NH1 E:ARG188 4.9 0.7 1.0
C F:SER42 4.9 0.1 1.0
F3 F:AF3201 4.9 0.8 1.0

Reference:

N.Dong, Y.Zhu, Q.Lu, L.Hu, Y.Zheng, F.Shao. Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase to RAB1 Inactivation to Counteract Host Defenses. Cell(Cambridge,Mass.) V. 150 1029 2012.
ISSN: ISSN 0092-8674
PubMed: 22939626
DOI: 10.1016/J.CELL.2012.06.050
Page generated: Mon Dec 14 15:30:04 2020

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