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Magnesium in PDB 7ady: Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

Enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

All present enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein:
1.18.6.1;

Protein crystallography data

The structure of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7ady was solved by M.Rohde, K.Grunau, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.66 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.576, 80.027, 107.200, 83.99, 72.48, 75.03
R / Rfree (%) 12.1 / 14.1

Other elements in 7ady:

The structure of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein also contains other interesting chemical elements:

Iron (Fe) 32 atoms
Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein (pdb code 7ady). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7ady:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7ady

Go back to Magnesium Binding Sites List in 7ady
Magnesium binding site 1 out of 4 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:9.2
occ:1.00
 OE2 B:GLU70 2.0 10.3 1.0
O B:HOH692 2.0 10.2 1.0
OD2 E:ASP314 2.0 10.6 1.0
O B:HOH709 2.1 9.9 1.0
O B:HOH868 2.1 10.4 1.0
O E:HOH991 2.1 10.3 1.0
CG E:ASP314 3.2 9.5 1.0
CD B:GLU70 3.2 10.0 1.0
CB E:ASP314 3.9 8.4 1.0
CG B:GLU70 3.9 8.5 1.0
O B:LYS69 4.1 8.6 1.0
NZ A:LYS414 4.1 10.8 1.0
NZ A:LYS413 4.1 10.6 1.0
O A:HOH889 4.1 12.6 1.0
OE1 B:GLU70 4.1 12.5 1.0
OD1 E:ASP314 4.2 10.7 1.0
OD1 B:ASP222 4.2 11.1 1.0
OH B:TYR437 4.2 13.8 1.0
O B:HOH696 4.2 10.5 1.0
OD2 E:ASP318 4.2 9.6 1.0
O B:SER223 4.2 9.9 1.0
O B:PHE68 4.5 9.5 1.0
O E:ASP314 4.5 9.0 1.0
C E:ASP314 4.6 8.2 1.0
N B:SER223 4.8 9.6 1.0
C B:LYS69 4.8 8.0 1.0
CA E:ASP314 4.8 8.5 1.0
N E:ALA315 4.9 8.3 1.0
O B:HOH989 5.0 24.9 1.0
CB B:LYS69 5.0 10.0 1.0

Magnesium binding site 2 out of 4 in 7ady

Go back to Magnesium Binding Sites List in 7ady
Magnesium binding site 2 out of 4 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:8.2
occ:1.00
 OE2 E:GLU70 2.0 9.5 1.0
O E:HOH670 2.0 9.7 1.0
OD2 B:ASP314 2.1 9.9 1.0
O B:HOH677 2.1 9.0 1.0
O E:HOH865 2.1 9.4 1.0
O B:HOH972 2.1 9.8 1.0
CD E:GLU70 3.2 8.4 1.0
CG B:ASP314 3.2 8.9 1.0
CG E:GLU70 3.9 8.2 1.0
CB B:ASP314 3.9 8.3 1.0
O E:LYS69 4.0 7.5 1.0
NZ D:LYS414 4.1 9.6 1.0
NZ D:LYS413 4.1 9.7 1.0
O D:HOH885 4.1 11.3 1.0
OE1 E:GLU70 4.1 11.1 1.0
OD2 B:ASP318 4.2 8.9 1.0
O E:HOH684 4.2 10.2 1.0
OD1 B:ASP314 4.2 10.3 1.0
OD1 E:ASP222 4.2 10.6 1.0
OH E:TYR437 4.2 12.8 1.0
O E:SER223 4.2 8.9 1.0
O E:PHE68 4.5 8.2 1.0
C B:ASP314 4.6 7.8 1.0
O B:ASP314 4.6 8.6 1.0
N E:SER223 4.8 8.9 1.0
C E:LYS69 4.8 6.9 1.0
CA B:ASP314 4.9 8.5 1.0
N B:ALA315 4.9 7.6 1.0
CB E:LYS69 5.0 8.0 1.0
O E:HOH1018 5.0 23.1 1.0

Magnesium binding site 3 out of 4 in 7ady

Go back to Magnesium Binding Sites List in 7ady
Magnesium binding site 3 out of 4 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:15.5
occ:1.00
 O C:HOH377 2.0 14.4 1.0
O C:HOH319 2.0 15.3 1.0
O C:HOH450 2.1 18.0 1.0
O C:HOH443 2.1 15.9 1.0
O A:HOH909 2.1 14.8 1.0
O C:HOH465 2.1 17.9 1.0
OE1 C:GLU14 4.0 15.4 1.0
O C:HOH451 4.1 18.1 1.0
O A:HOH750 4.2 18.9 1.0
O A:HOH818 4.2 15.5 1.0
O A:HOH862 4.2 15.8 1.0
O A:HOH1140 4.2 25.5 1.0
O C:HOH456 4.3 22.7 1.0
OE2 C:GLU15 4.4 17.6 1.0
O C:HOH454 4.4 27.3 1.0
O C:HOH439 4.5 16.4 1.0
O C:ALA11 4.6 13.2 1.0
CB C:ALA11 4.6 15.0 1.0
O A:ALA373 4.7 11.5 1.0
CA C:ALA11 4.7 13.0 1.0
CD C:GLU14 4.7 13.7 1.0
O A:HOH941 4.9 17.7 1.0
CG C:GLU14 4.9 13.3 1.0
CB C:GLU14 4.9 12.2 1.0
O A:HOH882 4.9 21.3 1.0
CB C:GLU15 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in 7ady

Go back to Magnesium Binding Sites List in 7ady
Magnesium binding site 4 out of 4 in the Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:16.2
occ:1.00
 O F:HOH313 2.0 15.1 1.0
O F:HOH426 2.1 18.5 1.0
O F:HOH416 2.1 15.7 1.0
O F:HOH437 2.1 18.7 1.0
O D:HOH912 2.1 16.0 1.0
O F:HOH327 2.1 15.1 1.0
OE1 F:GLU14 3.9 16.3 1.0
O D:HOH896 4.2 20.3 1.0
O D:HOH803 4.2 15.8 1.0
O F:HOH427 4.2 21.0 1.0
O D:HOH879 4.2 14.8 1.0
O D:HOH1163 4.2 29.0 1.0
OE2 F:GLU15 4.4 18.7 1.0
O F:HOH428 4.4 22.0 1.0
O F:HOH430 4.4 32.9 1.0
O F:HOH415 4.5 16.6 1.0
O F:ALA11 4.6 13.6 1.0
O D:ALA373 4.6 10.6 1.0
CB F:ALA11 4.7 17.8 1.0
CD F:GLU14 4.7 13.7 1.0
CA F:ALA11 4.8 15.0 1.0
CG F:GLU14 4.9 14.0 1.0
CB F:GLU14 4.9 13.3 1.0
O F:HOH367 4.9 21.1 1.0
O D:HOH878 4.9 16.8 1.0
CB F:GLU15 4.9 16.0 1.0

Reference:

M.Rohde, K.Grunau, O.Einsle. Co Binding to the Fev Cofactor of Co-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32915491
DOI: 10.1002/ANIE.202010790
Page generated: Thu Aug 14 00:44:04 2025

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