Magnesium in PDB 7aiz: Vanadium Nitrogenase Vfe Protein, High Co State

Enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State

All present enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State:
1.18.6.1;

Protein crystallography data

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

Resolution Low / High (Å) 48.39 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.521, 80.041, 107.21, 84, 72.48, 75.03
R / Rfree (%) 12.4 / 14.6

Other elements in 7aiz:

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

Magnesium binding site 1 out of 4 in 7aiz

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Magnesium binding site 1 out of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

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

b:10.5
occ:1.00
OE2 B:GLU70 2.0 11.4 1.0
O B:HOH668 2.0 11.6 1.0
OD2 E:ASP314 2.1 11.4 1.0
O E:HOH674 2.1 10.7 1.0
O B:HOH839 2.1 11.6 1.0
O E:HOH979 2.1 11.1 1.0
CD B:GLU70 3.2 11.0 1.0
CG E:ASP314 3.2 10.4 1.0
CB E:ASP314 3.9 10.1 1.0
CG B:GLU70 4.0 10.2 1.0
O B:LYS69 4.0 9.7 1.0
NZ A:LYS414 4.1 11.8 1.0
OE1 B:GLU70 4.1 13.3 1.0
NZ A:LYS413 4.1 11.8 1.0
O A:HOH887 4.1 14.4 1.0
OD1 E:ASP314 4.2 12.3 1.0
O B:HOH678 4.2 11.8 1.0
OD1 B:ASP222 4.2 12.3 1.0
OD2 E:ASP318 4.2 11.0 1.0
O B:SER223 4.2 11.1 1.0
OH B:TYR437 4.2 14.9 1.0
O B:PHE68 4.4 10.5 1.0
O E:ASP314 4.5 10.5 1.0
C E:ASP314 4.6 9.5 1.0
N B:SER223 4.8 11.2 1.0
C B:LYS69 4.8 9.4 1.0
CA E:ASP314 4.8 9.7 1.0
N E:ALA315 4.9 9.5 1.0
CB B:LYS69 5.0 11.4 1.0

Magnesium binding site 2 out of 4 in 7aiz

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Magnesium binding site 2 out of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

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

b:9.8
occ:1.00
OE2 E:GLU70 2.0 10.9 1.0
O E:HOH658 2.0 11.2 1.0
OD2 B:ASP314 2.0 11.3 1.0
O B:HOH677 2.1 10.1 1.0
O B:HOH947 2.1 11.1 1.0
O E:HOH858 2.1 10.7 1.0
CG B:ASP314 3.2 10.1 1.0
CD E:GLU70 3.2 10.3 1.0
CB B:ASP314 3.9 9.1 1.0
CG E:GLU70 4.0 9.3 1.0
NZ D:LYS414 4.0 11.3 1.0
O E:LYS69 4.0 9.1 1.0
NZ D:LYS413 4.1 11.0 1.0
OE1 E:GLU70 4.1 12.6 1.0
O D:HOH865 4.1 12.5 1.0
OD1 B:ASP314 4.2 11.5 1.0
OD2 B:ASP318 4.2 10.6 1.0
O E:HOH670 4.2 11.5 1.0
OD1 E:ASP222 4.2 11.6 1.0
OH E:TYR437 4.2 14.7 1.0
O E:SER223 4.2 10.1 1.0
O E:PHE68 4.5 10.1 1.0
O B:ASP314 4.6 9.8 1.0
C B:ASP314 4.6 9.2 1.0
C E:LYS69 4.8 8.6 1.0
N E:SER223 4.8 10.1 1.0
CA B:ASP314 4.8 9.7 1.0
N B:ALA315 4.9 9.0 1.0
CB E:LYS69 5.0 10.0 1.0

Magnesium binding site 3 out of 4 in 7aiz

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Magnesium binding site 3 out of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

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

b:15.1
occ:1.00
O C:HOH356 2.0 14.9 1.0
O C:HOH440 2.0 15.5 1.0
O A:HOH915 2.1 14.7 1.0
O C:HOH451 2.1 16.8 1.0
O C:HOH310 2.1 15.6 1.0
O C:HOH463 2.1 17.1 1.0
OE1 C:GLU14 4.0 16.2 1.0
O C:HOH448 4.2 18.4 1.0
O A:HOH805 4.2 14.9 1.0
O A:HOH755 4.2 18.4 1.0
O A:HOH856 4.2 15.2 1.0
O A:HOH1123 4.3 24.1 1.0
O C:HOH452 4.3 20.5 1.0
OE2 C:GLU15 4.4 17.3 1.0
O C:HOH436 4.4 16.8 1.0
O C:HOH453 4.5 25.6 1.0
O C:ALA11 4.6 13.9 1.0
CB C:ALA11 4.6 15.3 1.0
O A:ALA373 4.6 12.1 1.0
CA C:ALA11 4.7 14.3 1.0
CD C:GLU14 4.8 14.3 1.0
O A:HOH885 4.9 17.0 1.0
CB C:GLU14 4.9 13.0 1.0
CB C:GLU15 4.9 15.0 1.0
CG C:GLU14 4.9 14.1 1.0
O A:HOH892 4.9 20.2 1.0

Magnesium binding site 4 out of 4 in 7aiz

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Magnesium binding site 4 out of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State


Mono view


Stereo pair view

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

b:16.0
occ:1.00
O F:HOH310 2.0 15.4 1.0
O D:HOH904 2.1 16.2 1.0
O F:HOH429 2.1 18.4 1.0
O F:HOH332 2.1 15.7 1.0
O F:HOH414 2.1 16.4 1.0
O F:HOH435 2.1 18.1 1.0
OE1 F:GLU14 4.0 16.7 1.0
O D:HOH909 4.1 19.0 1.0
O F:HOH427 4.2 20.1 1.0
O D:HOH793 4.2 15.3 1.0
O D:HOH859 4.2 15.1 1.0
O D:HOH1148 4.2 25.6 1.0
OE2 F:GLU15 4.4 18.1 1.0
O F:HOH430 4.4 21.5 1.0
O F:HOH412 4.4 16.1 1.0
O F:HOH425 4.4 30.4 1.0
O F:ALA11 4.5 15.3 1.0
O D:ALA373 4.6 12.0 1.0
CB F:ALA11 4.7 17.8 1.0
CD F:GLU14 4.7 14.9 1.0
CA F:ALA11 4.8 15.5 1.0
CB F:GLU15 4.9 15.6 1.0
CG F:GLU14 4.9 14.0 1.0
O D:HOH874 4.9 16.8 1.0
O D:HOH835 4.9 20.3 1.0
CB F:GLU14 4.9 13.8 1.0

Reference:

M.Rohde, K.Laun, I.Zebger, S.T.Stripp, O.Einsle. Two Ligand-Binding Sites in Co-Reducing V Nitrogenase Reveal A General Mechanistic Principle Sci Adv 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABG4474
Page generated: Sun Jul 11 15:23:41 2021

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