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Magnesium in PDB 7adr: Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein

Enzymatic activity of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein

All present enzymatic activity of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein:
1.18.6.1;

Protein crystallography data

The structure of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7adr 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) 48.45 / 1.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.579, 79.934, 107.223, 84.11, 72.42, 75.19
R / Rfree (%) 10.2 / 11.7

Other elements in 7adr:

The structure of Co Bound As Bridging Ligand at 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein (pdb code 7adr). 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7adr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7adr

Go back to Magnesium Binding Sites List in 7adr
Magnesium binding site 1 out of 4 in the Co Bound As Bridging Ligand at 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:10.8
occ:1.00
 OE2 B:GLU70 2.0 12.1 1.0
O B:HOH662 2.0 12.1 1.0
OD2 E:ASP314 2.1 12.4 1.0
O E:HOH688 2.1 11.5 1.0
O B:HOH815 2.1 12.4 1.0
O E:HOH1001 2.1 12.2 1.0
CD B:GLU70 3.2 11.7 1.0
CG E:ASP314 3.2 11.2 1.0
CG B:GLU70 3.9 10.3 1.0
CB E:ASP314 3.9 10.3 1.0
NZ A:LYS414 4.0 12.6 1.0
O B:LYS69 4.1 10.0 1.0
NZ A:LYS413 4.1 12.4 1.0
OE1 B:GLU70 4.1 14.3 1.0
O A:HOH849 4.1 15.0 1.0
OD1 E:ASP314 4.2 12.7 1.0
O B:HOH667 4.2 12.7 1.0
OD2 E:ASP318 4.2 11.5 1.0
OH B:TYR437 4.2 14.6 1.0
OD1 B:ASP222 4.2 13.1 1.0
O B:SER223 4.2 11.7 1.0
O B:PHE68 4.4 10.9 1.0
O E:ASP314 4.6 10.3 1.0
C E:ASP314 4.6 9.6 1.0
N B:SER223 4.8 11.9 1.0
C B:LYS69 4.8 9.0 1.0
CA E:ASP314 4.9 9.8 1.0
N E:ALA315 4.9 9.5 1.0
O B:HOH989 5.0 26.0 1.0
CB B:LYS69 5.0 11.1 1.0

Magnesium binding site 2 out of 4 in 7adr

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Magnesium binding site 2 out of 4 in the Co Bound As Bridging Ligand at 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:9.7
occ:1.00
 OE2 E:GLU70 2.0 10.9 1.0
O E:HOH668 2.0 11.6 1.0
OD2 B:ASP314 2.1 11.4 1.0
O B:HOH660 2.1 10.2 1.0
O E:HOH843 2.1 10.9 1.0
O B:HOH981 2.1 11.7 1.0
CG B:ASP314 3.2 10.4 1.0
CD E:GLU70 3.2 9.8 1.0
CB B:ASP314 3.9 9.3 1.0
CG E:GLU70 3.9 8.9 1.0
O E:LYS69 4.0 8.6 1.0
NZ D:LYS414 4.0 11.4 1.0
NZ D:LYS413 4.1 11.1 1.0
OE1 E:GLU70 4.1 12.8 1.0
O D:HOH857 4.1 13.5 1.0
OD2 B:ASP318 4.1 10.6 1.0
O E:HOH696 4.2 12.0 1.0
OD1 B:ASP314 4.2 11.7 1.0
OD1 E:ASP222 4.2 11.9 1.0
OH E:TYR437 4.2 13.7 1.0
O E:SER223 4.2 10.6 1.0
O E:PHE68 4.4 9.6 1.0
O B:ASP314 4.6 9.7 1.0
C B:ASP314 4.6 8.7 1.0
C E:LYS69 4.8 8.3 1.0
N E:SER223 4.8 10.4 1.0
CA B:ASP314 4.9 9.3 1.0
N B:ALA315 4.9 8.9 1.0
O E:HOH1012 4.9 22.9 1.0
CB E:LYS69 5.0 9.9 1.0

Magnesium binding site 3 out of 4 in 7adr

Go back to Magnesium Binding Sites List in 7adr
Magnesium binding site 3 out of 4 in the Co Bound As Bridging Ligand at 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:15.9
occ:1.00
 O C:HOH313 2.0 16.3 1.0
O C:HOH446 2.0 16.3 1.0
O C:HOH452 2.0 18.6 1.0
O C:HOH355 2.1 15.4 1.0
O C:HOH466 2.1 17.9 1.0
O A:HOH884 2.1 15.3 1.0
OE1 C:GLU14 4.0 17.0 1.0
O A:HOH737 4.1 20.3 1.0
O C:HOH451 4.2 19.3 1.0
O A:HOH784 4.2 16.1 1.0
O A:HOH831 4.2 16.4 1.0
O A:HOH1136 4.2 26.3 1.0
O C:HOH457 4.3 22.1 1.0
OE2 C:GLU15 4.4 20.0 1.0
O C:HOH442 4.4 18.1 1.0
O C:HOH458 4.5 26.5 1.0
O C:ALA11 4.6 14.1 1.0
CB C:ALA11 4.6 15.8 1.0
O A:ALA373 4.6 12.2 1.0
CA C:ALA11 4.7 14.2 1.0
CD C:GLU14 4.8 15.5 1.0
O A:HOH891 4.9 18.9 1.0
CG C:GLU14 4.9 15.5 1.0
CB C:GLU14 4.9 13.9 1.0
O A:HOH896 4.9 21.0 1.0
CB C:GLU15 4.9 16.2 1.0

Magnesium binding site 4 out of 4 in 7adr

Go back to Magnesium Binding Sites List in 7adr
Magnesium binding site 4 out of 4 in the Co Bound As Bridging Ligand at 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 Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:15.6
occ:1.00
 O F:HOH314 2.0 15.6 1.0
O F:HOH331 2.0 15.6 1.0
O F:HOH440 2.0 18.6 1.0
O F:HOH419 2.1 15.9 1.0
O F:HOH429 2.1 17.7 1.0
O D:HOH876 2.1 15.7 1.0
OE1 F:GLU14 4.0 15.8 1.0
O D:HOH1156 4.1 30.8 1.0
O D:HOH890 4.2 20.1 1.0
O D:HOH816 4.2 15.4 1.0
O F:HOH428 4.2 20.9 1.0
O D:HOH800 4.2 15.0 1.0
OE2 F:GLU15 4.4 19.1 1.0
O F:HOH434 4.4 22.5 1.0
O F:HOH431 4.4 30.9 1.0
O F:HOH416 4.5 17.0 1.0
O F:ALA11 4.6 14.1 1.0
O D:ALA373 4.6 11.0 1.0
CB F:ALA11 4.7 17.3 1.0
CD F:GLU14 4.7 14.6 1.0
CA F:ALA11 4.8 15.2 1.0
CG F:GLU14 4.9 14.7 1.0
CB F:GLU14 4.9 13.7 1.0
O D:HOH864 4.9 21.4 1.0
O D:HOH920 4.9 17.8 1.0
CB F:GLU15 4.9 16.5 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: Wed Oct 2 09:14:28 2024

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