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Sodium in PDB 6o7s: Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State

Enzymatic activity of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State

All present enzymatic activity of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State, PDB code: 6o7s was solved by H.L.Rutledge, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.45 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.775, 128.050, 107.539, 90.00, 108.97, 90.00
R / Rfree (%) 17 / 20.8

Other elements in 6o7s:

The structure of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 28 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State (pdb code 6o7s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State, PDB code: 6o7s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6o7s

Go back to Sodium Binding Sites List in 6o7s
Sodium binding site 1 out of 2 in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:28.6
occ:1.00
SG A:CYS88 2.4 23.3 1.0
S4B B:LPJ601 2.5 21.8 1.0
S2B B:LPJ601 2.5 21.6 1.0
S1 B:LPJ601 2.5 26.0 1.0
FE4 B:LPJ601 2.7 25.2 1.0
FE8 B:LPJ601 2.7 26.6 0.9
H A:CYS88 2.7 24.6 1.0
FE7 B:LPJ601 2.9 17.5 1.0
FE6 B:LPJ601 3.0 20.4 1.0
N A:CYS88 3.1 20.4 1.0
HA A:CYS88 3.4 27.1 1.0
CB A:CYS88 3.5 24.4 1.0
HA3 A:GLY87 3.5 24.8 1.0
CA A:CYS88 3.6 22.5 1.0
S3A B:LPJ601 3.6 24.8 1.0
HB3 A:CYS88 3.9 29.4 1.0
C A:GLY87 3.9 22.0 1.0
S3B B:LPJ601 4.0 22.9 1.0
CA A:GLY87 4.1 20.6 1.0
HB2 A:CYS88 4.3 29.4 1.0
HE2 A:TYR91 4.3 23.3 1.0
H A:GLY87 4.4 27.6 1.0
FE2 B:LPJ601 4.5 27.2 1.0
HD2 A:TYR91 4.5 25.1 1.0
SG B:CYS95 4.6 22.2 1.0
N A:GLY87 4.6 23.0 1.0
HD2 B:TYR98 4.7 26.5 1.0
HB3 B:CYS95 4.8 27.2 1.0
HB3 A:GLU153 4.8 30.9 1.0
S4A B:LPJ601 4.9 24.8 1.0
HA B:CYS95 4.9 25.2 1.0
O A:GLY87 4.9 22.4 1.0
HB2 A:PRO85 5.0 27.6 1.0
HA2 A:GLY87 5.0 24.8 1.0
SG B:CYS70 5.0 19.8 1.0

Sodium binding site 2 out of 2 in 6o7s

Go back to Sodium Binding Sites List in 6o7s
Sodium binding site 2 out of 2 in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:24.7
occ:1.00
S2B D:LPJ601 2.4 21.2 1.0
S4B D:LPJ601 2.4 20.4 1.0
SG C:CYS88 2.5 20.2 1.0
FE8 D:LPJ601 2.5 26.0 0.9
S1 D:LPJ601 2.5 23.1 1.0
FE7 D:LPJ601 2.6 17.8 1.0
FE6 D:LPJ601 2.7 19.6 1.0
FE4 D:LPJ601 2.8 22.7 1.0
H C:CYS88 2.9 24.7 1.0
N C:CYS88 3.3 20.5 1.0
HA3 C:GLY87 3.5 22.4 1.0
CB C:CYS88 3.7 21.8 1.0
HA C:CYS88 3.7 22.2 1.0
S3B D:LPJ601 3.7 19.2 1.0
CA C:CYS88 3.8 18.5 1.0
S3A D:LPJ601 3.8 25.0 1.0
C C:GLY87 4.1 19.5 1.0
HB3 C:CYS88 4.1 26.3 1.0
CA C:GLY87 4.2 18.6 1.0
H C:GLY87 4.4 23.6 1.0
HE2 C:TYR91 4.4 20.7 1.0
HB2 C:CYS88 4.5 26.3 1.0
SG D:CYS95 4.5 23.8 1.0
FE2 D:LPJ601 4.6 23.4 1.0
N C:GLY87 4.6 19.6 1.0
HB3 D:CYS95 4.7 24.4 1.0
HD2 C:TYR91 4.8 21.9 1.0
SG D:CYS70 4.8 18.3 1.0
HB2 C:PRO85 4.8 24.7 1.0
HB3 C:GLU153 4.8 25.5 1.0
SG D:CYS153 4.8 23.1 1.0
HD2 C:PRO85 4.9 26.5 1.0
S4A D:LPJ601 4.9 21.0 1.0
HA D:CYS95 5.0 25.8 1.0
HA2 C:GLY87 5.0 22.4 1.0

Reference:

H.L.Rutledge, J.Rittle, L.M.Williamson, W.A.Xu, D.M.Gagnon, F.A.Tezcan. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J.Am.Chem.Soc. V. 141 10091 2019.
ISSN: ESSN 1520-5126
PubMed: 31146522
DOI: 10.1021/JACS.9B04555
Page generated: Tue Dec 15 12:41:12 2020

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