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Sodium in PDB 8e3u: Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation

Enzymatic activity of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation

All present enzymatic activity of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation:
1.18.6.1;

Protein crystallography data

The structure of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3u 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) 79.89 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.259, 129.009, 107.76, 90, 109.22, 90
R / Rfree (%) 20.2 / 25.3

Other elements in 8e3u:

The structure of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Molybdenum (Mo) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation (pdb code 8e3u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8e3u

Go back to Sodium Binding Sites List in 8e3u
Sodium binding site 1 out of 2 in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:25.5
occ:0.70
S3A A:UFF601 2.1 40.5 1.0
SG B:CYS95 2.2 29.0 1.0
FE8 A:UFF601 2.4 34.5 0.8
S1 A:UFF601 2.4 32.6 1.0
FE4 A:UFF601 2.5 31.6 0.7
S2A A:UFF601 2.8 34.8 1.0
HA B:CYS95 3.0 39.3 1.0
FE2 A:UFF601 3.0 33.4 0.7
FE3 A:UFF601 3.1 32.2 0.8
FE5 A:UFF601 3.1 32.5 0.5
H B:CYS95 3.2 31.3 1.0
N B:CYS95 3.3 26.1 1.0
CB B:CYS95 3.4 36.4 1.0
CA B:CYS95 3.4 32.8 1.0
S4B A:UFF601 3.5 29.4 1.0
HB3 B:CYS95 3.8 43.7 1.0
HD2 B:TYR98 4.1 29.6 1.0
C B:GLY94 4.1 32.3 1.0
SG A:CYS88 4.2 29.2 1.0
S4A A:UFF601 4.2 27.8 1.0
HB2 B:CYS95 4.2 43.7 1.0
HA3 B:GLY94 4.3 41.3 1.0
HG B:SER92 4.3 61.4 1.0
FE6 A:UFF601 4.5 30.9 1.0
S3B A:UFF601 4.5 31.3 1.0
OG B:SER92 4.7 51.2 1.0
SG A:CYS62 4.7 36.2 1.0
HB B:THR152 4.7 35.7 1.0
S2B A:UFF601 4.7 24.5 1.0
CA B:GLY94 4.8 34.4 1.0
HE2 B:TYR98 4.8 40.6 1.0
O B:GLY94 4.8 30.4 1.0
HB3 A:CYS88 4.9 38.5 1.0
C B:CYS95 4.9 33.6 1.0
HG A:CYS62 4.9 43.5 1.0
CD2 B:TYR98 4.9 24.7 1.0
FE7 A:UFF601 5.0 29.1 1.0
HA A:CYS88 5.0 44.9 1.0

Sodium binding site 2 out of 2 in 8e3u

Go back to Sodium Binding Sites List in 8e3u
Sodium binding site 2 out of 2 in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:27.6
occ:0.75
S3A C:UFF601 2.2 34.9 1.0
S1 C:UFF601 2.2 35.8 1.0
SG D:CYS95 2.3 28.6 1.0
FE8 C:UFF601 2.5 34.8 0.8
FE4 C:UFF601 2.5 34.2 0.8
S2A C:UFF601 2.6 32.7 1.0
FE2 C:UFF601 2.6 36.2 0.7
FE3 C:UFF601 2.8 32.5 0.8
HA D:CYS95 3.1 33.9 1.0
H D:CYS95 3.1 39.0 1.0
N D:CYS95 3.3 32.5 1.0
CB D:CYS95 3.4 34.7 1.0
CA D:CYS95 3.4 28.2 1.0
S4B C:UFF601 3.7 32.7 1.0
HB3 D:CYS95 3.8 41.6 1.0
S4A C:UFF601 3.8 28.8 1.0
FE5 C:UFF601 3.9 40.4 0.7
HG D:SER92 4.0 47.7 1.0
C D:GLY94 4.0 32.2 1.0
HA3 D:GLY94 4.1 38.1 1.0
HD2 D:TYR98 4.2 38.0 1.0
HB2 D:CYS95 4.3 41.6 1.0
O D:HOH708 4.3 29.4 1.0
OG D:SER92 4.4 39.8 1.0
FE6 C:UFF601 4.4 31.8 1.0
SG C:CYS88 4.4 35.7 1.0
SG C:CYS154 4.6 40.5 1.0
CA D:GLY94 4.6 31.8 1.0
HB D:THR152 4.6 39.5 1.0
SG C:CYS62 4.7 40.1 1.0
S3B C:UFF601 4.7 36.7 1.0
HB2 D:SER92 4.7 45.0 1.0
O D:GLY94 4.7 27.2 1.0
HA3 C:GLY185 4.9 52.9 1.0
C D:CYS95 4.9 34.0 1.0
HB3 C:CYS88 5.0 46.8 1.0

Reference:

H.L.Rutledge, M.J.Field, J.Rittle, M.T.Green, F.A.Tezcan. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J.Am.Chem.Soc. V. 144 22101 2022.
ISSN: ESSN 1520-5126
PubMed: 36445204
DOI: 10.1021/JACS.2C09480
Page generated: Wed Oct 9 11:37:52 2024

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