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Nickel in PDB 7b1s: Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution

Enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution

All present enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution, PDB code: 7b1s was solved by T.Wagner, O.N.Lemaire, S.Engilberge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 0.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.736, 146.927, 113.128, 90, 106.98, 90
R / Rfree (%) 11.2 / 12.8

Other elements in 7b1s:

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 6 atoms
Manganese (Mn) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution (pdb code 7b1s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution, PDB code: 7b1s:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7b1s

Go back to Nickel Binding Sites List in 7b1s
Nickel binding site 1 out of 2 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:5.4
occ:1.00
NI C:USN301 0.0 5.4 1.0
ND C:USN301 2.1 5.0 1.0
NC C:USN301 2.1 5.5 1.0
NB C:USN301 2.1 4.8 1.0
NA C:USN301 2.1 4.8 1.0
S1 C:COM302 2.4 6.9 1.0
C4B C:USN301 3.0 5.6 1.0
C1C C:USN301 3.0 5.5 1.0
C1A C:USN301 3.0 5.0 1.0
C1D C:USN301 3.1 5.5 1.0
C4D C:USN301 3.1 5.4 1.0
C4C C:USN301 3.1 5.2 1.0
SD D:MET181 3.2 6.8 1.0
C1B C:USN301 3.2 5.0 1.0
C1 C:COM302 3.2 7.2 1.0
CHA C:USN301 3.3 5.5 1.0
C4A C:USN301 3.3 5.3 1.0
CHC C:USN301 3.3 5.6 1.0
CHB C:USN301 3.5 5.5 1.0
CHD C:USN301 3.5 5.6 1.0
N5B C:USN301 3.9 5.2 1.0
CE D:MET181 3.9 7.1 1.0
OH B:TYR391 4.1 6.7 1.0
C2 C:COM302 4.1 6.3 1.0
C3B C:USN301 4.3 5.6 1.0
OH A:TYR376 4.3 7.8 1.0
C3D C:USN301 4.3 5.6 1.0
C2C C:USN301 4.4 5.8 1.0
C2D C:USN301 4.4 5.7 1.0
C2A C:USN301 4.4 5.4 1.0
C3A C:USN301 4.4 5.5 1.0
C3C C:USN301 4.4 5.3 1.0
C2B C:USN301 4.5 5.5 1.0
CG D:MET181 4.8 6.5 1.0
CE2 A:TYR376 4.9 7.1 1.0
CAA C:USN301 4.9 6.6 1.0
CAB C:USN301 4.9 6.4 1.0
C7D C:USN301 5.0 6.0 1.0
C2 C:USN301 5.0 6.0 1.0

Nickel binding site 2 out of 2 in 7b1s

Go back to Nickel Binding Sites List in 7b1s
Nickel binding site 2 out of 2 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum at 0.994-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1101

b:4.1
occ:1.00
NI D:USN1101 0.0 4.1 1.0
NC D:USN1101 2.1 4.4 1.0
ND D:USN1101 2.1 4.2 1.0
NB D:USN1101 2.1 4.0 1.0
NA D:USN1101 2.1 3.6 1.0
S1 F:COM401 2.5 6.0 1.0
C4B D:USN1101 3.0 3.6 1.0
C1C D:USN1101 3.0 3.9 1.0
C1A D:USN1101 3.0 3.7 1.0
C1D D:USN1101 3.1 4.2 1.0
C4D D:USN1101 3.1 4.3 1.0
C4C D:USN1101 3.1 4.1 1.0
SD A:MET181 3.2 5.5 1.0
C1 F:COM401 3.2 6.0 1.0
C1B D:USN1101 3.3 4.0 1.0
C4A D:USN1101 3.3 4.0 1.0
CHA D:USN1101 3.3 4.3 1.0
CHC D:USN1101 3.3 3.8 1.0
CHB D:USN1101 3.5 4.0 1.0
CHD D:USN1101 3.5 4.1 1.0
N5B D:USN1101 3.9 4.3 1.0
CE A:MET181 3.9 5.5 1.0
OH E:TYR391 4.0 5.7 1.0
C2 F:COM401 4.1 5.6 1.0
C3B D:USN1101 4.3 4.2 1.0
OH D:TYR376 4.3 6.6 1.0
C2C D:USN1101 4.3 4.4 1.0
C3D D:USN1101 4.4 4.1 1.0
C2A D:USN1101 4.4 3.9 1.0
C2D D:USN1101 4.4 3.9 1.0
C3A D:USN1101 4.4 3.8 1.0
C3C D:USN1101 4.4 4.2 1.0
C2B D:USN1101 4.5 4.2 1.0
CG A:MET181 4.8 5.2 1.0
CE2 D:TYR376 4.9 5.2 1.0
CAA D:USN1101 4.9 4.5 1.0
CAB D:USN1101 4.9 4.9 1.0
C7D D:USN1101 5.0 4.4 1.0
C2 D:USN1101 5.0 4.9 1.0

Reference:

C.J.Hahn, O.N.Lemaire, J.Kahnt, S.Engilberge, G.Wegener, T.Wagner. Crystal Structure of A Key Enzyme For Anaerobic Ethane Activation. Science V. 373 118 2021.
ISSN: ESSN 1095-9203
PubMed: 34210888
DOI: 10.1126/SCIENCE.ABG1765
Page generated: Thu Oct 10 09:06:32 2024

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