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Nickel in PDB 7b2c: Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

Enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

All present enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon, PDB code: 7b2c 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) 35.90 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.791, 147.186, 113.376, 90, 107.2, 90
R / Rfree (%) 17.4 / 20.1

Other elements in 7b2c:

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 17 atoms
Xenon (Xe) 16 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 5 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon (pdb code 7b2c). 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 Gassed with Xenon, PDB code: 7b2c:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7b2c

Go back to Nickel Binding Sites List in 7b2c
Nickel binding site 1 out of 2 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


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 Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1201

b:14.0
occ:1.00
NI A:USN1201 0.0 14.0 1.0
NB A:USN1201 2.0 10.4 1.0
ND A:USN1201 2.1 10.8 1.0
NC A:USN1201 2.1 11.2 1.0
NA A:USN1201 2.1 9.9 1.0
S1 A:COM1205 2.4 8.9 1.0
C4B A:USN1201 2.9 9.4 1.0
C1A A:USN1201 3.0 10.5 1.0
C4D A:USN1201 3.0 10.1 1.0
C1C A:USN1201 3.0 9.3 1.0
C1D A:USN1201 3.1 10.8 1.0
SD D:MET181 3.1 15.6 1.0
C1B A:USN1201 3.1 9.4 1.0
C4C A:USN1201 3.1 11.3 1.0
C4A A:USN1201 3.2 9.5 1.0
CHC A:USN1201 3.3 10.1 1.0
CHA A:USN1201 3.3 10.7 1.0
CHB A:USN1201 3.3 9.6 1.0
C1 A:COM1205 3.4 8.9 1.0
CHD A:USN1201 3.5 11.0 1.0
N5B A:USN1201 3.8 7.9 1.0
CE D:MET181 3.9 14.2 1.0
OH B:TYR391 4.0 14.3 1.0
C2 A:COM1205 4.2 8.4 1.0
C3B A:USN1201 4.3 9.8 1.0
C3D A:USN1201 4.3 8.8 1.0
C2D A:USN1201 4.4 9.5 1.0
OH A:TYR376 4.4 14.5 1.0
C3C A:USN1201 4.4 9.1 1.0
C2C A:USN1201 4.4 8.5 1.0
C3A A:USN1201 4.4 8.4 1.0
C2B A:USN1201 4.4 8.8 1.0
C2A A:USN1201 4.5 9.6 1.0
CG D:MET181 4.8 16.5 1.0
CAB A:USN1201 4.9 11.1 1.0
CAA A:USN1201 4.9 7.8 1.0
C6B A:USN1201 4.9 8.5 1.0
CE2 A:TYR376 4.9 15.5 1.0

Nickel binding site 2 out of 2 in 7b2c

Go back to Nickel Binding Sites List in 7b2c
Nickel binding site 2 out of 2 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


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 Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni1101

b:11.6
occ:1.00
NI F:USN1101 0.0 11.6 1.0
NC F:USN1101 2.0 9.1 1.0
ND F:USN1101 2.0 8.8 1.0
NB F:USN1101 2.1 9.1 1.0
NA F:USN1101 2.1 8.6 1.0
S1 F:COM1102 2.5 11.3 1.0
C1A F:USN1101 2.9 8.5 1.0
C4B F:USN1101 2.9 9.7 1.0
C1C F:USN1101 2.9 9.3 1.0
C4D F:USN1101 3.0 8.7 1.0
C1D F:USN1101 3.0 9.5 1.0
C4C F:USN1101 3.1 9.8 1.0
SD A:MET181 3.2 12.1 1.0
C1B F:USN1101 3.2 9.9 1.0
CHA F:USN1101 3.2 8.5 1.0
C1 F:COM1102 3.2 8.8 1.0
CHC F:USN1101 3.3 9.4 1.0
C4A F:USN1101 3.4 8.6 1.0
CHD F:USN1101 3.5 9.7 1.0
CHB F:USN1101 3.6 8.9 1.0
N5B F:USN1101 3.9 9.6 1.0
CE A:MET181 4.0 9.5 1.0
OH E:TYR391 4.0 11.3 1.0
C2 F:COM1102 4.1 8.8 1.0
C2C F:USN1101 4.3 9.9 1.0
C3B F:USN1101 4.3 10.3 1.0
C2D F:USN1101 4.3 9.0 1.0
OH D:TYR376 4.3 8.7 1.0
C3D F:USN1101 4.3 8.7 1.0
C3C F:USN1101 4.3 9.4 1.0
C2A F:USN1101 4.4 8.5 1.0
C3A F:USN1101 4.5 8.6 1.0
C2B F:USN1101 4.5 9.3 1.0
CG A:MET181 4.8 13.6 1.0
CE2 D:TYR376 4.9 9.3 1.0
C2 F:USN1101 4.9 9.0 1.0
C7D F:USN1101 4.9 10.3 1.0
CAB F:USN1101 4.9 11.0 1.0
CAA F:USN1101 5.0 9.4 1.0
C6B F:USN1101 5.0 10.2 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: Sat Aug 21 17:30:59 2021

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