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Nickel in PDB 7b2h: Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

Enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

All present enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h 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) 48.17 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.719, 116.386, 123.07, 90, 92.36, 90
R / Rfree (%) 17.7 / 20.4

Other elements in 7b2h:

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon also contains other interesting chemical elements:

Magnesium (Mg) 15 atoms
Xenon (Xe) 12 atoms
Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon (pdb code 7b2h). 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 7b2h

Go back to Nickel Binding Sites List in 7b2h
Nickel binding site 1 out of 2 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni608

b:42.3
occ:1.00
NI A:F43608 0.0 42.3 1.0
ND A:F43608 2.0 41.2 1.0
NC A:F43608 2.0 39.6 1.0
NB A:F43608 2.0 43.1 1.0
NA A:F43608 2.1 39.8 1.0
OE1 D:GLN147 2.4 35.6 1.0
C4B A:F43608 2.9 41.8 1.0
C1A A:F43608 2.9 37.9 1.0
S1 A:COM601 3.0 49.0 1.0
C1C A:F43608 3.0 38.3 1.0
C1D A:F43608 3.0 39.7 1.0
C4C A:F43608 3.0 38.0 1.0
C4D A:F43608 3.1 38.1 1.0
C1B A:F43608 3.1 41.1 1.0
C4A A:F43608 3.2 38.4 1.0
CHA A:F43608 3.2 36.7 1.0
CHC A:F43608 3.3 38.6 1.0
CHB A:F43608 3.3 38.7 1.0
CD D:GLN147 3.4 39.7 1.0
CHD A:F43608 3.4 38.3 1.0
NE2 D:GLN147 3.6 39.2 1.0
N5B A:F43608 3.7 38.5 1.0
C1 A:COM601 3.9 49.6 1.0
C2 A:COM601 4.0 52.4 1.0
C3A A:F43608 4.2 37.6 1.0
C3B A:F43608 4.2 42.3 1.0
OH B:TYR367 4.2 37.9 1.0
C2A A:F43608 4.3 37.5 1.0
C3D A:F43608 4.3 37.0 1.0
C2D A:F43608 4.3 38.4 1.0
OH A:TYR333 4.3 40.2 1.0
C3C A:F43608 4.3 38.1 1.0
C2C A:F43608 4.3 38.6 1.0
C2B A:F43608 4.3 41.4 1.0
CAA A:F43608 4.5 37.8 1.0
CG D:GLN147 4.7 38.1 1.0
CAB A:F43608 4.8 42.1 1.0
C7D A:F43608 4.8 38.2 1.0
C6B A:F43608 4.8 39.0 1.0

Nickel binding site 2 out of 2 in 7b2h

Go back to Nickel Binding Sites List in 7b2h
Nickel binding site 2 out of 2 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni601

b:41.1
occ:1.00
NI D:F43601 0.0 41.1 1.0
NC D:F43601 2.0 41.8 1.0
ND D:F43601 2.0 38.9 1.0
NB D:F43601 2.0 42.7 1.0
NA D:F43601 2.1 39.2 1.0
OE1 A:GLN147 2.2 40.8 1.0
C1A D:F43601 2.9 37.1 1.0
C4B D:F43601 2.9 41.8 1.0
C1C D:F43601 3.0 40.3 1.0
C1D D:F43601 3.0 36.8 1.0
C4C D:F43601 3.0 39.8 1.0
C4D D:F43601 3.1 34.6 1.0
S1 D:COM602 3.1 54.0 1.0
C1 D:COM602 3.1 54.0 1.0
C1B D:F43601 3.1 42.7 1.0
C4A D:F43601 3.2 39.5 1.0
CHA D:F43601 3.2 34.4 1.0
CD A:GLN147 3.3 43.8 1.0
CHC D:F43601 3.3 40.2 1.0
CHB D:F43601 3.3 41.0 1.0
CHD D:F43601 3.4 37.6 1.0
N5B D:F43601 3.7 43.9 1.0
NE2 A:GLN147 3.7 44.5 1.0
C3A D:F43601 4.2 38.9 1.0
C3B D:F43601 4.2 44.6 1.0
C2A D:F43601 4.3 38.1 1.0
OH E:TYR367 4.3 44.2 1.0
C3D D:F43601 4.3 34.2 1.0
C2D D:F43601 4.3 35.7 1.0
C2C D:F43601 4.3 40.6 1.0
C3C D:F43601 4.3 40.6 1.0
C2B D:F43601 4.3 44.8 1.0
OH D:TYR333 4.4 34.6 1.0
CAA D:F43601 4.5 38.6 1.0
C2 D:COM602 4.6 57.1 1.0
CG A:GLN147 4.6 45.5 1.0
CAB D:F43601 4.8 45.6 1.0
C7D D:F43601 4.8 37.7 1.0
O1S D:COM602 4.9 62.6 1.0
C6B D:F43601 4.9 45.5 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 17:30:58 2021

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