Nickel in PDB 7sxm: Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

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

The structure of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 7sxm was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.63 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.956, 115.741, 123.4, 90, 92.53, 90
R / Rfree (%)	17.8 / 21.8

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

Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom
Xenon	(Xe)	8 atoms

The binding sites of Nickel atom in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis (pdb code 7sxm). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 7sxm:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:33.0 occ:1.00 NI A:F43601 0.0 33.0 1.0 NC A:F43601 2.1 32.0 1.0 ND A:F43601 2.1 30.9 1.0 NA A:F43601 2.1 29.7 1.0 NB A:F43601 2.1 32.8 1.0 OE1 A:GLN147 2.3 29.0 1.0 S1 D:COM602 2.5 35.6 1.0 C1A A:F43601 3.0 31.3 1.0 C4B A:F43601 3.0 33.2 1.0 C1C A:F43601 3.0 29.8 1.0 C1D A:F43601 3.1 27.3 1.0 C4D A:F43601 3.1 30.3 1.0 C4C A:F43601 3.1 31.0 1.0 C1B A:F43601 3.3 32.4 1.0 C4A A:F43601 3.3 31.4 1.0 CD A:GLN147 3.3 32.2 1.0 CHA A:F43601 3.3 29.0 1.0 CHC A:F43601 3.3 31.3 1.0 CHB A:F43601 3.5 30.9 1.0 CHD A:F43601 3.5 27.4 1.0 C1 D:COM602 3.5 37.1 1.0 NE2 A:GLN147 3.8 28.7 1.0 N5B A:F43601 3.9 33.3 1.0 C2 D:COM602 4.0 38.1 1.0 OH E:TYR367 4.2 32.6 0.6 OH D:TYR333 4.2 29.3 1.0 C3A A:F43601 4.3 31.2 1.0 C2A A:F43601 4.4 29.4 1.0 C3D A:F43601 4.4 28.7 1.0 C3B A:F43601 4.4 35.6 1.0 C2D A:F43601 4.4 27.7 1.0 C2C A:F43601 4.4 28.6 1.0 C3C A:F43601 4.5 31.4 1.0 C2B A:F43601 4.5 34.1 1.0 CG A:GLN147 4.7 31.0 1.0 CAA A:F43601 4.7 29.9 1.0 C7D A:F43601 5.0 29.3 1.0 CE2 D:TYR333 5.0 24.3 1.0 CAB A:F43601 5.0 32.8 1.0

Nickel binding site 2 out of 2 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni608 b:29.0 occ:1.00 NI A:F43608 0.0 29.0 1.0 NC A:F43608 2.0 26.6 1.0 ND A:F43608 2.1 26.5 1.0 NB A:F43608 2.1 26.7 1.0 NA A:F43608 2.1 27.4 1.0 OE1 D:GLN147 2.3 27.4 1.0 S1 A:COM605 2.5 31.2 1.0 C1A A:F43608 3.0 24.5 1.0 C1C A:F43608 3.0 27.3 1.0 C4B A:F43608 3.0 30.2 1.0 C1D A:F43608 3.1 25.0 1.0 C4D A:F43608 3.1 24.0 1.0 C4C A:F43608 3.1 23.3 1.0 C1B A:F43608 3.2 28.3 1.0 CD D:GLN147 3.3 31.0 1.0 C4A A:F43608 3.3 26.6 1.0 CHC A:F43608 3.3 27.9 1.0 CHA A:F43608 3.4 24.3 1.0 CHD A:F43608 3.5 24.7 1.0 CHB A:F43608 3.5 28.5 1.0 C1 A:COM605 3.5 36.2 1.0 NE2 D:GLN147 3.7 27.7 1.0 N5B A:F43608 3.9 28.7 1.0 C2 A:COM605 3.9 34.1 1.0 OH A:TYR333 4.1 25.3 1.0 OH B:TYR367 4.2 29.6 0.6 C3A A:F43608 4.4 25.2 1.0 C3D A:F43608 4.4 21.8 1.0 C2A A:F43608 4.4 25.3 1.0 C3B A:F43608 4.4 30.5 1.0 C2D A:F43608 4.4 24.2 1.0 C2C A:F43608 4.4 26.7 1.0 C3C A:F43608 4.4 25.3 1.0 C2B A:F43608 4.5 29.8 1.0 CG D:GLN147 4.6 30.4 1.0 CAA A:F43608 4.8 25.6 1.0 C7D A:F43608 5.0 26.1 1.0 CAB A:F43608 5.0 28.4 1.0 CZ A:TYR333 5.0 25.0 1.0 CE2 A:TYR333 5.0 21.8 1.0

C.J.Ohmer, M.Dasgupta, A.Patwardhan, I.Bogacz, C.Kaminsky, M.D.Doyle, P.Y.Chen, S.M.Keable, H.Makita, P.S.Simon, R.Massad, T.Fransson, R.Chatterjee, A.Bhowmick, D.W.Paley, N.W.Moriarty, A.S.Brewster, L.B.Gee, R.Alonso-Mori, F.Moss, F.D.Fuller, A.Batyuk, N.K.Sauter, U.Bergmann, C.L.Drennan, V.K.Yachandra, J.Yano, J.F.Kern, S.W.Ragsdale. Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase. J.Inorg.Biochem. V. 230 11768 2022.
ISSN: ISSN 0162-0134
PubMed: 35202981
DOI: 10.1016/J.JINORGBIO.2022.111768