Nickel in PDB 5n28: Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form

All present enzymatic activity of Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form:
2.8.4.1;

The structure of Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form, PDB code: 5n28 was solved by T.Wagner, C.E.Wegner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.680, 81.160, 154.950, 90.00, 107.80, 90.00
R / Rfree (%)	19.3 / 20.4

The structure of Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form (pdb code 5n28). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form, PDB code: 5n28:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni604 b:88.5 occ:1.00 NI A:F43604 0.0 88.5 1.0 ND A:F43604 2.0 86.1 1.0 NC A:F43604 2.0 89.8 1.0 NB A:F43604 2.1 87.6 1.0 NA A:F43604 2.1 87.0 1.0 OE1 A:GLN150 2.1 0.8 1.0 S1 D:COM602 2.8 0.1 1.0 C4B A:F43604 2.9 87.8 1.0 C1A A:F43604 3.0 85.8 1.0 C1C A:F43604 3.0 90.5 1.0 C1D A:F43604 3.0 86.2 1.0 C4C A:F43604 3.0 89.3 1.0 C4D A:F43604 3.1 85.1 1.0 C1B A:F43604 3.1 86.1 1.0 C4A A:F43604 3.2 85.9 1.0 CD A:GLN150 3.2 0.3 1.0 CHA A:F43604 3.2 84.8 1.0 CHC A:F43604 3.3 89.3 1.0 CHB A:F43604 3.3 86.4 1.0 CHD A:F43604 3.4 87.3 1.0 C1 D:COM602 3.6 0.1 1.0 NE2 A:GLN150 3.7 0.6 1.0 N5B A:F43604 3.8 84.8 1.0 C3A A:F43604 4.2 86.4 1.0 C3B A:F43604 4.2 87.6 1.0 C2A A:F43604 4.3 85.2 1.0 C2D A:F43604 4.3 85.6 1.0 C3D A:F43604 4.3 84.6 1.0 C3C A:F43604 4.3 92.0 1.0 C2C A:F43604 4.3 92.0 1.0 C2B A:F43604 4.4 85.9 1.0 CG A:GLN150 4.4 0.2 1.0 C2 D:COM602 4.4 98.9 1.0 OH D:TYR335 4.5 87.7 1.0 OH E:TYR368 4.5 96.7 1.0 CAA A:F43604 4.6 88.0 1.0 CAB A:F43604 4.7 88.7 1.0 C7D A:F43604 4.9 86.3 1.0 C6B A:F43604 4.9 84.5 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Methyl-Coenzyme M Reductase III From Methanotorris Formicicus Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni601 b:66.7 occ:1.00 NI D:F43601 0.0 66.7 1.0 ND D:F43601 2.0 64.1 1.0 NC D:F43601 2.0 67.5 1.0 NB D:F43601 2.1 65.3 1.0 NA D:F43601 2.1 65.5 1.0 OE1 D:GLN150 2.1 88.8 1.0 S1 A:COM601 2.7 73.2 1.0 C4B D:F43601 2.9 65.9 1.0 C1A D:F43601 3.0 64.5 1.0 C1C D:F43601 3.0 67.7 1.0 C1D D:F43601 3.0 64.3 1.0 C4C D:F43601 3.0 67.0 1.0 C4D D:F43601 3.1 63.2 1.0 C1B D:F43601 3.1 64.4 1.0 C4A D:F43601 3.2 65.0 1.0 CHA D:F43601 3.2 62.7 1.0 CD D:GLN150 3.2 92.4 1.0 CHC D:F43601 3.3 66.6 1.0 CHB D:F43601 3.3 64.3 1.0 CHD D:F43601 3.4 65.4 1.0 C1 A:COM601 3.7 71.7 1.0 N5B D:F43601 3.8 63.4 1.0 NE2 D:GLN150 3.8 82.3 1.0 C3A D:F43601 4.2 66.2 1.0 C3B D:F43601 4.2 65.7 1.0 C2A D:F43601 4.3 65.6 1.0 C2 A:COM601 4.3 69.4 1.0 C3D D:F43601 4.3 64.1 1.0 C2D D:F43601 4.3 64.0 1.0 C3C D:F43601 4.3 67.9 1.0 OH B:TYR368 4.3 77.7 1.0 C2C D:F43601 4.3 68.4 1.0 C2B D:F43601 4.4 63.8 1.0 CG D:GLN150 4.5 79.5 1.0 OH A:TYR335 4.5 67.1 1.0 CAA D:F43601 4.6 68.6 1.0 CAB D:F43601 4.7 67.6 1.0 C7D D:F43601 4.9 65.0 1.0 C6B D:F43601 4.9 62.2 1.0

T.Wagner, C.E.Wegner, J.Kahnt, U.Ermler, S.Shima. Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase From Methanococcales and Methanobacteriales. J.Bacteriol. V. 199 2017.
ISSN: ESSN 1098-5530
PubMed: 28559298
DOI: 10.1128/JB.00197-17