Nickel in PDB 3m2v: Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

All present enzymatic activity of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues:
2.8.4.1;

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2v was solved by P.E.Cedervall, M.Dey, S.W.Ragsdale, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.016, 118.260, 122.387, 90.00, 91.84, 90.00
R / Rfree (%)	15 / 19.5

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Zinc	(Zn)	1 atom

The binding sites of Nickel atom in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m2v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2v:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1 b:9.3 occ:1.00 NI A:F431 0.0 9.3 1.0 NC A:F431 2.1 9.8 1.0 ND A:F431 2.1 8.6 1.0 NA A:F431 2.1 5.7 1.0 NB A:F431 2.1 10.3 1.0 OE1 A:GLN147 2.3 11.9 1.0 S1 D:COM552 2.5 16.0 0.9 C1C A:F431 3.0 10.1 1.0 C4B A:F431 3.0 8.9 1.0 C1A A:F431 3.0 7.9 1.0 C1D A:F431 3.1 7.2 1.0 C4C A:F431 3.1 12.0 1.0 C4D A:F431 3.1 8.3 1.0 C4A A:F431 3.2 10.2 1.0 CD A:GLN147 3.3 12.3 1.0 C1B A:F431 3.3 7.2 1.0 CHC A:F431 3.3 8.3 1.0 CHA A:F431 3.3 7.1 1.0 C1 D:COM552 3.4 18.4 0.9 CHB A:F431 3.5 8.9 1.0 CHD A:F431 3.5 7.3 1.0 NE2 A:GLN147 3.6 10.8 1.0 N5B A:F431 3.9 7.1 1.0 OH E:TYR367 4.0 16.6 1.0 C2 D:COM552 4.1 14.5 0.9 OH D:TYR333 4.3 12.6 1.0 C3A A:F431 4.3 7.0 1.0 C3B A:F431 4.3 11.3 1.0 C2C A:F431 4.3 8.5 1.0 C3D A:F431 4.4 8.3 1.0 C2D A:F431 4.4 6.9 1.0 C3C A:F431 4.4 6.9 1.0 C2A A:F431 4.4 7.7 1.0 C2B A:F431 4.5 8.5 1.0 CG A:GLN147 4.6 12.0 1.0 CAA A:F431 4.7 7.7 1.0 CAB A:F431 5.0 14.3 1.0

Nickel binding site 2 out of 2 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni551 b:8.7 occ:1.00 NI D:F43551 0.0 8.7 1.0 ND D:F43551 2.0 7.1 1.0 NC D:F43551 2.1 8.2 1.0 NB D:F43551 2.1 8.9 1.0 NA D:F43551 2.1 8.5 1.0 OE1 D:GLN147 2.3 13.4 1.0 S1 A:COM553 2.4 14.5 0.9 C1C D:F43551 3.0 7.6 1.0 C1A D:F43551 3.0 4.5 1.0 C4B D:F43551 3.0 6.9 1.0 C1D D:F43551 3.1 6.5 1.0 C4D D:F43551 3.1 7.7 1.0 C4C D:F43551 3.1 7.6 1.0 CHA D:F43551 3.2 4.8 1.0 C4A D:F43551 3.3 5.1 1.0 C1 A:COM553 3.3 15.6 0.9 C1B D:F43551 3.3 7.2 1.0 CHC D:F43551 3.3 7.1 1.0 CD D:GLN147 3.3 9.6 1.0 CHB D:F43551 3.5 4.3 1.0 CHD D:F43551 3.6 3.8 1.0 NE2 D:GLN147 3.7 8.2 1.0 N5B D:F43551 3.9 7.5 1.0 C2 A:COM553 4.1 12.6 0.9 OH B:TYR367 4.2 14.9 1.0 OH A:TYR333 4.2 8.5 1.0 C3D D:F43551 4.3 5.0 1.0 C3A D:F43551 4.3 7.5 1.0 C3B D:F43551 4.3 7.7 1.0 C2C D:F43551 4.3 8.4 1.0 C2D D:F43551 4.4 5.2 1.0 C2A D:F43551 4.4 5.3 1.0 C3C D:F43551 4.4 8.1 1.0 C2B D:F43551 4.5 9.1 1.0 CAA D:F43551 4.7 8.4 1.0 CG D:GLN147 4.7 10.4 1.0 CAB D:F43551 5.0 8.1 1.0 C6B D:F43551 5.0 9.3 1.0

P.E.Cedervall, M.Dey, A.R.Pearson, S.W.Ragsdale, C.M.Wilmot. Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues. Biochemistry V. 49 7683 2010.
ISSN: ISSN 0006-2960
PubMed: 20707311
DOI: 10.1021/BI100458D