Nickel in PDB 3m32: 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: 3m32 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)	20.28 / 1.35
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 (%)	14 / 15.7

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

Magnesium	(Mg)	9 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 3m32). 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: 3m32:
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:7.6 occ:1.00 NI A:F431 0.0 7.6 1.0 ND A:F431 2.0 7.4 1.0 NC A:F431 2.0 7.0 1.0 NA A:F431 2.1 7.0 1.0 NB A:F431 2.1 8.1 1.0 OS3 D:SHT555 2.1 9.9 0.5 OE1 A:GLN147 2.3 9.3 1.0 S1 D:COM554 2.5 9.8 0.5 C4B A:F431 3.0 8.1 1.0 C1A A:F431 3.0 6.1 1.0 C1C A:F431 3.0 7.9 1.0 C4D A:F431 3.1 6.8 1.0 C1D A:F431 3.1 8.2 1.0 C4C A:F431 3.1 8.2 1.0 C1B A:F431 3.2 7.5 1.0 SG2 D:SHT555 3.3 9.9 0.5 C1 D:COM554 3.3 11.0 0.5 C4A A:F431 3.3 6.7 1.0 CD A:GLN147 3.3 9.3 1.0 CHA A:F431 3.3 7.1 1.0 CHC A:F431 3.3 8.7 1.0 CHB A:F431 3.4 8.0 1.0 CHD A:F431 3.5 7.0 1.0 OS1 D:SHT555 3.5 11.2 0.5 NE2 A:GLN147 3.7 9.3 1.0 OS2 D:SHT555 3.8 12.5 0.5 N5B A:F431 3.9 8.4 1.0 C2 D:COM554 4.1 10.8 0.5 C3B A:F431 4.3 8.3 1.0 OH D:TYR333 4.3 11.9 1.0 OH E:TYR367 4.3 9.2 1.0 C3A A:F431 4.3 7.2 1.0 C3D A:F431 4.3 7.0 1.0 C2D A:F431 4.3 8.0 1.0 C2C A:F431 4.4 7.5 1.0 C2A A:F431 4.4 6.2 1.0 C3C A:F431 4.4 8.1 1.0 C2B A:F431 4.5 9.9 1.0 CAA A:F431 4.6 7.7 1.0 CD D:SHT555 4.6 13.1 0.5 CG A:GLN147 4.6 9.6 1.0 CAB A:F431 4.9 10.8 1.0 C7D A:F431 4.9 8.2 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:Ni552 b:8.2 occ:1.00 NI D:F43552 0.0 8.2 1.0 NC D:F43552 2.0 7.0 1.0 ND D:F43552 2.1 7.8 1.0 NA D:F43552 2.1 7.2 1.0 OS3 A:SHT555 2.1 12.5 0.5 NB D:F43552 2.1 8.3 1.0 OE1 D:GLN147 2.2 10.9 1.0 S1 A:COM554 2.4 12.7 0.5 C4B D:F43552 3.0 7.9 1.0 C1D D:F43552 3.0 8.2 1.0 C1A D:F43552 3.0 6.7 1.0 C4C D:F43552 3.1 6.8 1.0 C1C D:F43552 3.1 6.8 1.0 C4D D:F43552 3.1 6.8 1.0 C1B D:F43552 3.2 8.3 1.0 SG2 A:SHT555 3.2 9.8 0.5 C4A D:F43552 3.3 8.3 1.0 CHA D:F43552 3.3 7.2 1.0 CD D:GLN147 3.3 8.1 1.0 CHC D:F43552 3.3 7.2 1.0 C1 A:COM554 3.3 10.4 0.5 CHB D:F43552 3.5 8.5 1.0 OS1 A:SHT555 3.6 12.1 0.5 CHD D:F43552 3.6 8.4 1.0 NE2 D:GLN147 3.6 10.2 1.0 OS2 A:SHT555 3.6 10.6 0.5 N5B D:F43552 4.0 8.4 1.0 C2 A:COM554 4.1 12.3 0.5 OH A:TYR333 4.3 11.9 1.0 C3B D:F43552 4.3 8.9 1.0 OH B:TYR367 4.3 9.8 1.0 C3A D:F43552 4.3 8.1 1.0 C3D D:F43552 4.3 6.8 1.0 C2A D:F43552 4.3 6.7 1.0 C2C D:F43552 4.4 7.9 1.0 C2D D:F43552 4.4 7.4 1.0 C3C D:F43552 4.4 8.4 1.0 C2B D:F43552 4.5 9.1 1.0 CAA D:F43552 4.6 8.1 1.0 CG D:GLN147 4.6 9.9 1.0 CD A:SHT555 4.6 7.0 0.5 CAB D:F43552 4.9 8.6 1.0 C7D D:F43552 5.0 8.5 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