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Nickel in PDB 3m2r: Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

Enzymatic activity of 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;

Protein crystallography data

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2r 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) 20.49 / 1.30
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 (%) 14.3 / 16.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m2r). 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: 3m2r:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3m2r

Go back to Nickel Binding Sites List in 3m2r
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:6.9
occ:1.00
NI A:F431 0.0 6.9 1.0
NC A:F431 2.0 6.7 1.0
NA A:F431 2.1 7.0 1.0
ND A:F431 2.1 6.3 1.0
NB A:F431 2.1 6.7 1.0
OE1 A:GLN147 2.3 9.7 1.0
S1 D:COM554 2.4 10.2 0.9
C4B A:F431 3.0 6.7 1.0
C1A A:F431 3.0 6.2 1.0
C1C A:F431 3.0 6.9 1.0
C1D A:F431 3.1 6.6 1.0
C4D A:F431 3.1 7.3 1.0
C4C A:F431 3.1 6.2 1.0
C1 D:COM554 3.2 11.7 0.9
C4A A:F431 3.2 5.4 1.0
C1B A:F431 3.2 6.4 1.0
CHA A:F431 3.3 7.3 1.0
CD A:GLN147 3.3 8.1 1.0
CHC A:F431 3.4 7.1 1.0
CHB A:F431 3.5 6.8 1.0
CHD A:F431 3.5 6.1 1.0
NE2 A:GLN147 3.7 8.4 1.0
N5B A:F431 3.9 6.8 1.0
C2 D:COM554 4.0 10.3 0.9
OH E:TYR367 4.2 9.9 1.0
C3A A:F431 4.3 7.1 1.0
C3B A:F431 4.3 6.6 1.0
OH D:TYR333 4.3 9.9 1.0
C2D A:F431 4.4 7.3 1.0
C2C A:F431 4.4 6.6 1.0
C3D A:F431 4.4 6.6 1.0
C2A A:F431 4.4 5.5 1.0
C3C A:F431 4.4 7.2 1.0
C2B A:F431 4.4 7.4 1.0
CAA A:F431 4.6 6.7 1.0
CG A:GLN147 4.7 7.9 1.0
CAB A:F431 4.9 7.0 1.0
C7D A:F431 4.9 6.6 1.0

Nickel binding site 2 out of 2 in 3m2r

Go back to Nickel Binding Sites List in 3m2r
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:7.9
occ:1.00
NI D:F43552 0.0 7.9 1.0
NC D:F43552 2.0 7.2 1.0
ND D:F43552 2.1 8.5 1.0
NB D:F43552 2.1 8.7 1.0
NA D:F43552 2.1 7.6 1.0
OE1 D:GLN147 2.3 10.7 1.0
S1 A:COM555 2.4 11.6 0.9
C1C D:F43552 3.0 7.8 1.0
C4B D:F43552 3.0 7.9 1.0
C1D D:F43552 3.0 9.0 1.0
C1A D:F43552 3.0 7.7 1.0
C4D D:F43552 3.1 6.5 1.0
C4C D:F43552 3.1 6.7 1.0
C1B D:F43552 3.2 8.5 1.0
C4A D:F43552 3.2 7.7 1.0
C1 A:COM555 3.3 11.6 0.9
CHA D:F43552 3.3 7.2 1.0
CD D:GLN147 3.3 7.5 1.0
CHC D:F43552 3.4 7.8 1.0
CHB D:F43552 3.5 8.2 1.0
CHD D:F43552 3.6 8.5 1.0
NE2 D:GLN147 3.6 9.5 1.0
N5B D:F43552 3.9 7.7 1.0
C2 A:COM555 4.1 12.8 0.9
OH B:TYR367 4.1 10.9 1.0
OH A:TYR333 4.3 10.4 1.0
C3B D:F43552 4.3 8.5 1.0
C3D D:F43552 4.3 6.8 1.0
C2C D:F43552 4.3 7.8 1.0
C3A D:F43552 4.4 7.7 1.0
C2A D:F43552 4.4 7.0 1.0
C2D D:F43552 4.4 8.0 1.0
C3C D:F43552 4.4 7.4 1.0
C2B D:F43552 4.5 7.3 1.0
CAA D:F43552 4.6 8.1 1.0
CG D:GLN147 4.6 8.8 1.0
CAB D:F43552 4.9 7.9 1.0
C7D D:F43552 5.0 7.9 1.0

Reference:

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
Page generated: Fri Sep 25 08:27:18 2020
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