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Nickel in PDB 3pot: Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

Enzymatic activity of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

All present enzymatic activity of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis:
2.8.4.1;

Protein crystallography data

The structure of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 3pot was solved by P.E.Cedervall, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.886, 118.165, 122.388, 90.00, 91.94, 90.00
R / Rfree (%) 13.2 / 15.6

Other elements in 3pot:

The structure of Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Potassium (K) 1 atom
Iodine (I) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis (pdb code 3pot). 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 Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 3pot:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3pot

Go back to Nickel Binding Sites List in 3pot
Nickel binding site 1 out of 2 in the Structural Analysis of A Ni(III)-Methyl Species in 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 Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni555

b:5.2
occ:1.00
 NI A:F43555 0.0 5.2 1.0
NC A:F43555 2.0 4.8 1.0
C1 D:06C556 2.1 4.8 0.5
ND A:F43555 2.1 5.0 1.0
NA A:F43555 2.1 5.1 1.0
NB A:F43555 2.1 5.1 1.0
OE1 A:GLN147 2.2 6.1 1.0
S1 D:COM555 2.4 7.7 0.5
C4B A:F43555 3.0 5.3 1.0
C1A A:F43555 3.0 4.8 1.0
C1C A:F43555 3.0 5.7 1.0
C4C A:F43555 3.1 5.2 1.0
C1D A:F43555 3.1 5.1 1.0
C4D A:F43555 3.1 5.0 1.0
C1B A:F43555 3.2 5.0 1.0
C4A A:F43555 3.2 5.1 1.0
CD A:GLN147 3.3 6.4 1.0
C1 D:COM555 3.3 7.3 0.5
CHA A:F43555 3.3 5.3 1.0
CHC A:F43555 3.3 5.3 1.0
CHB A:F43555 3.4 5.5 1.0
CHD A:F43555 3.5 4.4 1.0
NE2 A:GLN147 3.6 6.8 1.0
N5B A:F43555 3.9 5.6 1.0
C2 D:COM555 4.1 9.2 0.5
OH E:TYR367 4.1 8.0 1.0
OH D:TYR333 4.2 9.8 1.0
C3B A:F43555 4.3 5.5 1.0
C3A A:F43555 4.3 5.4 1.0
C2A A:F43555 4.3 5.1 1.0
C2C A:F43555 4.4 5.8 1.0
C3D A:F43555 4.4 4.7 1.0
C2D A:F43555 4.4 5.7 1.0
C3C A:F43555 4.4 5.3 1.0
C2B A:F43555 4.5 5.4 1.0
CAA A:F43555 4.6 6.0 1.0
CG A:GLN147 4.6 6.4 1.0
CAB A:F43555 4.9 6.4 1.0
C7D A:F43555 4.9 5.3 1.0

Nickel binding site 2 out of 2 in 3pot

Go back to Nickel Binding Sites List in 3pot
Nickel binding site 2 out of 2 in the Structural Analysis of A Ni(III)-Methyl Species in 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 Structural Analysis of A Ni(III)-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni552

b:6.0
occ:1.00
 NI D:F43552 0.0 6.0 1.0
NC D:F43552 2.0 6.2 1.0
NA D:F43552 2.1 5.4 1.0
ND D:F43552 2.1 5.5 1.0
C1 A:06C559 2.1 4.8 0.5
NB D:F43552 2.1 6.2 1.0
OE1 D:GLN147 2.2 7.8 1.0
S1 A:COM556 2.4 9.3 0.5
C4B D:F43552 3.0 6.2 1.0
C1A D:F43552 3.0 5.1 1.0
C1C D:F43552 3.0 5.8 1.0
C1D D:F43552 3.1 7.1 1.0
C4D D:F43552 3.1 6.0 1.0
C4C D:F43552 3.1 5.8 1.0
C1B D:F43552 3.2 6.3 1.0
CD D:GLN147 3.3 6.2 1.0
C4A D:F43552 3.3 5.9 1.0
C1 A:COM556 3.3 8.1 0.5
CHA D:F43552 3.3 6.5 1.0
CHC D:F43552 3.3 6.5 1.0
CHB D:F43552 3.4 5.9 1.0
CHD D:F43552 3.5 6.2 1.0
NE2 D:GLN147 3.6 7.2 1.0
N5B D:F43552 3.9 5.6 1.0
C2 A:COM556 4.0 11.2 0.5
OH B:TYR367 4.1 8.6 1.0
OH A:TYR333 4.2 10.4 1.0
C3B D:F43552 4.3 6.8 1.0
C3A D:F43552 4.3 6.4 1.0
C2A D:F43552 4.4 5.3 1.0
C3D D:F43552 4.4 6.2 1.0
C2C D:F43552 4.4 6.3 1.0
C2D D:F43552 4.4 5.5 1.0
C3C D:F43552 4.4 6.2 1.0
C2B D:F43552 4.5 6.8 1.0
CG D:GLN147 4.6 7.6 1.0
CAA D:F43552 4.6 7.2 1.0
CAB D:F43552 4.9 6.7 1.0
C7D D:F43552 4.9 6.3 1.0

Reference:

P.E.Cedervall, M.Dey, X.Li, R.Sarangi, B.Hedman, S.W.Ragsdale, C.M.Wilmot. Structural Analysis of A Ni-Methyl Species in Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis. J.Am.Chem.Soc. V. 133 5626 2011.
ISSN: ISSN 0002-7863
PubMed: 21438550
DOI: 10.1021/JA110492P
Page generated: Wed Oct 9 17:42:12 2024

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