Atomistry » Nickel » PDB 3nbk-3qsf » 3pot
Atomistry »
  Nickel »
    PDB 3nbk-3qsf »
      3pot »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy