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Iodine 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:

Nickel (Ni) 2 atoms
Magnesium (Mg) 12 atoms
Potassium (K) 1 atom

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine 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 Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 3pot

Go back to Iodine Binding Sites List in 3pot
Iodine 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 Iodine with other atoms in the I 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:I559

b:8.0
occ:0.35
 I1 A:06C559 0.0 8.0 0.3
S2 A:COM556 0.1 7.2 0.5
O1S A:COM556 1.5 7.6 0.5
O3S A:COM556 1.5 11.7 0.5
C2 A:COM556 1.6 11.2 0.5
O2S A:COM556 1.6 9.5 0.5
C1 A:COM556 2.4 8.1 0.5
O A:HOH733 3.8 10.7 1.0
CD2 C:LEU117 3.9 8.2 1.0
CHC D:F43552 4.0 6.5 1.0
C4B D:F43552 4.0 6.2 1.0
CE1 B:PHE361 4.0 7.3 1.0
S1 A:COM556 4.0 9.3 0.5
C8B D:F43552 4.0 6.8 1.0
NB D:F43552 4.0 6.2 1.0
CD2 A:PHE443 4.1 6.2 1.0
C6B D:F43552 4.1 6.5 1.0
N A:TYR444 4.1 5.8 1.0
CB A:TYR444 4.1 6.6 1.0
C1 A:06C559 4.1 4.8 0.5
CB A:PHE443 4.1 6.7 1.0
NH1 C:ARG120 4.2 9.5 1.0
CD1 B:PHE361 4.2 6.5 1.0
N5B D:F43552 4.3 5.6 1.0
C1C D:F43552 4.4 5.8 1.0
C5C D:F43552 4.4 6.0 1.0
O7B D:F43552 4.5 7.5 1.0
CG A:PHE443 4.6 5.3 1.0
C3B D:F43552 4.7 6.8 1.0
C1B D:F43552 4.7 6.3 1.0
C2B D:F43552 4.8 6.8 1.0
CA A:TYR444 4.8 6.5 1.0
NC D:F43552 4.8 6.2 1.0
CE2 B:TYR367 4.9 6.5 1.0
CD2 A:TYR444 4.9 9.1 1.0
CA A:PHE443 5.0 6.0 1.0

Iodine binding site 2 out of 2 in 3pot

Go back to Iodine Binding Sites List in 3pot
Iodine 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 Iodine with other atoms in the I 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:I556

b:7.3
occ:0.35
 I1 D:06C556 0.0 7.3 0.3
S2 D:COM555 0.1 6.6 0.5
O1S D:COM555 1.5 8.1 0.5
O2S D:COM555 1.5 8.3 0.5
C2 D:COM555 1.5 9.2 0.5
O3S D:COM555 1.6 9.9 0.5
C1 D:COM555 2.4 7.3 0.5
O D:HOH713 3.8 9.4 1.0
CD2 F:LEU117 3.9 7.2 1.0
C4B A:F43555 4.0 5.3 1.0
CHC A:F43555 4.0 5.3 1.0
S1 D:COM555 4.0 7.7 0.5
CE1 E:PHE361 4.0 6.4 1.0
C8B A:F43555 4.0 6.3 1.0
NB A:F43555 4.1 5.1 1.0
C6B A:F43555 4.1 6.3 1.0
CD2 D:PHE443 4.1 5.8 1.0
N D:TYR444 4.1 5.8 1.0
CB D:TYR444 4.1 6.4 1.0
CB D:PHE443 4.2 5.9 1.0
C1 D:06C556 4.2 4.8 0.5
NH1 F:ARG120 4.2 8.4 1.0
CD1 E:PHE361 4.2 5.9 1.0
N5B A:F43555 4.4 5.6 1.0
O7B A:F43555 4.4 7.3 1.0
C1C A:F43555 4.4 5.7 1.0
C5C A:F43555 4.4 5.9 1.0
CG D:PHE443 4.6 5.0 1.0
C3B A:F43555 4.7 5.5 1.0
C1B A:F43555 4.7 5.0 1.0
C2B A:F43555 4.8 5.4 1.0
CA D:TYR444 4.8 5.8 1.0
CE2 E:TYR367 4.8 6.5 1.0
CD2 D:TYR444 4.9 8.0 1.0
NC A:F43555 4.9 4.8 1.0
CA D:PHE443 4.9 5.7 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: Sun Aug 11 16:07:21 2024

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