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Nickel in PDB 3sqg: Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats

Enzymatic activity of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats

All present enzymatic activity of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats, PDB code: 3sqg was solved by S.Shima, M.Krueger, T.Weinert, U.Demmer, R.K.Thauer, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 128.860, 412.490, 165.510, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.6

Other elements in 3sqg:

The structure of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats (pdb code 3sqg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats, PDB code: 3sqg:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3sqg

Go back to Nickel Binding Sites List in 3sqg
Nickel binding site 1 out of 3 in the Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1001

b:27.3
occ:1.00
NI A:M431001 0.0 27.3 1.0
N17 A:M431001 2.0 27.9 1.0
N09 A:M431001 2.0 24.5 1.0
N21 A:M431001 2.1 27.8 1.0
N13 A:M431001 2.2 28.6 1.0
OE1 A:GLN155 2.3 32.2 1.0
S1 D:COM1003 2.4 23.5 0.6
C08 A:M431001 3.0 25.5 1.0
C14 A:M431001 3.0 28.6 1.0
C06 A:M431001 3.1 25.7 1.0
C16 A:M431001 3.1 29.0 1.0
C18 A:M431001 3.1 28.6 1.0
C20 A:M431001 3.1 28.3 1.0
C10 A:M431001 3.2 26.8 1.0
C12 A:M431001 3.2 29.0 1.0
C07 A:M431001 3.3 25.5 1.0
C11 A:M431001 3.4 28.2 1.0
CD A:GLN155 3.4 31.6 1.0
C15 A:M431001 3.5 26.8 1.0
C19 A:M431001 3.5 29.1 1.0
C1 D:COM1003 3.6 17.5 0.6
NE2 A:GLN155 3.9 33.1 1.0
N51 A:M431001 4.0 30.3 1.0
OH E:TYR363 4.1 28.2 1.0
C2 D:COM1003 4.1 20.3 0.6
C52 A:M431001 4.2 21.7 1.0
C40 A:M431001 4.3 28.8 1.0
C58 A:M431001 4.3 23.6 1.0
OH D:TYR347 4.3 32.3 1.0
C35 A:M431001 4.4 31.4 1.0
C29 A:M431001 4.4 27.2 1.0
C22 A:M431001 4.4 29.4 1.0
C05 A:M431001 4.5 29.6 1.0
C46 A:M431001 4.5 36.6 1.0
C53 A:M431001 4.7 26.4 1.0
CG A:GLN155 4.7 29.7 1.0
C27 A:M431001 5.0 31.1 1.0

Nickel binding site 2 out of 3 in 3sqg

Go back to Nickel Binding Sites List in 3sqg
Nickel binding site 2 out of 3 in the Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1001

b:21.4
occ:1.00
NI D:M431001 0.0 21.4 1.0
N17 D:M431001 2.0 17.9 1.0
N09 D:M431001 2.0 15.8 1.0
N21 D:M431001 2.2 20.8 1.0
N13 D:M431001 2.2 19.1 1.0
OE1 D:GLN155 2.3 19.2 1.0
S1 A:COM1003 2.4 18.2 0.6
C08 D:M431001 3.0 19.2 1.0
C06 D:M431001 3.0 18.1 1.0
C14 D:M431001 3.0 20.4 1.0
C16 D:M431001 3.1 22.4 1.0
C18 D:M431001 3.1 19.6 1.0
C20 D:M431001 3.2 18.0 1.0
C10 D:M431001 3.2 20.5 1.0
C12 D:M431001 3.2 17.5 1.0
C07 D:M431001 3.2 18.3 1.0
CD D:GLN155 3.4 21.9 1.0
C11 D:M431001 3.4 16.5 1.0
C15 D:M431001 3.4 20.1 1.0
C19 D:M431001 3.6 18.8 1.0
C1 A:COM1003 3.8 14.2 0.6
NE2 D:GLN155 3.9 23.7 1.0
N51 D:M431001 3.9 17.4 1.0
C2 A:COM1003 4.1 16.2 0.6
OH B:TYR363 4.2 23.9 1.0
C52 D:M431001 4.2 21.7 1.0
OH A:TYR347 4.3 22.1 1.0
C40 D:M431001 4.4 21.3 1.0
C35 D:M431001 4.4 24.5 1.0
C58 D:M431001 4.4 21.8 1.0
C29 D:M431001 4.4 17.6 1.0
C05 D:M431001 4.4 19.3 1.0
C22 D:M431001 4.5 18.4 1.0
C46 D:M431001 4.5 16.5 1.0
C53 D:M431001 4.6 18.4 1.0
CG D:GLN155 4.7 21.8 1.0
C49 D:M431001 4.9 20.5 1.0
CE2 A:TYR347 5.0 19.9 1.0

Nickel binding site 3 out of 3 in 3sqg

Go back to Nickel Binding Sites List in 3sqg
Nickel binding site 3 out of 3 in the Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Methyl-Coenzyme M Reductase Purified From Black Sea Mats within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni1001

b:25.0
occ:1.00
NI G:M431001 0.0 25.0 1.0
N17 G:M431001 2.0 27.8 1.0
N09 G:M431001 2.0 27.4 1.0
N13 G:M431001 2.1 27.0 1.0
N21 G:M431001 2.2 19.6 1.0
S1 G:COM1003 2.4 28.5 0.6
C08 G:M431001 3.0 21.5 1.0
C16 G:M431001 3.1 26.6 1.0
C06 G:M431001 3.1 22.7 1.0
C14 G:M431001 3.1 28.4 1.0
C18 G:M431001 3.2 25.1 1.0
C12 G:M431001 3.2 28.4 1.0
C07 G:M431001 3.2 19.5 1.0
C20 G:M431001 3.2 20.8 1.0
C10 G:M431001 3.2 28.2 1.0
C15 G:M431001 3.5 26.8 1.0
C11 G:M431001 3.5 27.8 1.0
C19 G:M431001 3.6 22.3 1.0
C1 G:COM1003 3.8 17.2 0.6
C2 G:COM1003 3.8 22.2 0.6
N51 G:M431001 3.9 30.3 1.0
OH H:TYR363 4.0 30.9 1.0
OH G:TYR347 4.2 26.5 1.0
C52 G:M431001 4.3 22.4 1.0
C40 G:M431001 4.3 28.5 1.0
C58 G:M431001 4.4 25.4 1.0
C35 G:M431001 4.4 25.1 1.0
C29 G:M431001 4.4 26.0 1.0
C05 G:M431001 4.5 20.6 1.0
C22 G:M431001 4.5 21.4 1.0
C46 G:M431001 4.5 25.4 1.0
C53 G:M431001 4.7 28.5 1.0
C41 G:M431001 4.9 27.2 1.0
C49 G:M431001 4.9 32.2 1.0

Reference:

S.Shima, M.Krueger, T.Weinert, U.Demmer, J.Kahnt, R.K.Thauer, U.Ermler. Structure of A Methyl-Coenzyme M Reductase From Black Sea Mats That Oxidize Methane Anaerobically. Nature V. 481 98 2011.
ISSN: ISSN 0028-0836
PubMed: 22121022
DOI: 10.1038/NATURE10663
Page generated: Wed Oct 9 17:48:17 2024

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