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:
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
|