Nickel in PDB 7suc: Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
Enzymatic activity of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
All present enzymatic activity of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase:
2.8.4.1;
Protein crystallography data
The structure of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase, PDB code: 7suc
was solved by
C.J.Ohmer,
M.Dasgupta,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.25 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.082,
119.777,
123.21,
90,
91.73,
90
|
R / Rfree (%)
|
15.2 /
18.6
|
Other elements in 7suc:
The structure of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
(pdb code 7suc). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the
Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase, PDB code: 7suc:
Jump to Nickel binding site number:
1;
2;
Nickel binding site 1 out
of 2 in 7suc
Go back to
Nickel Binding Sites List in 7suc
Nickel binding site 1 out
of 2 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni602
b:21.3
occ:1.00
|
NI
|
A:F43602
|
0.0
|
21.3
|
1.0
|
ND
|
A:F43602
|
2.1
|
17.6
|
1.0
|
NC
|
A:F43602
|
2.1
|
20.2
|
1.0
|
NB
|
A:F43602
|
2.1
|
21.6
|
1.0
|
NA
|
A:F43602
|
2.1
|
20.0
|
1.0
|
OE1
|
A:GLN147
|
2.3
|
20.9
|
1.0
|
S1
|
a:COM604
|
2.4
|
24.3
|
1.0
|
C4B
|
A:F43602
|
3.0
|
23.5
|
1.0
|
C1C
|
A:F43602
|
3.0
|
20.9
|
1.0
|
C1A
|
A:F43602
|
3.0
|
19.5
|
1.0
|
C4D
|
A:F43602
|
3.1
|
20.1
|
1.0
|
C1D
|
A:F43602
|
3.1
|
21.4
|
1.0
|
H12
|
a:COM604
|
3.1
|
31.6
|
1.0
|
C4C
|
A:F43602
|
3.1
|
19.9
|
1.0
|
HHA2
|
A:F43602
|
3.2
|
23.5
|
1.0
|
C1B
|
A:F43602
|
3.2
|
20.6
|
1.0
|
C4A
|
A:F43602
|
3.3
|
19.7
|
1.0
|
CHC
|
A:F43602
|
3.3
|
21.6
|
1.0
|
CHA
|
A:F43602
|
3.3
|
19.6
|
1.0
|
C1
|
a:COM604
|
3.3
|
26.3
|
1.0
|
CD
|
A:GLN147
|
3.3
|
23.0
|
1.0
|
HE22
|
A:GLN147
|
3.3
|
24.8
|
1.0
|
HHB2
|
A:F43602
|
3.3
|
25.4
|
1.0
|
H4D
|
A:F43602
|
3.4
|
24.1
|
1.0
|
CHB
|
A:F43602
|
3.5
|
21.2
|
1.0
|
CHD
|
A:F43602
|
3.5
|
20.1
|
1.0
|
HH
|
b:TYR367
|
3.5
|
33.3
|
1.0
|
NE2
|
A:GLN147
|
3.7
|
20.7
|
1.0
|
HH
|
a:TYR333
|
3.7
|
25.4
|
1.0
|
H22
|
a:COM604
|
3.7
|
30.5
|
1.0
|
H4A
|
A:F43602
|
3.8
|
23.7
|
1.0
|
H5B
|
A:F43602
|
3.8
|
26.5
|
1.0
|
N5B
|
A:F43602
|
3.9
|
22.1
|
1.0
|
H11
|
a:COM604
|
4.1
|
31.6
|
1.0
|
C2
|
a:COM604
|
4.1
|
25.4
|
1.0
|
OH
|
b:TYR367
|
4.1
|
27.8
|
1.0
|
HAA1
|
A:F43602
|
4.2
|
25.3
|
1.0
|
HHC
|
A:F43602
|
4.2
|
25.9
|
1.0
|
HHA1
|
A:F43602
|
4.3
|
23.5
|
1.0
|
C3B
|
A:F43602
|
4.3
|
20.1
|
1.0
|
OH
|
a:TYR333
|
4.3
|
21.1
|
1.0
|
C3D
|
A:F43602
|
4.3
|
20.5
|
1.0
|
C2C
|
A:F43602
|
4.4
|
22.0
|
1.0
|
C2A
|
A:F43602
|
4.4
|
20.3
|
1.0
|
C2D
|
A:F43602
|
4.4
|
20.5
|
1.0
|
C3A
|
A:F43602
|
4.4
|
22.0
|
1.0
|
C3C
|
A:F43602
|
4.4
|
21.9
|
1.0
|
HHB1
|
A:F43602
|
4.4
|
25.4
|
1.0
|
C2B
|
A:F43602
|
4.5
|
21.3
|
1.0
|
HAB2
|
A:F43602
|
4.5
|
27.3
|
1.0
|
HE21
|
A:GLN147
|
4.6
|
24.8
|
1.0
|
HE2
|
a:TYR333
|
4.6
|
27.0
|
1.0
|
H3D
|
A:F43602
|
4.6
|
24.6
|
1.0
|
CG
|
A:GLN147
|
4.6
|
20.9
|
1.0
|
H21
|
a:COM604
|
4.7
|
30.5
|
1.0
|
HG3
|
A:GLN147
|
4.7
|
25.1
|
1.0
|
H2D
|
A:F43602
|
4.7
|
24.6
|
1.0
|
CAA
|
A:F43602
|
4.7
|
21.1
|
1.0
|
HBB1
|
A:F43602
|
4.8
|
25.3
|
1.0
|
HAA2
|
A:F43602
|
4.8
|
25.3
|
1.0
|
H8C1
|
A:F43602
|
4.8
|
27.2
|
1.0
|
H5C1
|
A:F43602
|
4.9
|
25.0
|
1.0
|
CAB
|
A:F43602
|
4.9
|
22.8
|
1.0
|
H9A3
|
A:F43602
|
4.9
|
23.5
|
1.0
|
C7D
|
A:F43602
|
5.0
|
20.3
|
1.0
|
HE1
|
A:MET150
|
5.0
|
31.1
|
1.0
|
H2C
|
A:F43602
|
5.0
|
26.4
|
1.0
|
|
Nickel binding site 2 out
of 2 in 7suc
Go back to
Nickel Binding Sites List in 7suc
Nickel binding site 2 out
of 2 in the Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Ni603
b:20.6
occ:1.00
|
NI
|
a:F43603
|
0.0
|
20.6
|
1.0
|
ND
|
a:F43603
|
2.0
|
17.3
|
1.0
|
NC
|
a:F43603
|
2.1
|
19.4
|
1.0
|
NB
|
a:F43603
|
2.1
|
20.6
|
1.0
|
NA
|
a:F43603
|
2.1
|
19.2
|
1.0
|
OE1
|
a:GLN147
|
2.3
|
18.8
|
1.0
|
S1
|
A:COM604
|
2.5
|
22.2
|
1.0
|
C4B
|
a:F43603
|
3.0
|
20.2
|
1.0
|
C1A
|
a:F43603
|
3.0
|
18.7
|
1.0
|
C1C
|
a:F43603
|
3.0
|
19.2
|
1.0
|
H12
|
A:COM604
|
3.0
|
28.4
|
1.0
|
C4D
|
a:F43603
|
3.1
|
20.6
|
1.0
|
C1D
|
a:F43603
|
3.1
|
19.1
|
1.0
|
C4C
|
a:F43603
|
3.1
|
18.6
|
1.0
|
HHA2
|
a:F43603
|
3.2
|
24.6
|
1.0
|
C1B
|
a:F43603
|
3.2
|
21.7
|
1.0
|
C4A
|
a:F43603
|
3.3
|
18.3
|
1.0
|
C1
|
A:COM604
|
3.3
|
23.6
|
1.0
|
CHA
|
a:F43603
|
3.3
|
20.5
|
1.0
|
CHC
|
a:F43603
|
3.3
|
21.3
|
1.0
|
HHB2
|
a:F43603
|
3.3
|
25.2
|
1.0
|
CD
|
a:GLN147
|
3.3
|
20.3
|
1.0
|
HE22
|
a:GLN147
|
3.3
|
26.7
|
1.0
|
H4D
|
a:F43603
|
3.4
|
24.7
|
1.0
|
CHB
|
a:F43603
|
3.4
|
21.0
|
1.0
|
HH
|
B:TYR367
|
3.5
|
31.6
|
1.0
|
CHD
|
a:F43603
|
3.5
|
20.8
|
1.0
|
HH
|
A:TYR333
|
3.7
|
27.3
|
1.0
|
NE2
|
a:GLN147
|
3.7
|
22.3
|
1.0
|
H4A
|
a:F43603
|
3.7
|
22.0
|
1.0
|
H22
|
A:COM604
|
3.8
|
26.6
|
1.0
|
H5B
|
a:F43603
|
3.8
|
22.6
|
1.0
|
N5B
|
a:F43603
|
3.9
|
18.8
|
1.0
|
H11
|
A:COM604
|
4.0
|
28.4
|
1.0
|
OH
|
B:TYR367
|
4.1
|
26.3
|
1.0
|
C2
|
A:COM604
|
4.1
|
22.2
|
1.0
|
HAA1
|
a:F43603
|
4.2
|
24.5
|
1.0
|
HHC
|
a:F43603
|
4.2
|
25.6
|
1.0
|
HHA1
|
a:F43603
|
4.2
|
24.6
|
1.0
|
C3B
|
a:F43603
|
4.3
|
20.9
|
1.0
|
OH
|
A:TYR333
|
4.3
|
22.8
|
1.0
|
C2A
|
a:F43603
|
4.3
|
20.1
|
1.0
|
C3D
|
a:F43603
|
4.3
|
18.4
|
1.0
|
C2D
|
a:F43603
|
4.4
|
18.0
|
1.0
|
C2C
|
a:F43603
|
4.4
|
20.1
|
1.0
|
C3A
|
a:F43603
|
4.4
|
20.0
|
1.0
|
HHB1
|
a:F43603
|
4.4
|
25.2
|
1.0
|
C3C
|
a:F43603
|
4.4
|
18.3
|
1.0
|
C2B
|
a:F43603
|
4.5
|
20.2
|
1.0
|
HE21
|
a:GLN147
|
4.5
|
26.7
|
1.0
|
HE2
|
A:TYR333
|
4.6
|
26.4
|
1.0
|
HAB2
|
a:F43603
|
4.6
|
23.6
|
1.0
|
H3D
|
a:F43603
|
4.6
|
22.1
|
1.0
|
CG
|
a:GLN147
|
4.6
|
18.4
|
1.0
|
CAA
|
a:F43603
|
4.7
|
20.4
|
1.0
|
HG3
|
a:GLN147
|
4.7
|
22.1
|
1.0
|
H2D
|
a:F43603
|
4.7
|
21.6
|
1.0
|
HBB1
|
a:F43603
|
4.7
|
22.7
|
1.0
|
HAA2
|
a:F43603
|
4.7
|
24.5
|
1.0
|
H21
|
A:COM604
|
4.8
|
26.6
|
1.0
|
H8C1
|
a:F43603
|
4.8
|
26.9
|
1.0
|
H5C1
|
a:F43603
|
4.9
|
25.2
|
1.0
|
H9A3
|
a:F43603
|
4.9
|
24.4
|
1.0
|
CAB
|
a:F43603
|
4.9
|
19.7
|
1.0
|
C7D
|
a:F43603
|
5.0
|
22.1
|
1.0
|
H2C
|
a:F43603
|
5.0
|
24.1
|
1.0
|
H3B
|
a:F43603
|
5.0
|
25.1
|
1.0
|
C6B
|
a:F43603
|
5.0
|
24.4
|
1.0
|
|
Reference:
C.J.Ohmer,
M.Dasgupta,
A.Patwardhan,
I.Bogacz,
C.Kaminsky,
M.D.Doyle,
P.Y.Chen,
S.M.Keable,
H.Makita,
P.S.Simon,
R.Massad,
T.Fransson,
R.Chatterjee,
A.Bhowmick,
D.W.Paley,
N.W.Moriarty,
A.S.Brewster,
L.B.Gee,
R.Alonso-Mori,
F.Moss,
F.D.Fuller,
A.Batyuk,
N.K.Sauter,
U.Bergmann,
C.L.Drennan,
V.K.Yachandra,
J.Yano,
J.F.Kern,
S.W.Ragsdale.
Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase. J.Inorg.Biochem. V. 230 11768 2022.
ISSN: ISSN 0162-0134
PubMed: 35202981
DOI: 10.1016/J.JINORGBIO.2022.111768
Page generated: Thu Oct 10 09:24:17 2024
|