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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:

Magnesium (Mg) 7 atoms

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

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