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Nickel in PDB 5mdk: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3):
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3), PDB code: 5mdk was solved by A.Schmidt, J.Kalms, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.110, 95.567, 119.828, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 15.3

Other elements in 5mdk:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 12 atoms
Chlorine (Cl) 5 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) (pdb code 5mdk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3), PDB code: 5mdk:

Nickel binding site 1 out of 1 in 5mdk

Go back to Nickel Binding Sites List in 5mdk
Nickel binding site 1 out of 1 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3)


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 An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form (Oxidized State - State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni704

b:19.7
occ:1.00
 NI L:NFV704 0.0 19.7 1.0
O4 L:NFV704 1.9 18.3 1.0
SG L:CYS75 2.2 18.9 1.0
SG L:CYS597 2.2 22.4 1.0
SG L:CYS78 2.4 18.2 1.0
SG L:CYS600 2.6 18.2 1.0
FE L:NFV704 2.9 16.7 1.0
CB L:CYS75 3.1 18.0 1.0
CB L:CYS597 3.2 19.2 1.0
CB L:CYS78 3.5 18.3 1.0
N L:CYS78 3.6 16.5 1.0
CB L:CYS600 3.7 17.6 1.0
C2 L:NFV704 4.0 17.2 1.0
C3 L:NFV704 4.1 16.1 1.0
NH1 L:ARG530 4.2 22.9 1.0
CA L:CYS78 4.2 17.8 1.0
CB L:VAL77 4.5 18.5 1.0
CZ L:ARG530 4.5 20.8 1.0
C1 L:NFV704 4.5 16.4 1.0
CA L:CYS75 4.5 16.9 1.0
CA L:CYS597 4.6 16.8 1.0
CA L:CYS600 4.7 16.6 1.0
N L:CYS600 4.7 15.8 1.0
C L:VAL77 4.7 18.2 1.0
NE L:ARG530 4.7 20.7 1.0
CD L:ARG530 4.8 20.3 1.0
N2 L:NFV704 4.9 17.4 1.0
N L:VAL77 4.9 17.5 1.0
CA L:VAL77 4.9 17.7 1.0

Reference:

J.Kalms, A.Schmidt, S.Frielingsdorf, T.Utesch, G.Gotthard, D.Von Stetten, P.Van Der Linden, A.Royant, M.A.Mroginski, P.Carpentier, O.Lenz, P.Scheerer. Tracking the Route of Molecular Oxygen in O2-Tolerant Membrane-Bound [Nife] Hydrogenase. Proc. Natl. Acad. Sci. V. 115 E2229 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29463722
DOI: 10.1073/PNAS.1712267115
Page generated: Wed Dec 16 01:41:41 2020

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