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Nickel in PDB 5mdl: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method, PDB code: 5mdl was solved by J.Kalms, A.Schmidt, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.134, 95.568, 119.686, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.3

Other elements in 5mdl:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method also contains other interesting chemical elements:

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

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method (pdb code 5mdl). 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 O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method, PDB code: 5mdl:

Nickel binding site 1 out of 1 in 5mdl

Go back to Nickel Binding Sites List in 5mdl
Nickel binding site 1 out of 1 in the Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method


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 O2-Derivatized Form By A "Soak-and-Freeze" Derivatization Method within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni701

b:16.2
occ:1.00
 NI L:NFV701 0.0 16.2 1.0
O4 L:NFV701 1.8 14.4 1.0
SG L:CYS597 2.2 18.1 1.0
SG L:CYS75 2.2 16.2 1.0
SG L:CYS78 2.4 12.7 1.0
SG L:CYS600 2.6 13.9 1.0
FE L:NFV701 2.9 13.0 1.0
CB L:CYS75 3.0 14.6 1.0
CB L:CYS597 3.2 15.0 1.0
CB L:CYS78 3.5 11.6 1.0
CB L:CYS600 3.6 11.5 1.0
N L:CYS78 3.7 13.2 1.0
C2 L:NFV701 3.9 13.2 1.0
C3 L:NFV701 4.1 13.1 1.0
CA L:CYS78 4.2 11.8 1.0
NH1 L:ARG530 4.3 15.4 1.0
CA L:CYS75 4.5 13.0 1.0
CB L:VAL77 4.5 13.9 1.0
CZ L:ARG530 4.6 14.0 1.0
C1 L:NFV701 4.6 13.0 1.0
CA L:CYS600 4.6 12.3 1.0
CA L:CYS597 4.6 12.4 1.0
N L:CYS600 4.6 11.6 1.0
NE L:ARG530 4.7 14.1 1.0
C L:VAL77 4.8 13.7 1.0
CD L:ARG530 4.8 13.0 1.0
N2 L:NFV701 4.8 12.5 1.0
N L:VAL77 5.0 12.5 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: Thu Oct 10 06:39:29 2024

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