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Nickel in PDB 6qii: Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

Enzymatic activity of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri

All present enzymatic activity of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri:
1.12.98.1;

Protein crystallography data

The structure of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qii was solved by Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.55 / 2.28
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 236.705, 236.705, 236.705, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.7

Other elements in 6qii:

The structure of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Xenon (Xe) 7 atoms
Iron (Fe) 19 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri (pdb code 6qii). 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 Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri, PDB code: 6qii:

Nickel binding site 1 out of 1 in 6qii

Go back to Nickel Binding Sites List in 6qii
Nickel binding site 1 out of 1 in the Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Xenon Derivatization of the F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni502

b:63.6
occ:0.90
 NI A:NFU502 0.0 63.6 0.9
SG A:CYS63 2.3 67.1 1.0
SG A:CYS432 2.4 67.5 1.0
SG A:CYS66 2.5 58.1 1.0
SG A:CYS435 2.6 58.9 1.0
FE A:NFU502 2.7 58.8 0.9
CB A:CYS432 3.2 47.8 1.0
CB A:CYS63 3.2 59.0 1.0
CB A:CYS66 3.7 56.7 1.0
C1 A:NFU502 3.7 53.5 0.9
CB A:CYS435 3.8 49.4 1.0
C2 A:NFU502 3.8 56.3 0.9
N A:CYS66 4.1 55.9 1.0
NH2 A:ARG380 4.2 54.8 1.0
C3 A:NFU502 4.4 58.1 0.9
CB A:ILE65 4.5 56.4 1.0
CA A:CYS66 4.5 64.1 1.0
CA A:CYS63 4.6 56.8 1.0
CA A:CYS432 4.6 53.2 1.0
N2 A:NFU502 4.7 53.5 0.9
N1 A:NFU502 4.7 49.8 0.9
CZ A:ARG380 4.7 61.2 1.0
CD A:ARG380 4.7 48.6 1.0
CA A:CYS435 4.8 50.5 1.0
N A:CYS435 4.8 47.6 1.0
NE A:ARG380 4.9 49.9 1.0
N A:ILE65 4.9 50.2 1.0
C A:ILE65 4.9 55.1 1.0

Reference:

Y.Ilina, C.Lorent, S.Katz, J.H.Jeoung, S.Shima, M.Horch, I.Zebger, H.Dobbek. X-Ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling By [Nife] Hydrogenases. Angew.Chem.Int.Ed.Engl. 2019.
ISSN: ESSN 1521-3773
PubMed: 31591784
DOI: 10.1002/ANIE.201908258
Page generated: Mon Aug 18 21:27:24 2025

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