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Nickel in PDB 6qgr: The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

Enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State

All present enzymatic activity of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State:
1.12.98.1;

Protein crystallography data

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr 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) 48.14 / 1.84
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 235.826, 235.826, 235.826, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 6qgr:

The structure of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 19 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State (pdb code 6qgr). 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 The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State, PDB code: 6qgr:

Nickel binding site 1 out of 1 in 6qgr

Go back to Nickel Binding Sites List in 6qgr
Nickel binding site 1 out of 1 in the The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The F420-Reducing [Nife] Hydrogenase Complex From Methanosarcina Barkeri at the Nia-S State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:33.7
occ:1.00
 NI A:NFU501 0.0 33.7 1.0
SG A:CYS63 2.3 31.6 1.0
SG A:CYS432 2.4 38.5 1.0
SG A:CYS66 2.5 33.7 1.0
SG A:CYS435 2.6 35.2 1.0
FE A:NFU501 2.7 32.2 1.0
CB A:CYS63 3.1 29.6 1.0
CB A:CYS432 3.2 31.9 1.0
CB A:CYS66 3.6 31.6 1.0
CB A:CYS435 3.7 30.1 1.0
C1 A:NFU501 3.7 30.1 1.0
C2 A:NFU501 3.8 34.7 1.0
N A:CYS66 3.9 35.5 1.0
CA A:CYS66 4.4 33.1 1.0
C3 A:NFU501 4.4 37.4 1.0
NH2 A:ARG380 4.5 27.0 1.0
CB A:ILE65 4.5 33.0 1.0
CA A:CYS63 4.5 31.3 1.0
N1 A:NFU501 4.6 29.6 1.0
CA A:CYS432 4.7 34.7 1.0
CA A:CYS435 4.7 27.6 1.0
N2 A:NFU501 4.7 28.5 1.0
N A:CYS435 4.7 32.8 1.0
CD A:ARG380 4.7 30.4 1.0
C A:ILE65 4.9 31.7 1.0
N A:ILE65 4.9 30.5 1.0
CZ A:ARG380 5.0 31.3 1.0
C A:CYS63 5.0 34.7 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: Thu Oct 10 08:46:04 2024

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