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Nickel in PDB 4iub: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form - Oxidized State 1

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form - Oxidized State 1

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form - Oxidized State 1:
1.12.5.1;

Protein crystallography data

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form - Oxidized State 1, PDB code: 4iub was solved by S.Frielingsdorf, A.Schmidt, J.Fritsch, O.Lenz, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.05 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.903, 95.390, 118.818, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 16.6

Other elements in 4iub:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form - Oxidized State 1 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 As-Isolated Form - Oxidized State 1 (pdb code 4iub). 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 1, PDB code: 4iub:

Nickel binding site 1 out of 1 in 4iub

Go back to Nickel Binding Sites List in 4iub
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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni701

b:10.1
occ:1.00
 NI L:NFV701 0.0 10.1 1.0
O4 L:NFV701 1.9 10.5 1.0
SG L:CYS75 2.2 13.7 1.0
SG L:CYS597 2.2 13.9 1.0
SG L:CYS78 2.4 12.2 1.0
SG L:CYS600 2.6 11.0 1.0
FE L:NFV701 2.9 8.5 1.0
CB L:CYS75 3.1 11.1 1.0
CB L:CYS597 3.2 12.4 1.0
CB L:CYS78 3.5 12.3 1.0
CB L:CYS600 3.6 10.1 1.0
N L:CYS78 3.7 11.8 1.0
C3 L:NFV701 4.0 8.8 1.0
C2 L:NFV701 4.2 8.4 1.0
NH1 L:ARG530 4.2 12.2 1.0
CA L:CYS78 4.2 12.7 1.0
C1 L:NFV701 4.5 7.9 1.0
CB L:VAL77 4.5 10.9 1.0
CA L:CYS75 4.5 9.9 1.0
CZ L:ARG530 4.5 13.3 1.0
N L:CYS600 4.6 8.2 1.0
CA L:CYS597 4.6 11.0 1.0
CA L:CYS600 4.6 8.5 1.0
NE L:ARG530 4.8 12.2 1.0
C L:VAL77 4.8 11.9 1.0
CD L:ARG530 4.8 11.2 1.0
N3 L:NFV701 4.9 8.7 1.0
N L:VAL77 4.9 10.7 1.0
CA L:VAL77 5.0 10.3 1.0

Reference:

S.Frielingsdorf, J.Fritsch, A.Schmidt, M.Hammer, J.Lowenstein, E.Siebert, V.Pelmenschikov, T.Jaenicke, J.Kalms, Y.Rippers, F.Lendzian, I.Zebger, C.Teutloff, M.Kaupp, R.Bittl, P.Hildebrandt, B.Friedrich, O.Lenz, P.Scheerer. Reversible [4FE-3S] Cluster Morphing in An O2-Tolerant [Nife] Hydrogenase. Nat.Chem.Biol. V. 10 378 2014.
ISSN: ISSN 1552-4450
PubMed: 24705592
DOI: 10.1038/NCHEMBIO.1500
Page generated: Wed Oct 9 18:15:07 2024

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