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Nickel in PDB 4iud: Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State

Enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State

All present enzymatic activity of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State:
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 with Ascorbate - Partly Reduced State, PDB code: 4iud was solved by M.Hammer, A.Schmidt, S.Frielingsdorf, 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) 34.42 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.775, 95.795, 120.679, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.5

Other elements in 4iud:

The structure of Crystal Structure of An O2-Tolerant [Nife]-Hydrogenase From Ralstonia Eutropha in Its As-Isolated Form with Ascorbate - Partly Reduced State also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 13 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 with Ascorbate - Partly Reduced State (pdb code 4iud). 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 with Ascorbate - Partly Reduced State, PDB code: 4iud:

Nickel binding site 1 out of 1 in 4iud

Go back to Nickel Binding Sites List in 4iud
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 with Ascorbate - Partly Reduced State


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 with Ascorbate - Partly Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni1001

b:12.8
occ:1.00
 NI L:NFV1001 0.0 12.8 1.0
O4 L:NFV1001 1.9 12.6 1.0
SG L:CSO597 2.2 12.6 0.5
SG L:CYS75 2.2 14.2 1.0
SG L:CSO597 2.3 11.8 0.5
OD L:CSO597 2.5 13.4 0.2
SG L:CYS78 2.5 10.9 1.0
SG L:CYS600 2.6 10.6 1.0
FE L:NFV1001 2.9 10.4 1.0
OD L:CSO597 3.0 11.7 0.2
CB L:CYS75 3.1 12.1 1.0
CB L:CSO597 3.2 11.5 0.5
CB L:CSO597 3.2 11.3 0.5
CB L:CYS78 3.6 12.7 1.0
CB L:CYS600 3.6 9.6 1.0
N L:CYS78 3.8 13.1 1.0
C2 L:NFV1001 4.0 10.5 1.0
C3 L:NFV1001 4.2 11.1 1.0
CA L:CYS78 4.3 12.8 1.0
NH1 L:ARG530 4.3 13.8 1.0
C1 L:NFV1001 4.5 10.3 1.0
CA L:CYS75 4.5 10.8 1.0
CB L:VAL77 4.5 12.9 1.0
CZ L:ARG530 4.6 13.2 1.0
N L:CYS600 4.6 9.1 1.0
CA L:CSO597 4.6 10.9 0.5
CA L:CSO597 4.6 11.0 0.5
CA L:CYS600 4.6 9.8 1.0
NE L:ARG530 4.8 12.4 1.0
C L:VAL77 4.9 13.1 1.0
N2 L:NFV1001 4.9 10.1 1.0
CD L:ARG530 4.9 12.1 1.0
N L:VAL77 5.0 12.0 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 18:15:41 2024

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