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Nickel in PDB 5d51: Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network

Enzymatic activity of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network

All present enzymatic activity of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network:
1.12.99.6;

Protein crystallography data

The structure of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network, PDB code: 5d51 was solved by J.Kalms, A.Schmidt, S.Frielingsdorf, P.Van Der Linden, D.Von Stetten, O.Lenz, P.Carpentier, P.Scheerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.387, 95.574, 119.752, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15

Other elements in 5d51:

The structure of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Krypton (Kr) 23 atoms
Iron (Fe) 13 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network (pdb code 5d51). 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 Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network, PDB code: 5d51:

Nickel binding site 1 out of 1 in 5d51

Go back to Nickel Binding Sites List in 5d51
Nickel binding site 1 out of 1 in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni701

b:15.9
occ:1.00
 NI L:NFV701 0.0 15.9 1.0
O4 L:NFV701 1.8 16.6 1.0
SG L:CYS597 2.2 18.7 1.0
SG L:CYS75 2.2 18.6 1.0
SG L:CYS78 2.4 14.6 1.0
SG L:CYS600 2.6 15.1 1.0
FE L:NFV701 2.8 13.9 1.0
CB L:CYS75 3.1 15.4 1.0
CB L:CYS597 3.2 15.1 1.0
CB L:CYS78 3.4 14.8 1.0
CB L:CYS600 3.6 14.8 1.0
N L:CYS78 3.6 13.8 1.0
C2 L:NFV701 3.9 13.4 1.0
C3 L:NFV701 4.1 13.9 1.0
CA L:CYS78 4.1 13.9 1.0
NH1 L:ARG530 4.2 18.8 1.0
CB L:VAL77 4.5 15.7 1.0
CA L:CYS75 4.5 14.4 1.0
C1 L:NFV701 4.5 13.8 1.0
CZ L:ARG530 4.5 16.7 1.0
CA L:CYS597 4.6 14.3 1.0
CA L:CYS600 4.6 14.6 1.0
N L:CYS600 4.7 12.9 1.0
C L:VAL77 4.7 13.6 1.0
NE L:ARG530 4.7 16.9 1.0
CD L:ARG530 4.8 15.6 1.0
N2 L:NFV701 4.8 13.8 1.0
N L:VAL77 5.0 14.2 1.0
CA L:VAL77 5.0 13.7 1.0
N3 L:NFV701 5.0 13.9 1.0

Reference:

J.Kalms, A.Schmidt, S.Frielingsdorf, P.Van Der Linden, D.Von Stetten, O.Lenz, P.Carpentier, P.Scheerer. Krypton Derivatization of An O2 -Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Tunnel Network For Gas Transport. Angew.Chem.Int.Ed.Engl. V. 55 5586 2016.
ISSN: ESSN 1521-3773
PubMed: 26913499
DOI: 10.1002/ANIE.201508976
Page generated: Mon Aug 18 19:59:37 2025

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