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Chlorine 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:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom
Krypton (Kr) 23 atoms
Iron (Fe) 13 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Krypton Derivatization of An O2-Tolerant Membrane-Bound [Nife] Hydrogenase Reveals A Hydrophobic Gas Tunnel Network, PDB code: 5d51:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5d51

Go back to Chlorine Binding Sites List in 5d51
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl715

b:25.8
occ:0.85
 O L:HOH824 2.6 23.1 1.0
O L:HOH1148 2.8 19.7 1.0
NE L:ARG88 3.0 16.1 1.0
NH1 L:ARG106 3.2 15.4 1.0
CD L:ARG106 3.4 14.8 1.0
NH2 L:ARG88 3.5 19.1 1.0
CZ L:ARG88 3.7 18.0 1.0
CD1 L:ILE98 3.8 17.5 1.0
CG L:ARG88 3.8 14.6 1.0
CD1 L:LEU84 3.8 13.6 1.0
CD L:ARG88 4.0 15.1 1.0
CZ L:ARG106 4.1 14.3 1.0
NE L:ARG106 4.2 14.7 1.0
O L:HOH951 4.2 26.7 1.0
CB L:ARG106 4.4 14.0 1.0
CG L:ARG106 4.5 14.7 1.0
O L:HOH1139 4.6 41.1 1.0
O L:HOH810 4.6 18.6 1.0
ND1 L:HIS103 4.7 24.6 1.0
OE2 L:GLU107 4.9 43.8 1.0
OE1 L:GLU91 5.0 17.0 1.0
CG L:LEU84 5.0 14.0 1.0

Chlorine binding site 2 out of 2 in 5d51

Go back to Chlorine Binding Sites List in 5d51
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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
S:Cl1011

b:26.3
occ:1.00
 O S:HOH1132 3.2 21.4 1.0
N S:CYS120 3.2 16.8 1.0
N S:GLY256 3.2 19.7 1.0
O S:HOH1144 3.3 30.3 1.0
CA S:CYS120 3.5 14.9 1.0
CB S:TRP118 3.7 20.6 1.0
CA S:GLY256 3.9 19.6 1.0
O S:GLU254 4.1 18.3 1.0
CD1 S:PHE257 4.1 18.9 1.0
N S:PHE257 4.2 17.1 1.0
C S:ASP255 4.2 19.4 1.0
N S:GLY119 4.3 17.8 1.0
CE1 S:PHE257 4.3 17.6 1.0
C S:TRP118 4.3 17.5 1.0
C S:GLY119 4.4 17.0 1.0
CA S:ASP255 4.4 18.9 1.0
C S:CYS120 4.4 14.0 1.0
CD1 S:TRP258 4.4 14.4 1.0
O S:CYS120 4.5 16.0 1.0
O S:SER114 4.5 17.9 1.0
C S:GLY256 4.5 18.2 1.0
CB S:SER114 4.5 16.9 1.0
CB S:CYS120 4.5 14.5 1.0
CG S:TRP118 4.6 21.8 1.0
O S:TRP118 4.7 21.0 1.0
CA S:TRP118 4.7 18.2 1.0
CA S:GLY119 4.7 16.5 1.0
OD1 S:ASP255 4.7 23.7 1.0
O S:HOH1237 4.7 22.9 1.0
NE1 S:TRP258 4.8 13.8 1.0
CD1 S:TRP118 4.8 22.6 1.0
C S:GLU254 4.9 17.6 1.0
O S:HOH1246 5.0 39.3 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: Sat Jul 12 01:06:29 2025

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