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Chlorine in PDB 9er7: Hydrogenase-1 Ni-Sco State

Enzymatic activity of Hydrogenase-1 Ni-Sco State

All present enzymatic activity of Hydrogenase-1 Ni-Sco State:
1.12.99.6;

Protein crystallography data

The structure of Hydrogenase-1 Ni-Sco State, PDB code: 9er7 was solved by S.B.Carr, W.Li, K.L.Wong, P.A.Ash, K.A.Vincent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.20 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.79, 96.01, 182.79, 90, 90, 90
R / Rfree (%) 16.9 / 18.9

Other elements in 9er7:

The structure of Hydrogenase-1 Ni-Sco State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hydrogenase-1 Ni-Sco State (pdb code 9er7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hydrogenase-1 Ni-Sco State, PDB code: 9er7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 9er7

Go back to Chlorine Binding Sites List in 9er7
Chlorine binding site 1 out of 4 in the Hydrogenase-1 Ni-Sco State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl404

b:21.4
occ:1.00
 O S:HOH618 2.9 18.3 1.0
N S:GLY256 3.1 16.4 1.0
N S:CYS120 3.2 15.4 1.0
O S:HOH667 3.2 28.0 1.0
CB S:TRP118 3.7 17.0 1.0
CA S:CYS120 3.7 14.2 1.0
CA S:GLY256 3.8 16.4 1.0
CG2 S:THR114 3.8 16.0 1.0
N S:GLY119 4.0 16.5 1.0
C S:TRP118 4.1 17.8 1.0
C S:GLY119 4.1 15.7 1.0
OD1 S:ASN255 4.2 19.6 1.0
C S:ASN255 4.2 16.9 1.0
O S:CYS120 4.3 14.0 1.0
CA S:GLY119 4.3 15.5 1.0
CA S:ASN255 4.3 16.1 1.0
O S:TRP118 4.3 18.2 1.0
N S:PHE257 4.4 16.2 1.0
O S:GLU254 4.4 15.9 1.0
C S:CYS120 4.4 13.9 1.0
C S:GLY256 4.5 16.1 1.0
CA S:TRP118 4.6 16.2 1.0
CD1 S:TRP258 4.6 15.4 1.0
O S:HOH571 4.6 31.2 1.0
CG S:TRP118 4.7 19.7 1.0
O S:THR114 4.9 14.0 1.0
CD1 S:PHE257 4.9 15.2 1.0
CB S:CYS120 4.9 14.3 1.0

Chlorine binding site 2 out of 4 in 9er7

Go back to Chlorine Binding Sites List in 9er7
Chlorine binding site 2 out of 4 in the Hydrogenase-1 Ni-Sco State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:21.1
occ:1.00
 O S:HOH579 3.1 22.6 1.0
O S:HOH534 3.1 27.2 1.0
O S:HOH520 3.2 25.3 1.0
N S:HIS13 3.3 14.3 1.0
NZ S:LYS98 3.3 24.1 1.0
CB S:ILE12 3.5 15.6 1.0
CA S:ILE12 3.5 13.4 1.0
OD2 S:ASP46 3.7 21.3 1.0
CE S:LYS98 3.7 22.7 1.0
O S:HIS13 3.9 14.2 1.0
CG2 S:ILE12 3.9 15.5 1.0
C S:ILE12 3.9 13.7 1.0
O S:HOH606 4.1 27.9 1.0
CD S:LYS98 4.1 21.8 1.0
CE2 S:TYR44 4.1 18.9 1.0
CA S:HIS13 4.2 13.9 1.0
CG S:ASP46 4.2 21.5 1.0
CB S:HIS13 4.4 14.3 1.0
C S:HIS13 4.5 13.9 1.0
CE1 S:PHE95 4.5 16.5 1.0
OH S:TYR44 4.5 20.6 1.0
CD2 S:HIS13 4.7 14.7 1.0
OD1 S:ASP46 4.7 23.5 1.0
CZ S:TYR44 4.8 18.0 1.0
O S:TRP11 4.8 14.8 1.0
N S:ILE12 4.8 14.2 1.0
CG1 S:ILE12 4.8 16.0 1.0
CG S:HIS13 4.9 14.2 1.0
CD1 S:PHE95 4.9 15.7 1.0
CB S:ASP46 5.0 21.5 1.0

Chlorine binding site 3 out of 4 in 9er7

Go back to Chlorine Binding Sites List in 9er7
Chlorine binding site 3 out of 4 in the Hydrogenase-1 Ni-Sco State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl404

b:21.8
occ:1.00
 O T:HOH604 3.0 18.6 1.0
N T:GLY256 3.1 16.4 1.0
N T:CYS120 3.1 16.5 1.0
O T:HOH662 3.2 30.7 1.0
CB T:TRP118 3.6 18.7 1.0
CA T:CYS120 3.7 14.5 1.0
CG2 T:THR114 3.7 18.1 1.0
CA T:GLY256 3.7 17.1 1.0
N T:GLY119 4.0 17.2 1.0
C T:TRP118 4.1 18.3 1.0
C T:GLY119 4.1 16.9 1.0
C T:ASN255 4.1 16.1 1.0
O T:TRP118 4.2 18.8 1.0
OD1 T:ASN255 4.2 21.2 1.0
CA T:GLY119 4.2 15.7 1.0
O T:CYS120 4.3 16.0 1.0
CA T:ASN255 4.3 16.7 1.0
N T:PHE257 4.4 16.6 1.0
C T:CYS120 4.4 15.8 1.0
O T:GLU254 4.5 15.9 1.0
CA T:TRP118 4.5 18.5 1.0
C T:GLY256 4.5 16.4 1.0
CD1 T:TRP258 4.6 14.4 1.0
O T:HOH616 4.6 30.9 1.0
CG T:TRP118 4.7 21.4 1.0
O T:THR114 4.8 15.7 1.0
CD1 T:PHE257 4.8 15.9 1.0
CB T:CYS120 4.9 15.9 1.0

Chlorine binding site 4 out of 4 in 9er7

Go back to Chlorine Binding Sites List in 9er7
Chlorine binding site 4 out of 4 in the Hydrogenase-1 Ni-Sco State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hydrogenase-1 Ni-Sco State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:21.0
occ:1.00
 O T:HOH607 3.1 24.1 1.0
O T:HOH599 3.1 20.9 1.0
O T:HOH554 3.2 25.8 1.0
NZ T:LYS98 3.3 22.5 1.0
N T:HIS13 3.3 14.9 1.0
CB T:ILE12 3.5 16.9 1.0
CA T:ILE12 3.6 14.8 1.0
CE T:LYS98 3.7 20.2 1.0
OD2 T:ASP46 3.8 21.1 1.0
O T:HIS13 3.9 17.0 1.0
CG2 T:ILE12 3.9 16.8 1.0
CD T:LYS98 4.0 21.2 1.0
C T:ILE12 4.0 16.2 1.0
CE2 T:TYR44 4.1 20.2 1.0
O T:HOH618 4.1 24.9 1.0
CA T:HIS13 4.3 15.8 1.0
CG T:ASP46 4.3 21.6 1.0
CB T:HIS13 4.4 17.1 1.0
CE1 T:PHE95 4.4 17.9 1.0
C T:HIS13 4.5 16.6 1.0
OH T:TYR44 4.6 19.5 1.0
CD2 T:HIS13 4.7 15.2 1.0
O T:TRP11 4.8 16.8 1.0
OD1 T:ASP46 4.8 22.1 1.0
CD1 T:PHE95 4.9 17.0 1.0
CG1 T:ILE12 4.9 17.4 1.0
CZ T:TYR44 4.9 19.9 1.0
N T:ILE12 4.9 15.5 1.0
CG T:HIS13 4.9 16.4 1.0

Reference:

S.B.Carr, W.Li, K.L.Wong, R.M.Evans, S.E.T.Kendall-Price, P.A.Ash, K.A.Vincent. Glutamate Flick Enables Proton Tunnelling During Fast Redox Biocatalysis To Be Published.
Page generated: Sun Jul 13 16:35:14 2025

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