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Chlorine in PDB 9era: Hydrogenase-1 Ni-Lii State

Enzymatic activity of Hydrogenase-1 Ni-Lii State

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

Protein crystallography data

The structure of Hydrogenase-1 Ni-Lii State, PDB code: 9era was solved by K.L.Wong, S.B.Carr, 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) 54.29 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.679, 97.072, 183.149, 90, 90, 90
R / Rfree (%) 20.4 / 22.2

Other elements in 9era:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hydrogenase-1 Ni-Lii State (pdb code 9era). 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-Lii State, PDB code: 9era:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 9era

Go back to Chlorine Binding Sites List in 9era
Chlorine binding site 1 out of 4 in the Hydrogenase-1 Ni-Lii 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-Lii State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl404

b:25.2
occ:1.00
 O S:HOH544 2.9 20.1 1.0
N S:GLY256 3.1 17.9 1.0
N S:CYS120 3.2 15.9 1.0
O S:HOH579 3.3 25.1 1.0
CB S:TRP118 3.6 19.3 1.0
CA S:GLY256 3.7 17.1 1.0
CA S:CYS120 3.7 15.9 1.0
CG2 S:THR114 3.7 17.8 1.0
N S:GLY119 4.1 18.0 1.0
C S:ASN255 4.1 17.2 1.0
OD1 S:ASN255 4.1 22.6 1.0
C S:TRP118 4.1 18.4 1.0
C S:GLY119 4.2 16.9 1.0
CA S:ASN255 4.3 17.6 1.0
CA S:GLY119 4.3 17.6 1.0
O S:CYS120 4.3 16.6 1.0
N S:PHE257 4.3 15.5 1.0
O S:GLU254 4.4 16.4 1.0
O S:HOH576 4.4 25.6 1.0
O S:TRP118 4.4 17.1 1.0
C S:GLY256 4.5 16.1 1.0
C S:CYS120 4.5 15.8 1.0
CA S:TRP118 4.5 18.2 1.0
CD1 S:TRP258 4.6 14.6 1.0
CG S:TRP118 4.6 20.8 1.0
CD1 S:PHE257 4.8 15.0 1.0
O S:THR114 4.8 14.3 1.0
CB S:CYS120 4.9 16.9 1.0

Chlorine binding site 2 out of 4 in 9era

Go back to Chlorine Binding Sites List in 9era
Chlorine binding site 2 out of 4 in the Hydrogenase-1 Ni-Lii 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-Lii State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:37.1
occ:1.00
 OD1 S:ASP46 2.8 27.4 1.0
O S:HOH519 2.9 22.9 1.0
N S:HIS13 3.1 13.6 1.0
NZ S:LYS98 3.2 39.0 1.0
CA S:ILE12 3.4 15.2 1.0
CG S:ASP46 3.5 24.0 1.0
CB S:ILE12 3.5 15.0 1.0
OD2 S:ASP46 3.6 23.6 1.0
C S:ILE12 3.8 15.2 1.0
CE1 S:TYR44 3.8 20.4 1.0
CG2 S:ILE12 3.9 15.7 1.0
O S:HIS13 3.9 14.6 1.0
CE S:LYS98 3.9 37.0 1.0
CA S:HIS13 4.1 14.1 1.0
OH S:TYR44 4.1 21.8 1.0
CB S:HIS13 4.3 14.6 1.0
CD2 S:HIS13 4.3 15.9 1.0
CD S:LYS98 4.3 33.4 1.0
C S:HIS13 4.4 15.7 1.0
CZ S:TYR44 4.5 20.6 1.0
O S:TRP11 4.6 16.5 1.0
CG S:HIS13 4.6 15.4 1.0
N S:ILE12 4.7 15.2 1.0
CB S:ASP46 4.8 20.3 1.0
CE1 S:PHE95 4.8 18.6 1.0
CD1 S:TYR44 4.8 19.7 1.0
CG1 S:ILE12 4.9 16.2 1.0

Chlorine binding site 3 out of 4 in 9era

Go back to Chlorine Binding Sites List in 9era
Chlorine binding site 3 out of 4 in the Hydrogenase-1 Ni-Lii 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-Lii State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl404

b:25.9
occ:1.00
 O T:HOH538 2.9 20.6 1.0
N T:GLY256 3.0 18.1 1.0
N T:CYS120 3.2 16.8 1.0
CA T:GLY256 3.6 17.3 1.0
CB T:TRP118 3.6 21.6 1.0
CA T:CYS120 3.7 15.5 1.0
CG2 T:THR114 3.8 17.2 1.0
C T:ASN255 4.0 17.8 1.0
N T:GLY119 4.1 17.4 1.0
C T:TRP118 4.1 18.8 1.0
OD1 T:ASN255 4.1 21.5 1.0
C T:GLY119 4.2 16.9 1.0
CA T:ASN255 4.2 19.1 1.0
O T:CYS120 4.3 15.4 1.0
N T:PHE257 4.3 16.6 1.0
CA T:GLY119 4.3 16.9 1.0
O T:GLU254 4.3 17.1 1.0
O T:TRP118 4.4 19.6 1.0
C T:GLY256 4.4 17.2 1.0
C T:CYS120 4.5 16.1 1.0
CA T:TRP118 4.5 18.9 1.0
CD1 T:TRP258 4.6 14.7 1.0
CG T:TRP118 4.7 23.6 1.0
CD1 T:PHE257 4.8 14.8 1.0
O T:THR114 4.8 16.4 1.0
CB T:CYS120 4.9 16.3 1.0

Chlorine binding site 4 out of 4 in 9era

Go back to Chlorine Binding Sites List in 9era
Chlorine binding site 4 out of 4 in the Hydrogenase-1 Ni-Lii 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-Lii State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:49.3
occ:1.00
 O T:HOH542 2.8 23.4 1.0
OD1 T:ASP46 2.8 23.0 0.8
N T:HIS13 3.1 17.6 1.0
NZ T:LYS98 3.2 38.5 1.0
OD2 T:ASP46 3.2 20.9 0.2
CA T:ILE12 3.4 17.6 1.0
CB T:ILE12 3.4 17.2 1.0
CG T:ASP46 3.5 23.0 0.8
OD2 T:ASP46 3.7 22.0 0.8
CG T:ASP46 3.7 21.3 0.2
C T:ILE12 3.8 18.4 1.0
CG2 T:ILE12 3.8 16.9 1.0
CE T:LYS98 3.8 37.4 1.0
O T:HIS13 3.8 18.8 1.0
OD1 T:ASP46 3.9 21.4 0.2
CE1 T:TYR44 3.9 21.9 1.0
CA T:HIS13 4.1 17.6 1.0
CD T:LYS98 4.2 35.7 1.0
CB T:HIS13 4.3 18.2 1.0
OH T:TYR44 4.3 24.7 1.0
CD2 T:HIS13 4.3 20.7 1.0
C T:HIS13 4.4 17.7 1.0
CZ T:TYR44 4.6 22.1 1.0
O T:TRP11 4.7 18.7 1.0
CE1 T:PHE95 4.7 19.7 1.0
CG T:HIS13 4.7 19.9 1.0
N T:ILE12 4.7 17.1 1.0
CG1 T:ILE12 4.8 17.0 1.0
CB T:ASP46 4.8 20.9 0.2
CD1 T:TYR44 4.9 20.5 1.0
CB T:ASP46 4.9 21.2 0.8
O T:ILE12 5.0 18.5 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 16:35:22 2025

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