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Chlorine in PDB 9er6: Hydrogenase-1 Ni-Si State

Enzymatic activity of Hydrogenase-1 Ni-Si State

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

Protein crystallography data

The structure of Hydrogenase-1 Ni-Si State, PDB code: 9er6 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) 65.50 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.8, 96.188, 182.582, 90, 90, 90
R / Rfree (%) 17.1 / 18.4

Other elements in 9er6:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hydrogenase-1 Ni-Si State (pdb code 9er6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hydrogenase-1 Ni-Si State, PDB code: 9er6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9er6

Go back to Chlorine Binding Sites List in 9er6
Chlorine binding site 1 out of 5 in the Hydrogenase-1 Ni-Si 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-Si State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl404

b:18.3
occ:1.00
 O S:HOH591 2.9 16.0 1.0
N S:GLY256 3.1 13.4 1.0
N S:CYS120 3.1 11.6 1.0
O S:HOH654 3.2 24.5 1.0
CB S:TRP118 3.6 14.2 1.0
CA S:CYS120 3.7 11.7 1.0
CG2 S:THR114 3.7 11.8 1.0
CA S:GLY256 3.7 13.7 1.0
N S:GLY119 4.0 13.5 1.0
C S:TRP118 4.1 14.6 1.0
C S:GLY119 4.1 12.8 1.0
C S:ASN255 4.2 14.0 1.0
OD1 S:ASN255 4.2 15.2 1.0
CA S:GLY119 4.2 12.5 1.0
O S:CYS120 4.3 11.0 1.0
CA S:ASN255 4.3 13.7 1.0
O S:TRP118 4.3 14.6 1.0
N S:PHE257 4.4 13.5 1.0
O S:GLU254 4.4 12.2 1.0
C S:CYS120 4.4 11.1 1.0
C S:GLY256 4.5 13.3 1.0
CA S:TRP118 4.5 12.9 1.0
CD1 S:TRP258 4.6 11.1 1.0
O S:HOH541 4.7 26.5 1.0
CG S:TRP118 4.7 16.8 1.0
O S:THR114 4.8 10.3 1.0
CD1 S:PHE257 4.8 11.6 1.0
CB S:CYS120 4.9 10.6 1.0

Chlorine binding site 2 out of 5 in 9er6

Go back to Chlorine Binding Sites List in 9er6
Chlorine binding site 2 out of 5 in the Hydrogenase-1 Ni-Si 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-Si State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:17.5
occ:1.00
 O S:HOH584 3.1 25.8 1.0
O S:HOH569 3.1 23.8 1.0
N S:HIS13 3.2 10.5 1.0
O S:HOH504 3.3 21.8 1.0
NZ S:LYS98 3.3 20.6 1.0
CB S:ILE12 3.5 10.7 1.0
CA S:ILE12 3.5 10.2 1.0
OD2 S:ASP46 3.7 21.3 1.0
CE S:LYS98 3.8 19.0 1.0
O S:HIS13 3.9 10.2 1.0
CG2 S:ILE12 3.9 11.1 1.0
C S:ILE12 3.9 10.8 1.0
O S:HOH595 4.1 24.6 1.0
CD S:LYS98 4.1 18.2 1.0
CE2 S:TYR44 4.1 14.8 1.0
CG S:ASP46 4.2 23.9 1.0
CA S:HIS13 4.2 10.3 1.0
CB S:HIS13 4.4 10.2 1.0
C S:HIS13 4.4 10.4 1.0
OH S:TYR44 4.5 17.3 1.0
CE1 S:PHE95 4.5 12.2 1.0
OD1 S:ASP46 4.6 25.7 1.0
CD2 S:HIS13 4.7 10.8 1.0
CZ S:TYR44 4.8 16.2 1.0
N S:ILE12 4.8 10.7 1.0
O S:TRP11 4.8 11.4 1.0
CG1 S:ILE12 4.9 11.5 1.0
CD1 S:PHE95 4.9 12.8 1.0
CG S:HIS13 4.9 10.3 1.0
CB S:ASP46 5.0 18.8 1.0

Chlorine binding site 3 out of 5 in 9er6

Go back to Chlorine Binding Sites List in 9er6
Chlorine binding site 3 out of 5 in the Hydrogenase-1 Ni-Si 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-Si State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl606

b:38.1
occ:1.00
 NE2 L:HIS421 3.2 21.2 1.0
O L:HOH1119 3.3 34.8 1.0
CD2 L:LEU417 3.5 15.9 1.0
CD2 L:LEU442 3.7 44.2 1.0
NE2 L:GLN446 3.9 18.0 1.0
OE1 L:GLN446 3.9 18.9 1.0
CD L:GLN446 3.9 19.1 1.0
CG L:LEU442 4.0 41.7 1.0
CE1 L:HIS421 4.1 23.5 1.0
CD2 L:HIS421 4.3 20.9 1.0
O L:HOH1021 4.7 22.5 1.0
CD1 L:LEU442 4.7 44.1 1.0
CG L:GLN446 4.8 17.6 1.0
CG2 L:ILE445 4.9 20.1 1.0
O L:LEU442 5.0 23.4 1.0

Chlorine binding site 4 out of 5 in 9er6

Go back to Chlorine Binding Sites List in 9er6
Chlorine binding site 4 out of 5 in the Hydrogenase-1 Ni-Si 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-Si State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl404

b:18.8
occ:1.00
 O T:HOH598 3.0 15.4 1.0
N T:CYS120 3.1 12.2 1.0
N T:GLY256 3.1 13.3 1.0
O T:HOH662 3.2 25.7 1.0
CB T:TRP118 3.6 15.2 1.0
CA T:CYS120 3.6 11.2 1.0
CG2 T:THR114 3.7 13.2 1.0
CA T:GLY256 3.7 12.7 1.0
N T:GLY119 4.0 13.5 1.0
C T:TRP118 4.0 14.8 1.0
C T:GLY119 4.1 11.9 1.0
C T:ASN255 4.2 13.2 1.0
CA T:GLY119 4.2 12.5 1.0
OD1 T:ASN255 4.2 16.4 1.0
O T:TRP118 4.2 15.7 1.0
O T:CYS120 4.3 11.3 1.0
CA T:ASN255 4.3 14.4 1.0
N T:PHE257 4.4 12.5 1.0
C T:CYS120 4.4 12.2 1.0
CA T:TRP118 4.5 14.5 1.0
O T:GLU254 4.5 12.5 1.0
C T:GLY256 4.5 12.7 1.0
CD1 T:TRP258 4.6 10.7 1.0
O T:HOH586 4.6 25.5 1.0
CG T:TRP118 4.7 16.1 1.0
O T:THR114 4.8 12.3 1.0
CB T:CYS120 4.8 11.3 1.0
CD1 T:PHE257 4.9 11.1 1.0

Chlorine binding site 5 out of 5 in 9er6

Go back to Chlorine Binding Sites List in 9er6
Chlorine binding site 5 out of 5 in the Hydrogenase-1 Ni-Si State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hydrogenase-1 Ni-Si State within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:17.3
occ:1.00
 O T:HOH616 3.1 20.0 1.0
O T:HOH596 3.1 17.1 1.0
O T:HOH533 3.3 24.8 1.0
N T:HIS13 3.3 11.9 1.0
NZ T:LYS98 3.3 19.8 1.0
CB T:ILE12 3.5 13.3 1.0
CA T:ILE12 3.6 12.6 1.0
OD2 T:ASP46 3.8 19.4 1.0
CE T:LYS98 3.8 18.9 1.0
O T:HIS13 3.9 12.7 1.0
CG2 T:ILE12 3.9 13.4 1.0
C T:ILE12 4.0 13.1 1.0
CD T:LYS98 4.0 19.2 1.0
CE2 T:TYR44 4.1 16.3 1.0
O T:HOH620 4.1 18.6 1.0
CA T:HIS13 4.3 12.1 1.0
CG T:ASP46 4.3 21.1 1.0
CB T:HIS13 4.4 12.2 1.0
CE1 T:PHE95 4.4 14.0 1.0
C T:HIS13 4.5 12.3 1.0
OH T:TYR44 4.6 16.7 1.0
CD2 T:HIS13 4.8 12.2 1.0
O T:TRP11 4.8 13.3 1.0
OD1 T:ASP46 4.8 20.4 1.0
CD1 T:PHE95 4.8 13.2 1.0
CG1 T:ILE12 4.9 14.6 1.0
CZ T:TYR44 4.9 16.7 1.0
N T:ILE12 4.9 13.1 1.0
CG T:HIS13 5.0 12.2 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 16:34:25 2025

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