Chlorine in PDB 5jrd: E. Coli Hydrogenase-1 Variant P508A

All present enzymatic activity of E. Coli Hydrogenase-1 Variant P508A:
1.12.99.6;

The structure of E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd was solved by S.B.Carr, S.E.V.Phillips, F.A.Armstrong, R.M.Evans, E.J.Brooke, S.T.A.Islam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.69 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.691, 98.589, 185.373, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.1

The structure of E. Coli Hydrogenase-1 Variant P508A also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	2 atoms
Iron	(Fe)	26 atoms

The binding sites of Chlorine atom in the E. Coli Hydrogenase-1 Variant P508A (pdb code 5jrd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the E. Coli Hydrogenase-1 Variant P508A, PDB code: 5jrd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ S:Cl404 b:15.0 occ:1.00 O S:HOH595 3.1 15.5 1.0 O S:HOH665 3.1 29.8 1.0 N S:GLY256 3.2 12.0 1.0 N S:CYS120 3.2 9.9 1.0 CB S:TRP118 3.7 13.0 1.0 CG2 S:THR114 3.7 12.5 1.0 CA S:CYS120 3.7 9.9 1.0 CA S:GLY256 3.9 12.9 1.0 N S:GLY119 4.1 11.4 1.0 C S:ASN255 4.2 11.6 1.0 C S:TRP118 4.2 11.4 1.0 OD1 S:ASN255 4.2 15.3 1.0 C S:GLY119 4.2 10.4 1.0 CA S:ASN255 4.2 12.1 1.0 CA S:GLY119 4.3 10.6 1.0 O S:CYS120 4.4 10.3 1.0 O S:TRP118 4.4 13.9 1.0 O S:GLU254 4.5 11.9 1.0 N S:PHE257 4.5 11.6 1.0 C S:CYS120 4.6 9.8 1.0 CA S:TRP118 4.6 11.6 1.0 O S:HOH670 4.6 22.0 1.0 C S:GLY256 4.7 11.7 1.0 CD1 S:TRP258 4.8 11.4 1.0 O S:HOH654 4.8 29.2 1.0 CG S:TRP118 4.8 14.9 1.0 CD1 S:PHE257 4.8 11.8 1.0 CB S:CYS120 4.9 10.3 1.0 O S:THR114 4.9 11.0 1.0

Chlorine binding site 2 out of 4 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ S:Cl405 b:24.0 occ:1.00 O S:HOH549 2.9 32.0 1.0 N S:HIS13 3.2 10.1 1.0 O S:HOH503 3.2 57.8 1.0 NZ S:LYS98 3.4 21.3 1.0 CB S:ILE12 3.5 11.3 1.0 OD2 S:ASP46 3.5 27.9 1.0 CA S:ILE12 3.5 10.3 1.0 CE S:LYS98 3.7 21.4 1.0 O S:HIS13 3.9 12.0 1.0 C S:ILE12 3.9 10.2 1.0 CG2 S:ILE12 3.9 12.3 1.0 CE1 S:TYR44 4.1 14.9 1.0 CG S:ASP46 4.1 24.6 1.0 CA S:HIS13 4.1 11.3 1.0 CD S:LYS98 4.2 19.7 1.0 CB S:HIS13 4.3 12.0 1.0 C S:HIS13 4.4 10.4 1.0 OH S:TYR44 4.5 18.3 1.0 OD1 S:ASP46 4.6 26.4 1.0 CD2 S:HIS13 4.6 14.0 1.0 CE1 S:PHE95 4.6 13.1 1.0 O S:TRP11 4.8 12.2 1.0 CZ S:TYR44 4.8 15.3 1.0 CG1 S:ILE12 4.8 12.6 1.0 N S:ILE12 4.9 10.6 1.0 CG S:HIS13 4.9 13.1 1.0 CB S:ASP46 4.9 20.1 1.0

Chlorine binding site 3 out of 4 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ T:Cl404 b:16.4 occ:1.00 O T:HOH622 3.1 16.4 1.0 O T:HOH661 3.1 30.1 1.0 N T:GLY256 3.1 12.3 1.0 N T:CYS120 3.2 11.2 1.0 CA T:CYS120 3.8 10.9 1.0 CG2 T:THR114 3.8 13.0 1.0 CB T:TRP118 3.8 15.0 1.0 CA T:GLY256 3.9 13.1 1.0 N T:GLY119 4.1 12.6 1.0 C T:ASN255 4.1 12.0 1.0 C T:TRP118 4.2 13.0 1.0 C T:GLY119 4.2 11.2 1.0 CA T:ASN255 4.2 12.0 1.0 OD1 T:ASN255 4.2 16.1 1.0 CA T:GLY119 4.3 12.1 1.0 O T:TRP118 4.4 15.3 1.0 O T:GLU254 4.4 13.0 1.0 O T:CYS120 4.5 11.2 1.0 N T:PHE257 4.5 12.1 1.0 O T:HOH671 4.6 22.6 1.0 C T:CYS120 4.6 10.9 1.0 C T:GLY256 4.6 12.0 1.0 CA T:TRP118 4.7 13.9 1.0 CD1 T:TRP258 4.7 12.2 1.0 CD1 T:PHE257 4.8 12.0 1.0 CG T:TRP118 4.8 17.2 1.0 O T:HOH660 4.9 29.6 1.0 CB T:CYS120 4.9 11.7 1.0 O T:THR114 5.0 12.1 1.0

Chlorine binding site 4 out of 4 in the E. Coli Hydrogenase-1 Variant P508A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of E. Coli Hydrogenase-1 Variant P508A within 5.0Å range: probe atom residue distance (Å) B Occ T:Cl405 b:26.2 occ:1.00 O T:HOH673 3.0 38.4 1.0 O T:HOH570 3.1 28.8 1.0 N T:HIS13 3.2 11.9 1.0 NZ T:LYS98 3.4 24.4 1.0 CB T:ILE12 3.5 12.2 1.0 OD2 T:ASP46 3.5 29.5 1.0 CA T:ILE12 3.5 12.2 1.0 CE T:LYS98 3.7 21.1 1.0 O T:HIS13 3.9 13.2 1.0 C T:ILE12 3.9 11.6 1.0 CG2 T:ILE12 3.9 13.1 1.0 CD T:LYS98 4.1 21.0 1.0 CG T:ASP46 4.1 25.8 1.0 CE1 T:TYR44 4.1 16.4 1.0 CA T:HIS13 4.2 11.7 1.0 CB T:HIS13 4.4 13.5 1.0 C T:HIS13 4.4 12.0 1.0 OD1 T:ASP46 4.6 27.7 1.0 OH T:TYR44 4.6 18.8 1.0 CE1 T:PHE95 4.6 14.6 1.0 CD2 T:HIS13 4.6 14.1 1.0 O T:TRP11 4.8 13.7 1.0 CG1 T:ILE12 4.9 12.9 1.0 N T:ILE12 4.9 10.9 1.0 CZ T:TYR44 4.9 15.6 1.0 CG T:HIS13 4.9 14.1 1.0 CB T:ASP46 4.9 20.4 1.0

E.J.Brooke, R.M.Evans, S.T.Islam, G.M.Roberts, S.A.Wehlin, S.B.Carr, S.E.Phillips, F.A.Armstrong. Importance of the Active Site "Canopy" Residues in An O2-Tolerant [Nife]-Hydrogenase. Biochemistry V. 56 132 2017.
ISSN: ISSN 1520-4995
PubMed: 28001048
DOI: 10.1021/ACS.BIOCHEM.6B00868