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Chlorine in PDB 5a4i: The Mechanism of Hydrogen Activation By Nife-Hydrogenases

Enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases

All present enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases:
1.12.99.6;

Protein crystallography data

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4i was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sargent, S.C.Carr, S.E.V.Phillips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.19 / 1.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.780, 97.580, 182.880, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14.7

Other elements in 5a4i:

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5a4i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5a4i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5a4i

Go back to Chlorine Binding Sites List in 5a4i
Chlorine binding site 1 out of 4 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:13.8
occ:1.00
 O S:HOH2044 3.1 14.5 1.0
O S:HOH2042 3.1 27.3 1.0
N S:GLY256 3.2 10.3 1.0
N S:CYS120 3.2 8.6 1.0
CB S:TRP118 3.7 11.7 1.0
CA S:CYS120 3.7 8.5 1.0
CG2 S:THR114 3.7 10.4 1.0
CA S:GLY256 3.8 10.8 1.0
N S:GLY119 4.1 9.8 1.0
C S:ASN255 4.1 10.9 1.0
C S:TRP118 4.1 10.5 1.0
C S:GLY119 4.2 8.5 1.0
OD1 S:ASN255 4.2 13.9 1.0
CA S:ASN255 4.2 10.2 1.0
CA S:GLY119 4.3 9.6 1.0
O S:TRP118 4.4 12.2 1.0
O S:CYS120 4.4 8.6 1.0
O S:GLU254 4.4 10.9 1.0
N S:PHE257 4.4 9.8 1.0
C S:CYS120 4.5 7.8 1.0
CA S:TRP118 4.6 10.4 1.0
O S:HOH2115 4.6 20.1 1.0
C S:GLY256 4.6 9.6 1.0
O S:HOH2046 4.6 24.2 1.0
CD1 S:TRP258 4.7 9.1 1.0
CG S:TRP118 4.7 13.4 1.0
CD1 S:PHE257 4.8 9.5 1.0
CB S:CYS120 4.9 8.7 1.0
O S:THR114 4.9 9.1 1.0

Chlorine binding site 2 out of 4 in 5a4i

Go back to Chlorine Binding Sites List in 5a4i
Chlorine binding site 2 out of 4 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl406

b:22.0
occ:1.00
 O S:HOH2002 3.0 25.0 1.0
N S:HIS13 3.2 8.2 1.0
NZ S:LYS98 3.3 20.7 1.0
OD2 S:ASP46 3.4 27.1 1.0
CB S:ILE12 3.5 9.3 1.0
CA S:ILE12 3.5 8.1 1.0
CE S:LYS98 3.7 17.7 1.0
O S:HIS13 3.8 9.8 1.0
C S:ILE12 3.9 8.9 1.0
CG2 S:ILE12 3.9 10.2 1.0
CD S:LYS98 4.1 16.9 1.0
CG S:ASP46 4.1 19.3 1.0
CA S:HIS13 4.1 8.9 1.0
CE1 S:TYR44 4.1 13.0 1.0
CB S:HIS13 4.3 11.2 1.0
C S:HIS13 4.4 8.7 1.0
OH S:TYR44 4.5 15.3 1.0
CE1 S:PHE95 4.5 12.0 1.0
CD2 S:HIS13 4.6 13.0 1.0
OD1 S:ASP46 4.6 22.5 1.0
O S:TRP11 4.7 10.4 1.0
CZ S:TYR44 4.8 13.2 1.0
N S:ILE12 4.8 8.3 1.0
CG S:HIS13 4.8 12.6 1.0
CG1 S:ILE12 4.9 10.6 1.0
CB S:ASP46 4.9 17.6 1.0
CE1 L:HIS30 5.0 15.4 1.0
CD1 S:PHE95 5.0 11.1 1.0

Chlorine binding site 3 out of 4 in 5a4i

Go back to Chlorine Binding Sites List in 5a4i
Chlorine binding site 3 out of 4 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:14.8
occ:1.00
 O T:HOH2034 3.0 14.8 1.0
O T:HOH2031 3.1 30.0 1.0
N T:GLY256 3.1 10.7 1.0
N T:CYS120 3.2 9.4 1.0
CB T:TRP118 3.7 14.4 1.0
CA T:CYS120 3.7 9.3 1.0
CG2 T:THR114 3.7 10.9 1.0
CA T:GLY256 3.9 11.4 1.0
N T:GLY119 4.0 10.3 1.0
C T:ASN255 4.1 11.1 1.0
C T:TRP118 4.1 11.3 1.0
CA T:ASN255 4.2 10.7 1.0
C T:GLY119 4.2 9.8 1.0
OD1 T:ASN255 4.2 15.2 1.0
CA T:GLY119 4.3 10.0 1.0
O T:GLU254 4.3 11.6 1.0
O T:TRP118 4.3 13.8 1.0
O T:CYS120 4.4 9.8 1.0
N T:PHE257 4.4 10.8 1.0
C T:CYS120 4.5 9.2 1.0
CA T:TRP118 4.6 12.4 1.0
O T:HOH2094 4.6 21.7 1.0
C T:GLY256 4.6 10.9 1.0
CD1 T:TRP258 4.7 9.9 1.0
CD1 T:PHE257 4.7 10.3 1.0
CG T:TRP118 4.7 16.8 1.0
O T:HOH2036 4.8 30.4 1.0
CB T:CYS120 4.9 9.3 1.0
O T:THR114 4.9 10.5 1.0

Chlorine binding site 4 out of 4 in 5a4i

Go back to Chlorine Binding Sites List in 5a4i
Chlorine binding site 4 out of 4 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl406

b:24.1
occ:1.00
 N T:HIS13 3.2 10.0 1.0
O T:HOH2003 3.2 23.1 1.0
NZ T:LYS98 3.2 22.6 1.0
OD2 T:ASP46 3.5 29.2 1.0
CB T:ILE12 3.5 10.8 1.0
CA T:ILE12 3.5 9.8 1.0
CE T:LYS98 3.7 18.7 1.0
O T:HIS13 3.8 11.5 1.0
C T:ILE12 3.9 9.6 1.0
CG2 T:ILE12 3.9 13.0 1.0
CD T:LYS98 4.0 18.1 1.0
CG T:ASP46 4.1 21.4 1.0
CE1 T:TYR44 4.1 14.5 1.0
CA T:HIS13 4.1 9.9 1.0
CB T:HIS13 4.3 12.2 1.0
C T:HIS13 4.4 9.6 1.0
CE1 T:PHE95 4.5 14.5 1.0
CD2 T:HIS13 4.5 12.8 1.0
OH T:TYR44 4.6 16.4 1.0
OD1 T:ASP46 4.6 22.9 1.0
O T:TRP11 4.7 12.0 1.0
CG1 T:ILE12 4.8 10.4 1.0
N T:ILE12 4.8 9.3 1.0
CG T:HIS13 4.8 13.7 1.0
CB T:ASP46 4.9 18.9 1.0
CZ T:TYR44 4.9 13.5 1.0
CD1 T:PHE95 5.0 13.4 1.0

Reference:

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong. Mechanism of Hydrogen Activation By [Nife] Hydrogenases. Nat. Chem. Biol. V. 12 46 2016.
ISSN: ESSN 1552-4469
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976
Page generated: Fri Jul 11 23:59:54 2025

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