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Chlorine in PDB 5a4f: 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: 5a4f was solved by R.M.Evans, E.J.Brooke, S.A.M.Wehlin, E.Nomerotskaia, F.Sargent, S.B.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) 91.64 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.757, 97.770, 183.288, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 15.7

Other elements in 5a4f:

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 5a4f). 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: 5a4f:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5a4f

Go back to Chlorine Binding Sites List in 5a4f
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:13.1
occ:1.00
 O S:HOH2048 3.1 13.2 1.0
O S:HOH2046 3.1 27.1 1.0
N S:GLY256 3.1 10.1 1.0
N S:CYS120 3.2 8.2 1.0
CB S:TRP118 3.7 11.5 1.0
CG2 S:THR114 3.7 9.3 1.0
CA S:CYS120 3.7 7.7 1.0
CA S:GLY256 3.9 10.1 1.0
N S:GLY119 4.0 9.3 1.0
OD1 S:ASN255 4.1 12.9 1.0
C S:ASN255 4.1 9.4 1.0
C S:TRP118 4.2 10.3 1.0
C S:GLY119 4.2 7.8 1.0
CA S:ASN255 4.2 9.8 1.0
CA S:GLY119 4.3 9.2 1.0
O S:TRP118 4.4 12.4 1.0
O S:CYS120 4.4 7.6 1.0
O S:GLU254 4.4 9.6 1.0
N S:PHE257 4.5 9.9 1.0
C S:CYS120 4.5 7.8 1.0
O S:HOH2122 4.6 19.7 1.0
CA S:TRP118 4.6 9.7 1.0
C S:GLY256 4.6 9.5 1.0
O S:HOH2050 4.7 24.3 1.0
CD1 S:TRP258 4.7 9.0 1.0
CG S:TRP118 4.7 14.0 1.0
CD1 S:PHE257 4.8 8.7 1.0
CB S:CYS120 4.8 7.9 1.0
O S:THR114 4.9 8.2 1.0

Chlorine binding site 2 out of 4 in 5a4f

Go back to Chlorine Binding Sites List in 5a4f
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:17.4
occ:1.00
 O L:HOH2030 3.0 25.1 1.0
O S:HOH2002 3.1 19.3 1.0
O L:HOH2032 3.2 28.4 1.0
N S:HIS13 3.2 8.6 1.0
NZ S:LYS98 3.3 17.2 1.0
CB S:ILE12 3.5 9.1 1.0
OD2 S:ASP46 3.6 21.2 1.0
CA S:ILE12 3.6 8.0 1.0
CE S:LYS98 3.7 15.1 1.0
O S:HIS13 3.9 10.3 1.0
CG2 S:ILE12 3.9 10.7 1.0
C S:ILE12 3.9 8.6 1.0
CD S:LYS98 4.0 15.3 1.0
CE1 S:TYR44 4.2 12.5 1.0
CG S:ASP46 4.2 16.4 1.0
CA S:HIS13 4.2 8.9 1.0
CB S:HIS13 4.4 10.2 1.0
C S:HIS13 4.4 8.3 1.0
CE1 S:PHE95 4.5 10.4 1.0
OH S:TYR44 4.6 13.6 1.0
CD2 S:HIS13 4.7 12.2 1.0
OD1 S:ASP46 4.7 19.4 1.0
O S:TRP11 4.8 10.7 1.0
CZ S:TYR44 4.8 11.3 1.0
CG1 S:ILE12 4.9 10.3 1.0
N S:ILE12 4.9 8.1 1.0
CG S:HIS13 4.9 11.1 1.0
CD1 S:PHE95 4.9 9.7 1.0
CB S:ASP46 5.0 16.4 1.0
OG S:SER90 5.0 17.5 0.5

Chlorine binding site 3 out of 4 in 5a4f

Go back to Chlorine Binding Sites List in 5a4f
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:14.2
occ:1.00
 O T:HOH2039 3.1 15.1 1.0
N T:GLY256 3.1 10.0 1.0
O T:HOH2037 3.1 29.8 1.0
N T:CYS120 3.2 8.6 1.0
CB T:TRP118 3.7 13.4 1.0
CA T:CYS120 3.7 9.3 1.0
CG2 T:THR114 3.7 10.3 1.0
CA T:GLY256 3.9 10.8 1.0
N T:GLY119 4.0 9.9 1.0
C T:ASN255 4.1 10.8 1.0
C T:TRP118 4.1 11.1 1.0
CA T:ASN255 4.2 10.3 1.0
C T:GLY119 4.2 8.9 1.0
OD1 T:ASN255 4.2 13.7 1.0
CA T:GLY119 4.3 9.0 1.0
O T:GLU254 4.4 11.0 1.0
O T:TRP118 4.4 13.2 1.0
O T:CYS120 4.4 8.6 1.0
N T:PHE257 4.4 10.2 1.0
O T:HOH2099 4.5 21.6 1.0
C T:CYS120 4.5 8.7 1.0
C T:GLY256 4.6 10.3 1.0
CA T:TRP118 4.6 11.6 1.0
CD1 T:TRP258 4.7 9.5 1.0
CG T:TRP118 4.7 14.9 1.0
CD1 T:PHE257 4.7 9.6 1.0
CB T:CYS120 4.9 9.1 1.0
O T:THR114 4.9 10.0 1.0

Chlorine binding site 4 out of 4 in 5a4f

Go back to Chlorine Binding Sites List in 5a4f
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:18.9
occ:1.00
 O T:HOH2003 3.2 18.6 1.0
NZ T:LYS98 3.2 18.9 1.0
N T:HIS13 3.3 9.6 1.0
CB T:ILE12 3.5 10.4 1.0
CA T:ILE12 3.6 9.3 1.0
OD2 T:ASP46 3.6 21.4 1.0
CE T:LYS98 3.6 16.5 1.0
CG2 T:ILE12 3.9 11.5 1.0
O T:HIS13 3.9 11.4 1.0
C T:ILE12 3.9 9.3 1.0
CD T:LYS98 4.0 16.0 1.0
CA T:HIS13 4.2 9.7 1.0
CE1 T:TYR44 4.2 13.9 1.0
CG T:ASP46 4.2 16.9 1.0
CB T:HIS13 4.4 11.3 1.0
C T:HIS13 4.4 9.1 1.0
CE1 T:PHE95 4.5 12.7 1.0
OH T:TYR44 4.6 15.2 1.0
CD2 T:HIS13 4.7 13.1 1.0
OD1 T:ASP46 4.8 20.1 1.0
O T:TRP11 4.8 11.6 1.0
CG1 T:ILE12 4.8 11.2 1.0
N T:ILE12 4.9 9.0 1.0
CD1 T:PHE95 4.9 12.2 1.0
CG T:HIS13 4.9 12.9 1.0
CZ T:TYR44 5.0 13.5 1.0
CB T:ASP46 5.0 15.9 1.0
CG T:LYS98 5.0 13.9 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 23:59:32 2025

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