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Chlorine in PDB 5adu: 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: 5adu was solved by R.Evans, E.J.Brooke, S.A.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) 92.78 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.855, 98.979, 185.207, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.2

Other elements in 5adu:

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

Chlorine binding site 1 out of 4 in 5adu

Go back to Chlorine Binding Sites List in 5adu
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:9.9
occ:1.00
 O S:HOH2054 3.1 10.7 1.0
O S:HOH2052 3.1 25.9 1.0
N S:GLY256 3.2 7.3 1.0
N S:CYS120 3.2 5.1 1.0
CB S:TRP118 3.7 7.5 1.0
CG2 S:THR114 3.7 6.2 1.0
CA S:CYS120 3.8 5.2 1.0
CA S:GLY256 3.9 7.1 1.0
N S:GLY119 4.1 6.3 1.0
C S:ASN255 4.2 6.7 1.0
C S:TRP118 4.2 6.4 1.0
C S:GLY119 4.2 5.1 1.0
OD1 S:ASN255 4.2 9.7 1.0
CA S:ASN255 4.2 7.1 1.0
CA S:GLY119 4.3 6.0 1.0
O S:TRP118 4.4 8.6 1.0
O S:CYS120 4.4 5.2 1.0
O S:GLU254 4.5 7.0 1.0
N S:PHE257 4.5 6.3 1.0
C S:CYS120 4.6 5.0 1.0
O S:HOH2139 4.6 15.3 1.0
CA S:TRP118 4.6 6.7 1.0
C S:GLY256 4.7 6.4 1.0
O S:HOH2056 4.7 23.1 1.0
CD1 S:TRP258 4.8 6.1 1.0
CG S:TRP118 4.8 9.5 1.0
CD1 S:PHE257 4.8 6.5 1.0
CB S:CYS120 4.9 5.4 1.0
O S:THR114 5.0 5.5 1.0

Chlorine binding site 2 out of 4 in 5adu

Go back to Chlorine Binding Sites List in 5adu
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:15.4
occ:1.00
 O S:HOH2003 3.0 21.8 1.0
O S:HOH2002 3.2 14.9 1.0
NZ S:LYS98 3.3 14.4 1.0
N S:HIS13 3.3 6.2 1.0
O L:HOH2033 3.3 26.1 1.0
CB S:ILE12 3.6 6.9 1.0
CA S:ILE12 3.6 6.1 1.0
OD2 S:ASP46 3.6 17.9 1.0
CE S:LYS98 3.7 12.8 1.0
O S:HOH2022 3.9 27.1 1.0
O S:HIS13 3.9 7.1 1.0
CG2 S:ILE12 3.9 7.8 1.0
C S:ILE12 4.0 6.2 1.0
CD S:LYS98 4.1 12.5 1.0
CE1 S:TYR44 4.2 10.3 1.0
CA S:HIS13 4.3 7.1 1.0
CG S:ASP46 4.3 14.5 1.0
CB S:HIS13 4.4 8.1 1.0
C S:HIS13 4.5 6.2 1.0
OH S:TYR44 4.6 12.2 1.0
CE1 S:PHE95 4.6 9.0 1.0
CD2 S:HIS13 4.7 9.5 1.0
OD1 S:ASP46 4.8 16.3 1.0
O S:TRP11 4.8 7.8 1.0
CG1 S:ILE12 4.9 7.7 1.0
N S:ILE12 4.9 6.0 1.0
CZ S:TYR44 4.9 9.8 1.0
CG S:HIS13 5.0 8.8 1.0

Chlorine binding site 3 out of 4 in 5adu

Go back to Chlorine Binding Sites List in 5adu
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:10.6
occ:1.00
 O T:HOH2042 3.1 12.0 1.0
O T:HOH2039 3.1 24.3 1.0
N T:GLY256 3.2 7.0 1.0
N T:CYS120 3.2 5.9 1.0
CB T:TRP118 3.7 8.7 1.0
CG2 T:THR114 3.8 7.0 1.0
CA T:CYS120 3.8 5.8 1.0
CA T:GLY256 3.9 7.7 1.0
N T:GLY119 4.1 6.8 1.0
C T:ASN255 4.1 7.2 1.0
C T:TRP118 4.2 7.5 1.0
C T:GLY119 4.2 5.5 1.0
CA T:ASN255 4.2 7.4 1.0
OD1 T:ASN255 4.2 10.7 1.0
CA T:GLY119 4.3 6.7 1.0
O T:TRP118 4.4 9.4 1.0
O T:GLU254 4.4 7.3 1.0
O T:CYS120 4.5 5.8 1.0
N T:PHE257 4.5 6.8 1.0
O T:HOH2113 4.6 16.2 1.0
C T:CYS120 4.6 5.5 1.0
CA T:TRP118 4.6 7.7 1.0
C T:GLY256 4.7 7.4 1.0
CD1 T:TRP258 4.8 6.9 1.0
CD1 T:PHE257 4.8 6.9 1.0
CG T:TRP118 4.8 10.4 1.0
O T:HOH2044 4.9 25.3 1.0
CB T:CYS120 4.9 6.2 1.0
O T:THR114 5.0 6.3 1.0

Chlorine binding site 4 out of 4 in 5adu

Go back to Chlorine Binding Sites List in 5adu
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:17.0
occ:1.00
 O T:HOH2003 3.2 14.6 1.0
NZ T:LYS98 3.2 16.1 1.0
N T:HIS13 3.3 6.6 1.0
CB T:ILE12 3.6 7.4 1.0
CA T:ILE12 3.6 6.6 1.0
OD2 T:ASP46 3.6 19.7 1.0
CE T:LYS98 3.7 15.3 1.0
CG2 T:ILE12 3.9 8.0 1.0
O T:HIS13 3.9 7.9 1.0
C T:ILE12 4.0 6.0 1.0
CD T:LYS98 4.1 14.2 1.0
CA T:HIS13 4.2 7.0 1.0
CE2 T:TYR44 4.3 11.5 1.0
CG T:ASP46 4.3 14.5 1.0
CB T:HIS13 4.4 8.2 1.0
C T:HIS13 4.5 6.7 1.0
CE1 T:PHE95 4.6 9.7 1.0
CD2 T:HIS13 4.7 9.6 1.0
OH T:TYR44 4.7 13.4 1.0
OD1 T:ASP46 4.8 16.6 1.0
O T:TRP11 4.8 8.5 1.0
N T:ILE12 4.9 6.4 1.0
CG1 T:ILE12 4.9 7.7 1.0
CG T:HIS13 4.9 9.3 1.0
CZ T:TYR44 5.0 10.2 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: Sat Jul 12 00:10:07 2025

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