Atomistry » Chlorine » PDB 5aaa-5afy » 5adu
Atomistry »
  Chlorine »
    PDB 5aaa-5afy »
      5adu »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy