Atomistry » Chlorine » PDB 3unk-3uwd » 3uqy
Atomistry »
  Chlorine »
    PDB 3unk-3uwd »
      3uqy »

Chlorine in PDB 3uqy: H2-Reduced Structure of E. Coli Hydrogenase-1

Enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1

All present enzymatic activity of H2-Reduced Structure of E. Coli Hydrogenase-1:
1.12.99.6;

Protein crystallography data

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.710, 97.400, 183.730, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 16

Other elements in 3uqy:

The structure of H2-Reduced Structure of E. Coli Hydrogenase-1 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 24 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the H2-Reduced Structure of E. Coli Hydrogenase-1 (pdb code 3uqy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the H2-Reduced Structure of E. Coli Hydrogenase-1, PDB code: 3uqy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3uqy

Go back to Chlorine Binding Sites List in 3uqy
Chlorine binding site 1 out of 5 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:12.9
occ:0.70
 O S:HOH548 2.8 13.1 1.0
N S:GLY256 3.0 8.2 1.0
N S:CYS120 3.1 5.4 1.0
O S:HOH599 3.2 26.4 1.0
CB S:TRP118 3.6 9.0 1.0
CA S:GLY256 3.6 9.7 1.0
CA S:CYS120 3.7 5.3 1.0
CG2 S:THR114 3.8 5.2 1.0
C S:TRP118 4.0 7.2 1.0
N S:GLY119 4.0 6.8 1.0
C S:ASN255 4.0 7.5 1.0
OD1 S:ASN255 4.1 10.7 1.0
C S:GLY119 4.1 5.0 1.0
O S:TRP118 4.1 9.4 1.0
CA S:ASN255 4.2 7.2 1.0
CA S:GLY119 4.2 6.4 1.0
O S:CYS120 4.3 6.1 1.0
N S:PHE257 4.4 6.9 1.0
CA S:TRP118 4.5 6.2 1.0
O S:GLU254 4.5 7.5 1.0
C S:CYS120 4.5 5.4 1.0
C S:GLY256 4.5 8.8 1.0
O S:HOH547 4.5 26.7 1.0
CG S:TRP118 4.6 11.1 1.0
CD1 S:TRP258 4.7 6.4 1.0
O S:THR114 4.9 6.2 1.0
O S:HOH605 4.9 30.2 1.0
CD1 S:PHE257 4.9 6.5 1.0
CB S:CYS120 4.9 6.5 1.0
CG S:ASN255 5.0 10.3 1.0

Chlorine binding site 2 out of 5 in 3uqy

Go back to Chlorine Binding Sites List in 3uqy
Chlorine binding site 2 out of 5 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl406

b:22.9
occ:0.50
 O S:HOH658 2.1 21.6 0.5
N S:ARG174 3.1 10.1 1.0
CB S:ASP173 3.5 9.6 1.0
CG S:ARG174 3.6 17.5 1.0
CB S:ARG174 3.6 14.7 1.0
CA S:ASP173 3.8 10.3 1.0
C S:ASP173 4.0 9.8 1.0
O M:HOH1253 4.0 49.0 1.0
CA S:ARG174 4.0 12.6 1.0
CD S:ARG174 4.0 25.5 1.0
O S:HOH705 4.3 35.6 1.0
NE S:ARG174 4.3 30.8 1.0
O S:HOH673 4.6 31.9 1.0
CG S:ASP173 4.6 8.0 1.0

Chlorine binding site 3 out of 5 in 3uqy

Go back to Chlorine Binding Sites List in 3uqy
Chlorine binding site 3 out of 5 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl607

b:21.3
occ:0.50
 O L:HOH947 2.9 31.9 1.0
N L:ARG500 3.0 10.2 1.0
O L:ARG500 3.4 11.0 1.0
CA L:CYS499 3.4 9.5 1.0
CB L:CYS499 3.6 9.3 1.0
C L:CYS499 3.7 9.9 1.0
O L:HOH1134 3.7 35.5 1.0
O L:HOH1088 3.9 33.7 1.0
CA L:ARG500 4.0 9.5 1.0
CG L:ARG500 4.1 14.8 1.0
C L:ARG500 4.1 8.8 1.0
O L:HOH937 4.4 37.1 1.0
O L:HOH1146 4.4 34.0 0.7
O L:ALA94 4.5 10.7 1.0
CB L:ARG500 4.6 14.1 1.0
N L:CYS499 4.8 10.4 1.0
O L:HOH921 4.8 32.1 1.0
O L:GLU498 4.8 13.4 1.0
O L:CYS499 4.9 11.1 1.0

Chlorine binding site 4 out of 5 in 3uqy

Go back to Chlorine Binding Sites List in 3uqy
Chlorine binding site 4 out of 5 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:15.8
occ:0.80
 O T:HOH547 2.9 13.4 1.0
N T:GLY256 3.0 8.8 1.0
N T:CYS120 3.1 6.9 1.0
O T:HOH589 3.2 28.0 1.0
CB T:TRP118 3.6 10.1 1.0
CA T:GLY256 3.6 10.2 1.0
CA T:CYS120 3.6 6.2 1.0
CG2 T:THR114 3.8 7.1 1.0
C T:TRP118 3.9 8.6 1.0
N T:GLY119 4.0 7.7 1.0
O T:TRP118 4.1 10.2 1.0
OD1 T:ASN255 4.1 11.0 1.0
C T:ASN255 4.1 9.2 1.0
C T:GLY119 4.1 5.8 1.0
CA T:ASN255 4.2 7.4 1.0
CA T:GLY119 4.2 8.1 1.0
O T:CYS120 4.3 6.8 1.0
CA T:TRP118 4.4 9.4 1.0
C T:CYS120 4.4 6.6 1.0
N T:PHE257 4.4 8.4 1.0
O T:GLU254 4.5 8.7 1.0
C T:GLY256 4.5 8.9 1.0
O T:HOH567 4.6 28.3 1.0
CG T:TRP118 4.7 11.7 1.0
CD1 T:TRP258 4.7 5.8 1.0
O T:THR114 4.9 8.2 1.0
CB T:CYS120 4.9 5.8 1.0
CD1 T:PHE257 4.9 7.8 1.0
O T:HOH594 5.0 20.0 1.0

Chlorine binding site 5 out of 5 in 3uqy

Go back to Chlorine Binding Sites List in 3uqy
Chlorine binding site 5 out of 5 in the H2-Reduced Structure of E. Coli Hydrogenase-1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of H2-Reduced Structure of E. Coli Hydrogenase-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl604

b:23.0
occ:0.50
 O M:HOH1115 2.4 25.5 0.5
O M:HOH913 2.8 19.1 1.0
O T:HOH733 3.0 40.3 1.0
N M:ASN184 3.0 9.9 1.0
CD2 M:LEU179 3.7 17.7 1.0
CA M:ASN184 3.8 9.3 1.0
CA M:ARG183 3.8 9.5 1.0
C M:ARG183 3.9 10.4 1.0
CG M:ARG183 3.9 11.7 1.0
O M:HOH1261 4.3 31.0 1.0
CB M:ARG183 4.4 9.7 1.0
O M:PHE182 4.6 11.1 1.0
O T:HOH655 4.6 32.8 1.0
CB M:ASN184 4.7 11.1 1.0
CG M:LEU179 4.8 13.5 1.0
CB M:LEU179 4.9 10.6 1.0
N M:GLY185 4.9 11.7 1.0
C M:ASN184 4.9 10.0 1.0
N M:ARG183 5.0 8.5 1.0

Reference:

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109
Page generated: Fri Jul 11 11:26:01 2025

Last articles

Fe in 5TQN
Fe in 5TQO
Fe in 5TQP
Fe in 5TPG
Fe in 5TK5
Fe in 5TL8
Fe in 5T5I
Fe in 5TH5
Fe in 5T5M
Fe in 5TIA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy