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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: Sat Dec 12 10:15:50 2020

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