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Chlorine in PDB 3usc: Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form

Enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form, PDB code: 3usc 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.170, 98.160, 183.960, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 17.7

Other elements in 3usc:

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

Chlorine binding site 1 out of 5 in 3usc

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Chlorine binding site 1 out of 5 in the Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form


Mono view


Stereo pair view

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

b:13.9
occ:1.00
 O S:HOH547 3.0 14.7 1.0
N S:GLY256 3.1 10.5 1.0
N S:CYS120 3.2 5.0 1.0
O S:HOH602 3.2 20.4 1.0
CB S:TRP118 3.6 10.5 1.0
CG2 S:THR114 3.7 4.8 1.0
CA S:GLY256 3.7 8.6 1.0
CA S:CYS120 3.7 4.9 1.0
C S:ASN255 4.1 10.4 1.0
N S:GLY119 4.1 6.7 1.0
OD1 S:ASN255 4.1 14.2 1.0
C S:TRP118 4.1 8.1 1.0
CA S:ASN255 4.2 8.4 1.0
C S:GLY119 4.2 6.7 1.0
CA S:GLY119 4.3 5.5 1.0
O S:GLU254 4.4 7.1 1.0
O S:CYS120 4.4 5.4 1.0
N S:PHE257 4.4 6.8 1.0
O S:TRP118 4.4 8.1 1.0
C S:CYS120 4.5 5.5 1.0
C S:GLY256 4.6 9.1 1.0
CA S:TRP118 4.6 7.7 1.0
O S:HOH546 4.6 15.5 1.0
O S:HOH608 4.6 20.1 1.0
CG S:TRP118 4.7 11.2 1.0
CD1 S:TRP258 4.7 6.4 1.0
CD1 S:PHE257 4.7 6.7 1.0
O S:THR114 4.9 6.0 1.0
CB S:CYS120 4.9 4.7 1.0

Chlorine binding site 2 out of 5 in 3usc

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Chlorine binding site 2 out of 5 in the Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form


Mono view


Stereo pair view

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

b:9.2
occ:0.70
 O S:HOH607 3.0 20.2 1.0
O S:HOH567 3.1 21.4 1.0
N S:HIS13 3.1 5.7 1.0
OD2 S:ASP46 3.4 23.5 1.0
NZ S:LYS98 3.4 19.5 1.0
CB S:ILE12 3.5 6.3 1.0
CA S:ILE12 3.6 5.8 1.0
O S:HOH675 3.6 22.6 1.0
CE S:LYS98 3.7 20.6 1.0
O S:HIS13 3.8 8.4 1.0
C S:ILE12 3.9 6.6 1.0
CG2 S:ILE12 3.9 5.5 1.0
CD S:LYS98 4.0 17.4 1.0
CG S:ASP46 4.1 21.1 1.0
CA S:HIS13 4.1 6.3 1.0
CE1 S:TYR44 4.2 12.6 1.0
C S:HIS13 4.3 8.2 1.0
CB S:HIS13 4.3 6.8 1.0
OH S:TYR44 4.5 11.1 1.0
CE1 S:PHE95 4.5 8.2 1.0
ND1 S:HIS13 4.6 12.6 1.0
OD1 S:ASP46 4.6 25.7 1.0
O S:HOH580 4.6 22.2 1.0
O S:TRP11 4.8 8.2 1.0
CG1 S:ILE12 4.8 7.9 1.0
N S:ILE12 4.9 6.2 1.0
CZ S:TYR44 4.9 11.2 1.0
CB S:ASP46 4.9 13.9 1.0
CG S:HIS13 4.9 10.0 1.0
CD1 S:PHE95 5.0 7.7 1.0
CE1 L:HIS30 5.0 13.7 1.0

Chlorine binding site 3 out of 5 in 3usc

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Chlorine binding site 3 out of 5 in the Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:14.6
occ:1.00
 O T:HOH548 3.1 10.6 1.0
N T:GLY256 3.1 9.7 1.0
O T:HOH591 3.2 24.8 1.0
N T:CYS120 3.2 6.0 1.0
CB T:TRP118 3.6 10.2 1.0
CA T:CYS120 3.7 5.9 1.0
CG2 T:THR114 3.7 6.6 1.0
CA T:GLY256 3.8 7.5 1.0
N T:GLY119 4.0 8.4 1.0
C T:TRP118 4.1 9.2 1.0
OD1 T:ASN255 4.1 14.5 1.0
C T:ASN255 4.1 10.6 1.0
C T:GLY119 4.2 7.2 1.0
CA T:ASN255 4.2 10.1 1.0
CA T:GLY119 4.3 6.3 1.0
O T:TRP118 4.4 8.6 1.0
O T:CYS120 4.4 6.6 1.0
O T:GLU254 4.4 6.7 1.0
N T:PHE257 4.4 6.7 1.0
C T:CYS120 4.5 6.6 1.0
CA T:TRP118 4.5 9.1 1.0
C T:GLY256 4.6 9.7 1.0
O T:HOH570 4.6 20.0 1.0
CD1 T:TRP258 4.6 6.3 1.0
CG T:TRP118 4.7 12.4 1.0
CD1 T:PHE257 4.8 7.2 1.0
O T:HOH640 4.9 22.6 1.0
O T:THR114 4.9 7.3 1.0
CB T:CYS120 4.9 5.6 1.0

Chlorine binding site 4 out of 5 in 3usc

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Chlorine binding site 4 out of 5 in the Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl406

b:14.1
occ:0.70
 O T:HOH620 3.0 23.6 1.0
O T:HOH580 3.1 19.0 1.0
N T:HIS13 3.1 8.7 1.0
NZ T:LYS98 3.2 21.9 1.0
OD2 T:ASP46 3.3 25.1 1.0
CB T:ILE12 3.5 8.3 1.0
CA T:ILE12 3.5 7.7 1.0
O T:HOH672 3.5 25.5 1.0
O T:HIS13 3.8 9.2 1.0
C T:ILE12 3.8 7.0 1.0
CG2 T:ILE12 3.9 7.6 1.0
CE T:LYS98 3.9 22.1 1.0
CG T:ASP46 4.0 22.1 1.0
CA T:HIS13 4.1 7.8 1.0
CD T:LYS98 4.1 18.8 1.0
CE1 T:TYR44 4.2 13.6 1.0
CB T:HIS13 4.3 7.6 1.0
C T:HIS13 4.3 9.0 1.0
OD1 T:ASP46 4.4 26.1 1.0
ND1 T:HIS13 4.5 14.2 1.0
OH T:TYR44 4.6 14.2 1.0
CE1 T:PHE95 4.6 9.2 1.0
O T:TRP11 4.7 7.2 1.0
N T:ILE12 4.9 6.5 1.0
CB T:ASP46 4.9 15.3 1.0
CZ T:TYR44 4.9 14.1 1.0
CG1 T:ILE12 4.9 9.3 1.0
CG T:HIS13 4.9 11.6 1.0

Chlorine binding site 5 out of 5 in 3usc

Go back to Chlorine Binding Sites List in 3usc
Chlorine binding site 5 out of 5 in the Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl407

b:34.5
occ:0.70
 N T:ARG174 3.3 11.8 1.0
CG T:ARG174 3.4 16.6 0.4
CB T:ASP173 3.5 10.2 1.0
CD T:ARG174 3.6 19.2 0.4
CG T:ARG174 3.6 17.1 0.6
CB T:ARG174 3.8 14.7 0.4
CB T:ARG174 3.8 15.2 0.6
CA T:ASP173 3.9 11.0 1.0
C T:ASP173 4.0 11.8 1.0
CA T:ARG174 4.2 14.2 0.6
CA T:ARG174 4.2 13.9 0.4
NE T:ARG174 4.4 17.5 0.4
NH2 T:ARG174 4.4 33.6 0.6
CD T:ARG174 4.5 26.4 0.6
CZ T:ARG174 4.6 36.2 0.6
NE T:ARG174 4.6 32.9 0.6
CG T:ASP173 4.7 11.1 1.0
NH2 T:ARG174 4.8 23.3 0.4
CZ T:ARG174 4.9 22.7 0.4

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 11:27:17 2025

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