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Chlorine in PDB 3use: Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

Enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use 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) 29.82 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.930, 97.790, 183.290, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 16.8

Other elements in 3use:

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 32 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form (pdb code 3use). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3use

Go back to Chlorine Binding Sites List in 3use
Chlorine binding site 1 out of 3 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated 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 Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl408

b:13.3
occ:1.00
O S:HOH550 3.0 14.9 1.0
N S:GLY256 3.1 9.9 1.0
N S:CYS120 3.2 6.2 1.0
O S:HOH603 3.2 20.2 1.0
CB S:TRP118 3.7 11.2 1.0
CA S:CYS120 3.7 6.2 1.0
CA S:GLY256 3.7 8.8 1.0
CG2 S:THR114 3.7 6.8 1.0
C S:ASN255 4.1 9.0 1.0
N S:GLY119 4.1 7.9 1.0
OD1 S:ASN255 4.1 14.0 1.0
C S:GLY119 4.2 7.1 1.0
C S:TRP118 4.2 7.6 1.0
CA S:ASN255 4.2 6.9 1.0
CA S:GLY119 4.3 7.8 1.0
O S:CYS120 4.4 6.1 1.0
N S:PHE257 4.4 7.0 1.0
O S:GLU254 4.4 8.8 1.0
O S:TRP118 4.4 10.8 1.0
C S:CYS120 4.5 6.3 1.0
C S:GLY256 4.5 9.0 1.0
O S:HOH548 4.5 19.7 1.0
CA S:TRP118 4.6 8.7 1.0
O S:HOH608 4.6 29.9 1.0
CD1 S:TRP258 4.6 7.7 1.0
CG S:TRP118 4.7 12.8 1.0
CD1 S:PHE257 4.7 5.1 1.0
O S:THR114 4.9 7.8 1.0
CB S:CYS120 4.9 6.6 1.0

Chlorine binding site 2 out of 3 in 3use

Go back to Chlorine Binding Sites List in 3use
Chlorine binding site 2 out of 3 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated 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 Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl409

b:13.2
occ:1.00
O T:HOH547 3.1 14.9 1.0
N T:GLY256 3.1 8.8 1.0
N T:CYS120 3.1 6.9 1.0
O T:HOH587 3.2 29.0 1.0
CA T:CYS120 3.6 6.3 1.0
CB T:TRP118 3.6 10.3 1.0
CG2 T:THR114 3.7 7.4 1.0
CA T:GLY256 3.8 8.9 1.0
N T:GLY119 4.0 9.0 1.0
C T:TRP118 4.1 10.7 1.0
C T:ASN255 4.1 10.4 1.0
C T:GLY119 4.1 8.4 1.0
OD1 T:ASN255 4.1 14.7 1.0
CA T:ASN255 4.2 10.8 1.0
CA T:GLY119 4.3 7.7 1.0
O T:CYS120 4.3 6.2 1.0
O T:TRP118 4.3 11.3 1.0
O T:GLU254 4.4 9.4 1.0
N T:PHE257 4.4 9.1 1.0
C T:CYS120 4.4 6.9 1.0
CA T:TRP118 4.5 10.1 1.0
C T:GLY256 4.5 9.2 1.0
O T:HOH569 4.6 24.7 1.0
CD1 T:TRP258 4.6 7.0 1.0
CG T:TRP118 4.7 11.7 1.0
CD1 T:PHE257 4.8 7.3 1.0
CB T:CYS120 4.8 6.0 1.0
O T:HOH635 4.9 28.1 1.0
O T:THR114 4.9 6.9 1.0

Chlorine binding site 3 out of 3 in 3use

Go back to Chlorine Binding Sites List in 3use
Chlorine binding site 3 out of 3 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated 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 Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl606

b:28.3
occ:0.50
O M:HOH1153 2.2 23.1 0.5
N M:TYR356 2.8 10.7 1.0
O M:TYR356 3.2 11.1 1.0
O M:HOH774 3.4 16.1 1.0
CA M:ARG355 3.5 10.2 1.0
CB M:ASP359 3.6 14.1 1.0
O M:TYR354 3.6 11.9 1.0
C M:ARG355 3.6 10.1 1.0
CA M:TYR356 3.8 11.3 1.0
C M:TYR356 4.0 11.0 1.0
CB M:TYR356 4.0 10.9 1.0
OD2 M:ASP359 4.0 22.5 1.0
CG M:ASP359 4.3 17.4 1.0
CZ3 M:TRP373 4.3 18.9 1.0
O M:HOH1044 4.4 29.6 1.0
CB M:ARG355 4.4 12.0 1.0
C M:TYR354 4.4 11.2 1.0
N M:ARG355 4.5 10.7 1.0
CG2 M:VAL349 4.5 10.2 1.0
CA M:ASP359 4.6 12.6 1.0
CE3 M:TRP373 4.6 17.3 1.0
N M:ASP359 4.7 12.1 1.0
O M:HOH989 4.7 28.8 1.0
NH2 M:ARG394 4.8 17.8 1.0
O M:ARG355 4.8 10.3 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 10:15:56 2020

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