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Chlorine in PDB 5lry: E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D

Enzymatic activity of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D

All present enzymatic activity of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D:
1.12.99.6;

Protein crystallography data

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry was solved by S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.79 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.756, 98.746, 185.243, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 16.3

Other elements in 5lry:

The structure of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D 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 E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D (pdb code 5lry). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D, PDB code: 5lry:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5lry

Go back to Chlorine Binding Sites List in 5lry
Chlorine binding site 1 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Cl405

b:14.1
occ:1.00
O S:HOH595 3.1 11.6 0.9
O S:HOH671 3.1 27.0 1.0
N S:GLY256 3.1 9.7 1.0
N S:CYS120 3.2 8.7 1.0
CB S:TRP118 3.8 11.8 1.0
CA S:CYS120 3.8 8.7 1.0
CG2 S:THR114 3.8 8.6 1.0
CA S:GLY256 3.9 9.7 1.0
N S:GLY119 4.1 9.7 1.0
OD1 S:ASN255 4.1 13.8 1.0
C S:ASN255 4.1 10.0 1.0
C S:TRP118 4.2 10.5 1.0
CA S:ASN255 4.2 10.4 1.0
C S:GLY119 4.2 9.1 1.0
CA S:GLY119 4.3 9.5 1.0
O S:TRP118 4.4 11.5 1.0
O S:CYS120 4.4 8.1 1.0
O S:GLU254 4.5 9.3 1.0
N S:PHE257 4.5 9.5 1.0
O S:HOH685 4.6 17.8 1.0
C S:CYS120 4.6 8.1 1.0
CA S:TRP118 4.6 10.7 1.0
C S:GLY256 4.7 9.6 1.0
O S:HOH660 4.7 22.1 0.9
CG S:TRP118 4.8 13.2 1.0
CD1 S:TRP258 4.8 8.3 1.0
CD1 S:PHE257 4.9 9.3 1.0
CB S:CYS120 4.9 8.6 1.0
O S:THR114 4.9 8.8 1.0

Chlorine binding site 2 out of 2 in 5lry

Go back to Chlorine Binding Sites List in 5lry
Chlorine binding site 2 out of 2 in the E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E Coli [Nife] Hydrogenase Hyd-1 Mutant E28D within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl405

b:14.9
occ:1.00
O T:HOH672 3.0 27.6 1.0
O T:HOH635 3.1 12.5 0.9
N T:GLY256 3.1 10.3 1.0
N T:CYS120 3.2 9.6 1.0
CB T:TRP118 3.7 13.1 1.0
CA T:CYS120 3.7 9.3 1.0
CG2 T:THR114 3.8 10.0 1.0
CA T:GLY256 3.9 10.3 1.0
N T:GLY119 4.0 10.6 1.0
C T:ASN255 4.1 11.1 1.0
C T:TRP118 4.1 11.4 1.0
CA T:ASN255 4.1 11.6 1.0
OD1 T:ASN255 4.2 15.2 1.0
C T:GLY119 4.2 10.1 1.0
CA T:GLY119 4.3 10.3 1.0
O T:TRP118 4.4 12.4 1.0
O T:GLU254 4.4 10.6 1.0
N T:PHE257 4.5 9.8 1.0
O T:CYS120 4.5 8.5 1.0
CA T:TRP118 4.6 12.1 1.0
O T:HOH674 4.6 20.2 1.0
C T:CYS120 4.6 9.0 1.0
C T:GLY256 4.6 10.1 1.0
CG T:TRP118 4.8 14.7 1.0
O T:HOH666 4.8 27.0 0.9
CD1 T:TRP258 4.8 8.8 1.0
CD1 T:PHE257 4.8 9.0 1.0
CB T:CYS120 4.9 9.5 1.0
O T:THR114 4.9 9.8 1.0

Reference:

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J.Am.Chem.Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798
Page generated: Sat Dec 12 12:04:00 2020

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