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Chlorine in PDB 3myr: Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

Enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State

All present enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr was solved by H.Ogata, P.Kellers, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.750, 216.960, 119.800, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.8

Other elements in 3myr:

The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Magnesium (Mg) 4 atoms
Iron (Fe) 52 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State (pdb code 3myr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3myr

Go back to Chlorine Binding Sites List in 3myr
Chlorine binding site 1 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2004

b:20.5
occ:1.00
O A:HOH3328 3.1 17.5 1.0
N A:ASN236 3.2 14.8 1.0
O A:HOH3314 3.3 16.3 1.0
N A:ASP237 3.3 16.0 1.0
N A:MET154 3.6 17.1 1.0
CB A:PRO153 3.6 13.8 1.0
CD A:PRO153 3.6 12.8 1.0
CA A:ASN236 3.7 14.6 1.0
CG A:PRO153 3.7 13.1 1.0
CG2 A:ILE152 3.8 16.1 1.0
N A:PRO153 3.9 17.1 1.0
CB A:MET154 4.0 17.2 1.0
C A:ASN236 4.1 15.8 1.0
CG A:MET154 4.1 20.9 1.0
C A:TRP235 4.1 15.4 1.0
CE A:MET154 4.2 29.8 1.0
CA A:PRO153 4.3 17.0 1.0
CA A:ASP237 4.3 19.6 1.0
C A:PRO153 4.4 20.2 1.0
CA A:MET154 4.4 17.7 1.0
CA A:TRP235 4.5 14.8 1.0
O A:LYS234 4.6 15.8 1.0
C A:ILE152 4.9 16.7 1.0
SD A:MET154 5.0 31.2 1.0

Chlorine binding site 2 out of 4 in 3myr

Go back to Chlorine Binding Sites List in 3myr
Chlorine binding site 2 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2004

b:20.5
occ:1.00
O C:HOH3354 3.1 16.5 1.0
O C:HOH3577 3.2 16.1 1.0
N C:ASN236 3.2 18.5 1.0
N C:ASP237 3.4 19.2 1.0
N C:MET154 3.5 16.9 1.0
CB C:PRO153 3.6 14.6 1.0
CA C:ASN236 3.7 17.6 1.0
CD C:PRO153 3.7 12.2 1.0
CG C:PRO153 3.8 17.8 1.0
CG2 C:ILE152 3.8 17.6 1.0
CB C:MET154 3.9 20.7 1.0
CE C:MET154 4.0 27.8 1.0
CG C:MET154 4.1 25.8 1.0
C C:ASN236 4.1 17.9 1.0
N C:PRO153 4.1 15.4 1.0
C C:TRP235 4.2 19.5 1.0
CA C:ASP237 4.3 21.6 1.0
CA C:PRO153 4.3 14.6 1.0
CA C:MET154 4.4 18.9 1.0
C C:PRO153 4.4 18.2 1.0
CA C:TRP235 4.5 19.4 1.0
O C:LYS234 4.6 19.7 1.0
SD C:MET154 4.9 30.9 1.0
C C:ILE152 4.9 15.8 1.0

Chlorine binding site 3 out of 4 in 3myr

Go back to Chlorine Binding Sites List in 3myr
Chlorine binding site 3 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl2004

b:24.4
occ:1.00
O E:HOH3206 3.1 17.4 1.0
O E:HOH3216 3.1 20.6 1.0
N E:ASN236 3.2 20.6 1.0
N E:ASP237 3.3 21.6 1.0
N E:MET154 3.6 20.5 1.0
CB E:PRO153 3.6 18.5 1.0
CD E:PRO153 3.7 19.6 1.0
CA E:ASN236 3.8 21.6 1.0
CG2 E:ILE152 3.8 18.8 1.0
CG E:PRO153 3.8 20.0 1.0
CE E:MET154 3.9 29.2 1.0
CB E:MET154 4.0 23.1 1.0
N E:PRO153 4.1 21.3 1.0
C E:ASN236 4.1 21.2 1.0
C E:TRP235 4.1 21.4 1.0
CG E:MET154 4.2 24.8 1.0
CA E:ASP237 4.2 24.6 1.0
CA E:PRO153 4.3 21.0 1.0
C E:PRO153 4.4 21.7 1.0
CA E:MET154 4.4 22.1 1.0
CA E:TRP235 4.5 22.0 1.0
O E:LYS234 4.6 23.2 1.0
C E:ILE152 4.9 21.2 1.0
SD E:MET154 5.0 31.8 1.0

Chlorine binding site 4 out of 4 in 3myr

Go back to Chlorine Binding Sites List in 3myr
Chlorine binding site 4 out of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State


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 [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl2004

b:21.2
occ:1.00
O G:HOH3053 3.1 19.1 1.0
N G:ASN236 3.2 18.1 1.0
O G:HOH3104 3.3 18.1 1.0
N G:ASP237 3.4 21.3 1.0
N G:MET154 3.5 16.7 1.0
CB G:PRO153 3.5 16.2 1.0
CA G:ASN236 3.7 19.6 1.0
CD G:PRO153 3.7 15.1 1.0
CG2 G:ILE152 3.9 19.5 1.0
CG G:PRO153 3.9 15.2 1.0
CB G:MET154 3.9 20.7 1.0
CE G:MET154 4.0 31.4 1.0
N G:PRO153 4.0 19.1 1.0
C G:ASN236 4.1 19.3 1.0
C G:TRP235 4.2 20.1 1.0
CA G:PRO153 4.2 17.9 1.0
CG G:MET154 4.3 20.9 1.0
C G:PRO153 4.3 19.1 1.0
CA G:ASP237 4.4 23.8 1.0
CA G:MET154 4.4 19.3 1.0
CA G:TRP235 4.5 19.1 1.0
O G:LYS234 4.6 18.6 1.0
C G:ILE152 4.9 19.4 1.0
SD G:MET154 4.9 30.1 1.0

Reference:

H.Ogata, P.Kellers, W.Lubitz. The Crystal Structure of the [Nife] Hydrogenase From the Photosynthetic Bacterium Allochromatium Vinosum: Characterization of the Oxidized Enzyme (Ni-A State). J.Mol.Biol. V. 402 428 2010.
ISSN: ISSN 0022-2836
PubMed: 20673834
DOI: 10.1016/J.JMB.2010.07.041
Page generated: Sun Jul 21 00:27:36 2024

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