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Chlorine in PDB 3omi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.064, 131.519, 175.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 3omi:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation (pdb code 3omi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3omi

Go back to Chlorine Binding Sites List in 3omi
Chlorine binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl614

b:39.3
occ:1.00
 O A:HOH832 3.0 53.6 1.0
O A:HOH828 3.1 30.9 1.0
N A:HIS26 3.3 37.3 1.0
N A:MET133 3.4 43.2 1.0
O A:THR24 3.7 44.7 1.0
CD2 A:HIS26 3.7 36.6 1.0
CB A:HIS26 3.8 36.4 1.0
CA A:ALA132 3.9 44.5 1.0
CA A:ASN25 3.9 40.3 1.0
CB A:ALA132 4.0 44.4 1.0
C A:ASN25 4.1 38.9 1.0
CA A:HIS26 4.1 36.7 1.0
CG A:HIS26 4.1 36.8 1.0
CG A:MET133 4.2 41.4 1.0
C A:ALA132 4.2 44.0 1.0
CB A:MET133 4.2 42.3 1.0
CG A:PRO136 4.2 44.6 1.0
CB A:PRO136 4.4 44.5 1.0
CA A:MET133 4.4 42.6 1.0
ND2 A:ASN25 4.5 41.4 1.0
C A:THR24 4.6 45.0 1.0
N A:ASN25 4.7 42.4 1.0
CG A:ASN25 4.7 40.5 1.0
O A:MET133 4.8 42.8 1.0
CB A:ASN25 4.9 40.5 1.0
CA A:PRO136 4.9 44.5 1.0

Chlorine binding site 2 out of 2 in 3omi

Go back to Chlorine Binding Sites List in 3omi
Chlorine binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl611

b:66.7
occ:1.00
 N C:MET133 2.9 62.9 1.0
O C:HOH731 3.1 54.2 1.0
CD2 C:HIS26 3.5 61.9 1.0
CA C:ALA132 3.5 63.1 1.0
N C:HIS26 3.5 62.5 1.0
CB C:ALA132 3.6 63.1 1.0
C C:ALA132 3.7 63.1 1.0
CG C:MET133 3.8 62.7 1.0
CB C:MET133 3.8 62.8 1.0
CB C:HIS26 3.8 61.2 1.0
CA C:MET133 3.9 62.7 1.0
CG C:HIS26 4.0 61.7 1.0
O C:THR24 4.0 68.0 1.0
CA C:HIS26 4.3 61.2 1.0
CA C:ASN25 4.3 65.2 1.0
ND2 C:ASN25 4.4 66.2 1.0
CG C:PRO136 4.4 63.3 1.0
C C:ASN25 4.4 64.0 1.0
O C:MET133 4.5 62.9 1.0
CB C:PRO136 4.6 63.4 1.0
C C:MET133 4.7 63.0 1.0
NE2 C:HIS26 4.8 61.8 1.0
O C:ALA132 4.9 63.1 1.0
N C:ALA132 4.9 63.0 1.0
C C:THR24 5.0 68.2 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Fri Jul 11 08:46:44 2025

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