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Calcium 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
Chlorine (Cl) 2 atoms
Copper (Cu) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3omi

Go back to Calcium Binding Sites List in 3omi
Calcium 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 Calcium with other atoms in the Ca 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:Ca613

b:23.1
occ:1.00
 O A:GLY59 2.3 22.6 1.0
O A:GLU54 2.3 22.2 1.0
O A:ALA57 2.3 23.3 1.0
OE1 A:GLU54 2.4 21.1 1.0
OE1 A:GLN61 2.5 26.6 1.0
O A:HOH810 2.6 19.4 1.0
O A:HOH817 2.6 19.3 1.0
C A:GLU54 3.4 21.7 1.0
CD A:GLU54 3.5 21.2 1.0
C A:GLY59 3.5 23.4 1.0
C A:ALA57 3.5 23.5 1.0
CD A:GLN61 3.6 26.3 1.0
CG A:GLU54 4.0 20.9 1.0
NE2 A:GLN61 4.0 23.7 1.0
CA A:GLU54 4.0 21.7 1.0
CA A:VAL60 4.1 23.1 1.0
N A:ALA57 4.2 24.5 1.0
N A:VAL60 4.3 23.3 1.0
N A:GLN61 4.3 24.9 1.0
C A:PRO58 4.3 23.8 1.0
CA A:ALA57 4.3 24.1 1.0
O A:PRO58 4.4 23.6 1.0
N A:GLY59 4.5 23.4 1.0
N A:PRO58 4.5 23.7 1.0
N A:LEU55 4.5 22.2 1.0
OE2 A:GLU54 4.6 20.6 1.0
CA A:GLY59 4.6 22.8 1.0
CA A:PRO58 4.6 23.2 1.0
C A:VAL60 4.6 24.4 1.0
CB A:GLU54 4.6 21.2 1.0
O61 A:DMU603 4.7 35.6 0.8
O A:MET53 4.8 21.3 1.0
CB A:ALA57 4.8 23.7 1.0
CA A:LEU55 4.8 22.1 1.0
CG A:GLN61 4.8 24.7 1.0
OD1 A:ASP485 4.8 23.4 1.0
C A:LEU55 4.9 22.7 1.0
CB A:GLN61 5.0 25.7 1.0

Calcium binding site 2 out of 2 in 3omi

Go back to Calcium Binding Sites List in 3omi
Calcium 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 Calcium with other atoms in the Ca 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:Ca610

b:34.0
occ:1.00
 O C:GLU54 2.3 33.6 1.0
O C:ALA57 2.3 33.5 1.0
OE1 C:GLU54 2.3 32.0 1.0
O C:GLY59 2.4 35.6 1.0
OE1 C:GLN61 2.5 40.7 1.0
O C:HOH722 2.6 28.1 1.0
O C:HOH735 2.7 36.3 1.0
C C:GLU54 3.4 33.7 1.0
C C:ALA57 3.5 33.8 1.0
CD C:GLU54 3.5 33.6 1.0
CD C:GLN61 3.5 40.6 1.0
C C:GLY59 3.5 36.0 1.0
NE2 C:GLN61 3.9 39.3 1.0
CA C:GLU54 3.9 33.7 1.0
CG C:GLU54 4.0 33.6 1.0
CA C:VAL60 4.1 37.2 1.0
N C:ALA57 4.2 34.6 1.0
N C:GLN61 4.2 39.5 1.0
C C:PRO58 4.2 35.2 1.0
N C:VAL60 4.2 36.5 1.0
CA C:ALA57 4.3 34.4 1.0
O C:PRO58 4.4 35.1 1.0
N C:GLY59 4.4 35.3 1.0
N C:PRO58 4.5 34.1 1.0
N C:LEU55 4.5 33.3 1.0
OE2 C:GLU54 4.5 32.9 1.0
CA C:PRO58 4.5 34.5 1.0
C C:VAL60 4.6 38.7 1.0
CB C:GLU54 4.6 33.4 1.0
OD1 C:ASP485 4.6 31.6 1.0
CA C:GLY59 4.7 35.5 1.0
CB C:ALA57 4.7 34.2 1.0
O C:MET53 4.8 34.9 1.0
CA C:LEU55 4.8 33.2 1.0
CG C:GLN61 4.8 40.0 1.0
O61 C:DMU602 4.9 40.1 1.0
CB C:GLN61 5.0 40.2 1.0
C C:LEU55 5.0 33.9 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: Tue Jul 8 15:08:45 2025

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