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Calcium in PDB 3oma: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation, PDB code: 3oma 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) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.019, 131.579, 176.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 3oma:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 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 K362M Mutation (pdb code 3oma). 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 K362M Mutation, PDB code: 3oma:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3oma

Go back to Calcium Binding Sites List in 3oma
Calcium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca553

b:30.1
occ:1.00
 O A:GLU54 2.3 29.2 1.0
O A:ALA57 2.3 29.3 1.0
O A:GLY59 2.3 28.5 1.0
OE1 A:GLU54 2.4 27.1 1.0
OE1 A:GLN61 2.4 31.7 1.0
O A:HOH771 2.6 24.2 1.0
O A:HOH758 2.6 23.6 1.0
C A:GLU54 3.4 29.0 1.0
CD A:GLN61 3.5 30.1 1.0
CD A:GLU54 3.5 27.3 1.0
C A:ALA57 3.5 29.9 1.0
C A:GLY59 3.6 29.4 1.0
NE2 A:GLN61 3.9 29.0 1.0
CG A:GLU54 4.0 28.0 1.0
CA A:GLU54 4.0 28.7 1.0
CA A:VAL60 4.2 28.8 1.0
N A:ALA57 4.2 31.1 1.0
C A:PRO58 4.2 29.9 1.0
N A:GLN61 4.3 29.9 1.0
O A:PRO58 4.3 31.0 1.0
N A:VAL60 4.3 28.9 1.0
CA A:ALA57 4.3 30.9 1.0
N A:GLY59 4.4 29.9 1.0
N A:PRO58 4.5 30.1 1.0
N A:LEU55 4.5 29.1 1.0
OE2 A:GLU54 4.6 28.2 1.0
CA A:PRO58 4.6 29.8 1.0
O61 A:DMU1005 4.6 45.9 0.8
CA A:GLY59 4.6 29.3 1.0
C A:VAL60 4.6 29.6 1.0
CB A:GLU54 4.6 28.2 1.0
CB A:ALA57 4.7 29.8 1.0
CG A:GLN61 4.7 29.2 1.0
O A:MET53 4.7 29.0 1.0
OD1 A:ASP485 4.8 28.6 1.0
CA A:LEU55 4.8 28.9 1.0
CB A:GLN61 4.9 30.0 1.0
C A:LEU55 5.0 29.6 1.0

Calcium binding site 2 out of 2 in 3oma

Go back to Calcium Binding Sites List in 3oma
Calcium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7

b:45.8
occ:1.00
 O C:GLU54 2.3 44.5 1.0
O C:ALA57 2.3 43.4 1.0
OE1 C:GLU54 2.4 43.9 1.0
O C:GLY59 2.4 44.2 1.0
O C:HOH586 2.5 32.4 1.0
OE1 C:GLN61 2.5 47.5 1.0
O C:HOH597 2.6 45.7 1.0
C C:GLU54 3.4 44.5 1.0
C C:ALA57 3.5 44.1 1.0
CD C:GLU54 3.5 44.2 1.0
C C:GLY59 3.5 45.0 1.0
CD C:GLN61 3.6 47.1 1.0
NE2 C:GLN61 3.9 46.0 1.0
CA C:GLU54 4.0 44.4 1.0
CG C:GLU54 4.0 44.5 1.0
CA C:VAL60 4.1 46.8 1.0
N C:ALA57 4.2 45.4 1.0
C C:PRO58 4.2 44.4 1.0
N C:VAL60 4.3 45.7 1.0
N C:GLN61 4.3 48.9 1.0
O C:PRO58 4.3 44.5 1.0
CA C:ALA57 4.3 44.8 1.0
N C:GLY59 4.4 44.5 1.0
N C:PRO58 4.4 44.0 1.0
N C:LEU55 4.5 44.7 1.0
CA C:PRO58 4.6 44.2 1.0
OE2 C:GLU54 4.6 43.2 1.0
CA C:GLY59 4.6 44.4 1.0
CB C:GLU54 4.6 44.3 1.0
OD1 C:ASP485 4.6 35.6 1.0
C C:VAL60 4.7 48.1 1.0
CB C:ALA57 4.7 44.5 1.0
CA C:LEU55 4.8 44.9 1.0
O61 C:DMU10 4.8 81.3 1.0
O C:MET53 4.8 44.7 1.0
CG C:GLN61 4.9 48.7 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: Sat Jul 13 16:17:32 2024

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