Calcium in PDB 2gsm: Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides

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

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

Protein crystallography data

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm was solved by L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.020, 131.639, 176.802, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 2gsm:

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 (pdb code 2gsm). 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, PDB code: 2gsm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2gsm

Go back to Calcium Binding Sites List in 2gsm
Calcium binding site 1 out of 2 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3007

b:24.3
occ:1.00
O A:ALA57 2.3 24.7 1.0
O A:GLY59 2.3 21.4 1.0
O A:GLU54 2.4 22.2 1.0
OE1 A:GLU54 2.4 23.8 1.0
O A:HOH6547 2.5 20.4 1.0
NE2 A:GLN61 2.5 21.5 1.0
O A:HOH6559 2.6 23.1 1.0
C A:GLU54 3.5 23.1 1.0
C A:ALA57 3.5 23.8 1.0
C A:GLY59 3.5 21.9 1.0
CD A:GLU54 3.5 23.9 1.0
CD A:GLN61 3.6 27.4 1.0
CA A:GLU54 4.0 23.2 1.0
CG A:GLU54 4.0 22.6 1.0
OE1 A:GLN61 4.0 27.7 1.0
CA A:VAL60 4.1 22.0 1.0
N A:ALA57 4.2 23.8 1.0
C A:PRO58 4.2 23.3 1.0
N A:VAL60 4.2 22.2 1.0
N A:GLN61 4.3 24.3 1.0
CA A:ALA57 4.3 24.3 1.0
O A:PRO58 4.3 23.4 1.0
N A:GLY59 4.4 22.5 1.0
N A:PRO58 4.5 23.5 1.0
CA A:PRO58 4.6 23.2 1.0
CA A:GLY59 4.6 22.3 1.0
N A:LEU55 4.6 23.1 1.0
OE2 A:GLU54 4.6 23.6 1.0
CB A:GLU54 4.6 23.2 1.0
C A:VAL60 4.6 23.5 1.0
O A:HOH6585 4.7 30.1 1.0
CB A:ALA57 4.7 24.1 1.0
O A:MET53 4.8 23.8 1.0
CA A:LEU55 4.8 23.2 1.0
CG A:GLN61 4.9 25.4 1.0
CB A:GLN61 4.9 24.6 1.0
OD1 A:ASP485 5.0 24.5 1.0
C A:LEU55 5.0 23.3 1.0

Calcium binding site 2 out of 2 in 2gsm

Go back to Calcium Binding Sites List in 2gsm
Calcium binding site 2 out of 2 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4007

b:34.8
occ:1.00
O C:GLY59 2.3 32.3 1.0
O C:ALA57 2.3 32.3 1.0
O C:GLU54 2.3 34.4 1.0
OE1 C:GLU54 2.4 35.0 1.0
NE2 C:GLN61 2.4 34.0 1.0
O C:HOH1085 2.5 30.8 1.0
O C:HOH1107 2.6 38.3 1.0
C C:GLU54 3.4 33.6 1.0
CD C:GLN61 3.5 35.8 1.0
C C:ALA57 3.5 32.9 1.0
C C:GLY59 3.5 32.8 1.0
CD C:GLU54 3.5 33.5 1.0
OE1 C:GLN61 3.7 36.5 1.0
CA C:GLU54 3.9 33.0 1.0
CA C:VAL60 4.0 33.5 1.0
CG C:GLU54 4.1 33.1 1.0
N C:GLN61 4.2 35.6 1.0
N C:VAL60 4.2 32.8 1.0
N C:ALA57 4.2 34.6 1.0
C C:PRO58 4.3 33.0 1.0
CA C:ALA57 4.3 34.0 1.0
O C:PRO58 4.4 32.7 1.0
N C:PRO58 4.5 32.9 1.0
N C:GLY59 4.5 32.5 1.0
N C:LEU55 4.5 33.8 1.0
OE2 C:GLU54 4.6 33.4 1.0
C C:VAL60 4.6 34.8 1.0
CA C:PRO58 4.6 33.0 1.0
CA C:GLY59 4.6 32.5 1.0
CB C:GLU54 4.6 33.2 1.0
CB C:ALA57 4.6 34.4 1.0
O C:MET53 4.7 33.0 1.0
OD1 C:ASP485 4.8 31.5 1.0
CG C:GLN61 4.8 35.5 1.0
CA C:LEU55 4.8 33.7 1.0
O C:HOH1164 4.9 37.9 1.0
CB C:GLN61 5.0 35.6 1.0

Reference:

L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller. Identification of Conserved Lipid/Detergent-Binding Sites in A High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc.Natl.Acad.Sci.Usa V. 103 16117 2006.
ISSN: ISSN 0027-8424
PubMed: 17050688
DOI: 10.1073/PNAS.0606149103
Page generated: Sat Dec 12 03:38:40 2020

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