Calcium in PDB 5weh: Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

All present enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh was solved by J.Liu, F.Ferguson-Miller, Q.Ling, C.Hiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 3.45
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	339.221, 339.221, 89.199, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.2

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms

The binding sites of Calcium atom in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State (pdb code 5weh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:0.5 occ:1.00 O A:GLU54 2.2 0.9 1.0 O A:GLY59 2.2 0.7 1.0 O A:ALA57 2.5 0.3 1.0 OE1 A:GLN61 3.2 0.2 1.0 C A:GLU54 3.3 0.4 1.0 OE1 A:GLU54 3.4 0.3 1.0 C A:GLY59 3.4 0.7 1.0 C A:ALA57 3.6 0.4 1.0 C A:PRO58 3.8 0.2 1.0 CG A:GLU54 3.9 99.6 1.0 NE2 A:GLN61 3.9 0.9 1.0 CD A:GLN61 3.9 0.1 1.0 N A:GLY59 3.9 0.6 1.0 CD A:GLU54 4.0 0.0 1.0 O A:PRO58 4.0 0.7 1.0 CA A:PRO58 4.0 0.5 1.0 CA A:GLU54 4.1 0.8 1.0 OD1 A:ASP485 4.1 0.0 1.0 N A:VAL60 4.3 0.5 1.0 N A:LEU55 4.3 0.1 1.0 CA A:GLY59 4.3 0.9 1.0 CA A:VAL60 4.3 0.4 1.0 N A:PRO58 4.3 0.0 1.0 CA A:LEU55 4.4 0.8 1.0 N A:ALA57 4.4 0.9 1.0 CB A:GLU54 4.5 0.0 1.0 O A:ILE484 4.6 0.9 1.0 CA A:ALA57 4.7 0.5 1.0 C A:LEU55 4.8 0.4 1.0 N A:MET56 4.9 0.9 1.0 N A:GLN61 4.9 0.7 1.0 CG A:ASP485 4.9 0.6 1.0

Calcium binding site 2 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca606 b:0.7 occ:1.00 O G:GLU54 2.3 0.2 1.0 O G:GLY59 2.3 1.0 1.0 O G:ALA57 2.4 0.3 1.0 C G:GLU54 3.4 0.7 1.0 C G:GLY59 3.4 0.9 1.0 OE1 G:GLN61 3.4 0.8 1.0 C G:ALA57 3.5 0.1 1.0 C G:PRO58 3.6 0.1 1.0 OE1 G:GLU54 3.6 0.4 1.0 N G:GLY59 3.8 0.5 1.0 CA G:PRO58 3.8 0.6 1.0 OD1 G:ASP485 3.9 0.5 1.0 O G:PRO58 3.9 0.3 1.0 CG G:GLU54 4.0 0.2 1.0 NE2 G:GLN61 4.0 0.6 1.0 CD G:GLN61 4.1 0.6 1.0 N G:PRO58 4.2 0.3 1.0 CD G:GLU54 4.2 0.7 1.0 CA G:GLY59 4.2 0.1 1.0 CA G:GLU54 4.2 0.9 1.0 N G:LEU55 4.2 0.2 1.0 N G:VAL60 4.3 0.9 1.0 CA G:LEU55 4.3 0.6 1.0 N G:ALA57 4.4 0.2 1.0 CA G:VAL60 4.5 0.0 1.0 O G:ILE484 4.5 0.7 1.0 CA G:ALA57 4.6 0.5 1.0 CB G:GLU54 4.6 0.9 1.0 C G:LEU55 4.7 0.8 1.0 CG G:ASP485 4.8 0.6 1.0 N G:MET56 4.8 0.8 1.0 CE1 G:TYR486 4.9 0.7 1.0

J.Liu, C.Hiser, S.Ferguson-Miller. Role of Conformational Change and K-Path Ligands in Controlling Cytochrome C Oxidase Activity. Biochem. Soc. Trans. V. 45 1087 2017.
ISSN: ISSN 1470-8752
PubMed: 28842531
DOI: 10.1042/BST20160138