Calcium in PDB 6ci0: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation, PDB code: 6ci0 was solved by J.Liu, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.916, 130.969, 177.788, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.4

Other elements in 6ci0:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom
Cadmium (Cd) 2 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 E101A (II) Mutation (pdb code 6ci0). 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 E101A (II) Mutation, PDB code: 6ci0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6ci0

Go back to Calcium Binding Sites List in 6ci0
Calcium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca616

b:44.0
occ:1.00
 O A:GLU54 2.3 42.4 1.0
O A:GLY59 2.3 43.0 1.0
O A:ALA57 2.4 40.4 1.0
OE1 A:GLU54 2.4 39.3 1.0
OE1 A:GLN61 2.4 45.4 1.0
O A:HOH715 2.6 41.9 1.0
O A:HOH768 2.6 37.1 1.0
C A:GLU54 3.4 38.8 1.0
CD A:GLN61 3.4 47.5 1.0
CD A:GLU54 3.5 46.1 1.0
C A:GLY59 3.6 46.3 1.0
C A:ALA57 3.6 44.8 1.0
NE2 A:GLN61 3.8 43.5 1.0
CA A:GLU54 3.9 37.7 1.0
CG A:GLU54 4.0 38.9 1.0
CA A:VAL60 4.1 44.7 1.0
N A:ALA57 4.2 48.7 1.0
C A:PRO58 4.2 41.4 1.0
O A:PRO58 4.2 43.5 1.0
N A:GLN61 4.2 47.4 1.0
N A:VAL60 4.3 44.1 1.0
CA A:ALA57 4.4 47.4 1.0
N A:GLY59 4.5 43.7 1.0
N A:LEU55 4.5 42.4 1.0
O61 A:DMU604 4.5 46.2 0.8
N A:PRO58 4.5 45.6 1.0
OE2 A:GLU54 4.6 45.7 1.0
CB A:GLU54 4.6 37.5 1.0
C A:VAL60 4.6 45.0 1.0
CA A:PRO58 4.6 36.5 1.0
CA A:GLY59 4.6 40.0 1.0
CG A:GLN61 4.7 42.2 1.0
CB A:ALA57 4.7 40.1 1.0
O A:MET53 4.7 47.0 1.0
OD1 A:ASP485 4.8 45.1 1.0
CA A:LEU55 4.8 45.4 1.0
CB A:GLN61 4.9 41.8 1.0
N A:MET56 5.0 42.2 1.0
C A:LEU55 5.0 45.8 1.0

Calcium binding site 2 out of 2 in 6ci0

Go back to Calcium Binding Sites List in 6ci0
Calcium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:69.3
occ:1.00
 O C:GLU54 2.2 65.0 1.0
O C:GLY59 2.3 68.3 1.0
O C:ALA57 2.3 61.3 1.0
O C:HOH706 2.5 72.8 1.0
OE1 C:GLU54 2.5 59.7 1.0
OE1 C:GLN61 2.5 72.4 1.0
O C:HOH719 2.6 60.4 1.0
C C:GLU54 3.4 61.2 1.0
CD C:GLN61 3.4 67.7 1.0
C C:GLY59 3.5 60.2 1.0
C C:ALA57 3.5 69.9 1.0
CD C:GLU54 3.6 70.9 1.0
NE2 C:GLN61 3.7 65.5 1.0
CA C:GLU54 4.0 63.7 1.0
CG C:GLU54 4.0 72.2 1.0
C C:PRO58 4.1 70.7 1.0
O C:PRO58 4.1 72.3 1.0
CA C:VAL60 4.2 66.0 1.0
N C:ALA57 4.2 68.5 1.0
N C:VAL60 4.3 65.3 1.0
N C:GLN61 4.3 78.1 1.0
CA C:ALA57 4.4 70.5 1.0
N C:GLY59 4.4 68.2 1.0
N C:LEU55 4.5 66.8 1.0
N C:PRO58 4.5 65.6 1.0
CA C:PRO58 4.5 68.6 1.0
CA C:GLY59 4.6 58.2 1.0
CB C:GLU54 4.6 69.1 1.0
C C:VAL60 4.7 77.0 1.0
OE2 C:GLU54 4.7 65.9 1.0
OD1 C:ASP485 4.7 58.8 1.0
CA C:LEU55 4.7 64.8 1.0
CG C:GLN61 4.7 73.3 1.0
CB C:ALA57 4.7 66.3 1.0
O C:MET53 4.9 65.1 1.0
C C:LEU55 4.9 66.2 1.0
N C:MET56 4.9 68.6 1.0

Reference:

C.Hiser, J.Liu, S.Ferguson-Miller. The K-Path Entrance in Cytochrome C Oxidase Is Defined By Mutation of E101 and Controlled By An Adjacent Ligand Binding Domain. Biochim. Biophys. Acta V.1859 725 2018.
ISSN: ISSN 0006-3002
PubMed: 29626419
DOI: 10.1016/J.BBABIO.2018.03.017
Page generated: Sat Dec 12 06:01:26 2020

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