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Calcium in PDB 3fye: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

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

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

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 3fye was solved by L.Qin, D.A.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.613, 131.472, 176.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 3fye:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State 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 in the Reduced State (pdb code 3fye). 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 in the Reduced State, PDB code: 3fye:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3fye

Go back to Calcium Binding Sites List in 3fye
Calcium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca572

b:29.1
occ:1.00
 O A:GLY59 2.3 28.8 1.0
O A:GLU54 2.3 28.4 1.0
O A:ALA57 2.4 30.8 1.0
NE2 A:GLN61 2.4 31.6 1.0
OE1 A:GLU54 2.4 29.2 1.0
O A:HOH640 2.6 26.8 1.0
O A:HOH628 2.6 26.5 1.0
C A:GLU54 3.4 28.2 1.0
CD A:GLU54 3.5 28.4 1.0
C A:GLY59 3.5 29.5 1.0
CD A:GLN61 3.6 33.9 1.0
C A:ALA57 3.6 31.1 1.0
OE1 A:GLN61 4.0 36.0 1.0
CA A:GLU54 4.0 28.4 1.0
CG A:GLU54 4.0 28.3 1.0
CA A:VAL60 4.1 29.2 1.0
N A:GLN61 4.2 31.2 1.0
N A:VAL60 4.3 29.4 1.0
N A:ALA57 4.3 31.7 1.0
C A:PRO58 4.3 30.6 1.0
O A:PRO58 4.4 30.2 1.0
CA A:ALA57 4.4 31.6 1.0
N A:GLY59 4.5 30.1 1.0
N A:LEU55 4.5 28.4 1.0
N A:PRO58 4.6 30.8 1.0
OE2 A:GLU54 4.6 28.2 1.0
C A:VAL60 4.6 30.4 1.0
O61 A:DMU577 4.6 44.1 0.8
CA A:GLY59 4.6 29.1 1.0
CB A:GLU54 4.7 28.3 1.0
CA A:PRO58 4.7 30.7 1.0
O A:MET53 4.7 28.2 1.0
CB A:ALA57 4.8 31.0 1.0
CG A:GLN61 4.8 32.3 1.0
CA A:LEU55 4.8 28.7 1.0
CB A:GLN61 4.9 31.9 1.0
OD1 A:ASP485 4.9 30.0 1.0
C A:LEU55 5.0 29.2 1.0

Calcium binding site 2 out of 2 in 3fye

Go back to Calcium Binding Sites List in 3fye
Calcium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca572

b:43.5
occ:1.00
 O C:ALA57 2.3 39.5 1.0
O C:GLU54 2.3 41.9 1.0
OE1 C:GLU54 2.3 39.2 1.0
O C:GLY59 2.3 41.7 1.0
NE2 C:GLN61 2.4 46.4 1.0
O C:HOH1085 2.6 32.8 1.0
O C:HOH1107 2.7 46.5 1.0
C C:GLU54 3.4 41.9 1.0
CD C:GLU54 3.5 41.6 1.0
C C:ALA57 3.5 40.4 1.0
C C:GLY59 3.5 42.2 1.0
CD C:GLN61 3.5 47.2 1.0
OE1 C:GLN61 3.9 46.9 1.0
CA C:GLU54 3.9 42.1 1.0
CG C:GLU54 4.0 42.4 1.0
CA C:VAL60 4.1 43.6 1.0
N C:ALA57 4.2 41.5 1.0
N C:VAL60 4.2 43.0 1.0
N C:GLN61 4.3 45.9 1.0
CA C:ALA57 4.3 40.9 1.0
C C:PRO58 4.3 41.3 1.0
N C:GLY59 4.4 41.4 1.0
O C:PRO58 4.5 41.0 1.0
N C:PRO58 4.5 40.5 1.0
N C:LEU55 4.5 41.5 1.0
OE2 C:GLU54 4.5 40.0 1.0
CB C:GLU54 4.6 42.0 1.0
CB C:ALA57 4.6 40.9 1.0
CA C:GLY59 4.6 41.6 1.0
C C:VAL60 4.6 45.1 1.0
OD1 C:ASP485 4.7 36.6 1.0
CA C:PRO58 4.7 41.0 1.0
O C:MET53 4.8 42.7 1.0
CG C:GLN61 4.8 47.0 1.0
O61 C:DMU1005 4.8 57.1 0.8
CA C:LEU55 4.8 41.2 1.0
CB C:GLN61 4.9 46.6 1.0

Reference:

L.Qin, J.Liu, D.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller. Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Tue Jul 8 12:34:15 2025

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