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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
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 Bound with Cyanide, PDB code: 3fyi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.344, 131.877, 176.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 3fyi:

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

Calcium binding site 1 out of 2 in 3fyi

Go back to Calcium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca571

b:27.1
occ:1.00
O A:GLU54 2.3 25.8 1.0
O A:GLY59 2.4 26.0 1.0
O A:ALA57 2.4 26.2 1.0
OE1 A:GLU54 2.4 25.3 1.0
NE2 A:GLN61 2.4 24.9 1.0
O A:HOH628 2.6 25.1 1.0
O A:HOH639 2.7 22.2 1.0
C A:GLU54 3.4 25.5 1.0
CD A:GLU54 3.5 25.5 1.0
C A:ALA57 3.5 26.1 1.0
CD A:GLN61 3.5 27.0 1.0
C A:GLY59 3.6 26.0 1.0
OE1 A:GLN61 4.0 28.9 1.0
CA A:GLU54 4.0 25.7 1.0
CG A:GLU54 4.0 25.5 1.0
CA A:VAL60 4.1 25.1 1.0
N A:ALA57 4.2 26.8 1.0
N A:GLN61 4.3 26.0 1.0
C A:PRO58 4.3 26.2 1.0
N A:VAL60 4.3 25.3 1.0
CA A:ALA57 4.3 26.9 1.0
O A:PRO58 4.4 25.9 1.0
N A:GLY59 4.5 26.0 1.0
N A:PRO58 4.5 26.0 1.0
N A:LEU55 4.5 25.5 1.0
OE2 A:GLU54 4.6 26.0 1.0
CA A:PRO58 4.6 25.8 1.0
C A:VAL60 4.6 26.0 1.0
CA A:GLY59 4.6 25.4 1.0
CB A:GLU54 4.7 25.4 1.0
O61 A:DMU576 4.7 41.4 0.8
O A:MET53 4.7 24.9 1.0
CB A:ALA57 4.7 25.8 1.0
CG A:GLN61 4.8 26.0 1.0
CA A:LEU55 4.8 25.4 1.0
OD1 A:ASP485 4.8 28.6 1.0
CB A:GLN61 4.8 26.5 1.0
C A:LEU55 5.0 25.5 1.0

Calcium binding site 2 out of 2 in 3fyi

Go back to Calcium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca571

b:40.3
occ:1.00
O C:ALA57 2.2 38.4 1.0
OE1 C:GLU54 2.2 37.6 1.0
O C:GLU54 2.3 39.9 1.0
O C:GLY59 2.3 40.1 1.0
NE2 C:GLN61 2.5 43.6 1.0
O C:HOH1107 2.6 45.0 1.0
O C:HOH1085 2.6 33.7 1.0
CD C:GLU54 3.4 39.6 1.0
C C:GLU54 3.4 39.8 1.0
C C:ALA57 3.4 39.0 1.0
C C:GLY59 3.5 40.4 1.0
CD C:GLN61 3.5 43.7 1.0
OE1 C:GLN61 3.8 42.5 1.0
CG C:GLU54 4.0 40.0 1.0
CA C:GLU54 4.0 39.9 1.0
CA C:VAL60 4.1 41.7 1.0
N C:ALA57 4.1 39.4 1.0
C C:PRO58 4.2 39.9 1.0
CA C:ALA57 4.2 39.3 1.0
N C:VAL60 4.2 40.9 1.0
N C:GLN61 4.3 43.9 1.0
O C:PRO58 4.4 39.7 1.0
N C:GLY59 4.4 39.8 1.0
N C:PRO58 4.4 39.3 1.0
OE2 C:GLU54 4.4 39.0 1.0
N C:LEU55 4.5 39.4 1.0
CA C:PRO58 4.5 39.5 1.0
CA C:GLY59 4.6 39.8 1.0
CB C:GLU54 4.6 39.8 1.0
CB C:ALA57 4.6 39.0 1.0
C C:VAL60 4.7 43.2 1.0
OD1 C:ASP485 4.7 33.9 1.0
O C:MET53 4.8 40.5 1.0
CA C:LEU55 4.8 39.5 1.0
O61 C:DMU1005 4.8 59.1 0.8
CG C:GLN61 4.8 44.4 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: Wed Oct 28 08:10:58 2020

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