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: Sat Dec 12 04:12:22 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy