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Calcium in PDB 3dtu: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid:
1.9.3.1;

Protein crystallography data

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

Resolution Low / High (Å) 40.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.243, 132.052, 167.966, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.2

Other elements in 3dtu:

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

Magnesium (Mg) 2 atoms
Cadmium (Cd) 5 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 Complexed with Deoxycholic Acid (pdb code 3dtu). 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 Complexed with Deoxycholic Acid, PDB code: 3dtu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3dtu

Go back to Calcium Binding Sites List in 3dtu
Calcium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:27.4
occ:1.00
 OE1 A:GLU54 2.3 22.8 1.0
O A:GLU54 2.3 29.3 1.0
O A:ALA57 2.3 29.8 1.0
O A:GLY59 2.3 31.0 1.0
NE2 A:GLN61 2.4 31.5 1.0
O A:HOH1563 2.5 30.4 1.0
O A:HOH1550 2.6 29.2 1.0
C A:GLU54 3.4 29.2 1.0
CD A:GLU54 3.4 26.9 1.0
C A:ALA57 3.5 29.9 1.0
CD A:GLN61 3.5 34.4 1.0
C A:GLY59 3.5 30.8 1.0
OE1 A:GLN61 4.0 34.5 1.0
CG A:GLU54 4.0 27.0 1.0
CA A:GLU54 4.0 28.6 1.0
CA A:VAL60 4.1 30.1 1.0
N A:ALA57 4.2 31.0 1.0
N A:GLN61 4.3 31.8 1.0
N A:VAL60 4.3 30.5 1.0
CA A:ALA57 4.3 30.5 1.0
C A:PRO58 4.3 30.5 1.0
N A:GLY59 4.4 30.6 1.0
OE2 A:GLU54 4.5 25.5 1.0
O A:PRO58 4.5 30.8 1.0
N A:PRO58 4.5 29.8 1.0
N A:LEU55 4.5 29.2 1.0
CA A:GLY59 4.6 30.6 1.0
O61 A:DMU1005 4.6 50.5 0.8
CB A:GLU54 4.6 28.4 1.0
CA A:PRO58 4.6 30.2 1.0
C A:VAL60 4.6 31.2 1.0
CB A:ALA57 4.7 30.7 1.0
O A:MET53 4.7 28.9 1.0
CG A:GLN61 4.8 31.8 1.0
CA A:LEU55 4.8 29.3 1.0
OD1 A:ASP485 4.8 30.3 1.0
CB A:GLN61 4.9 31.9 1.0
C A:LEU55 5.0 30.3 1.0
N A:MET56 5.0 31.1 1.0

Calcium binding site 2 out of 2 in 3dtu

Go back to Calcium Binding Sites List in 3dtu
Calcium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca571

b:32.6
occ:1.00
 O C:ALA57 2.3 30.8 1.0
OE1 C:GLU54 2.3 26.7 1.0
O C:GLU54 2.4 31.9 1.0
O C:GLY59 2.4 34.4 1.0
NE2 C:GLN61 2.5 35.0 1.0
O C:HOH642 2.5 30.9 1.0
O C:HOH629 2.6 28.2 1.0
C C:GLU54 3.4 32.1 1.0
CD C:GLU54 3.4 30.6 1.0
C C:ALA57 3.5 31.4 1.0
C C:GLY59 3.6 34.1 1.0
CD C:GLN61 3.6 36.2 1.0
OE1 C:GLN61 3.9 37.8 1.0
CA C:GLU54 4.0 32.1 1.0
CG C:GLU54 4.0 30.8 1.0
CA C:VAL60 4.1 34.6 1.0
N C:ALA57 4.2 31.6 1.0
N C:GLN61 4.2 35.9 1.0
C C:PRO58 4.3 32.6 1.0
N C:VAL60 4.3 34.5 1.0
CA C:ALA57 4.3 31.7 1.0
O C:PRO58 4.4 32.7 1.0
N C:GLY59 4.5 33.0 1.0
N C:PRO58 4.5 31.5 1.0
OE2 C:GLU54 4.5 28.5 1.0
N C:LEU55 4.5 31.5 1.0
CA C:PRO58 4.6 31.9 1.0
C C:VAL60 4.6 35.8 1.0
CB C:GLU54 4.6 31.5 1.0
CA C:GLY59 4.6 33.2 1.0
CB C:ALA57 4.7 31.6 1.0
O C:MET53 4.7 33.5 1.0
CA C:LEU55 4.8 31.4 1.0
O61 C:DMU567 4.8 78.5 1.0
OD1 C:ASP485 4.8 31.4 1.0
CG C:GLN61 4.8 36.7 1.0
C C:LEU55 4.9 31.8 1.0
N C:MET56 4.9 32.0 1.0
CB C:GLN61 5.0 36.3 1.0

Reference:

L.Qin, D.A.Mills, L.Buhrow, C.Hiser, S.Ferguson-Miller. A Conserved Steroid Binding Site in Cytochrome C Oxidase. Biochemistry V. 47 9931 2008.
ISSN: ISSN 0006-2960
PubMed: 18759498
DOI: 10.1021/BI8013483
Page generated: Sat Dec 12 04:09:21 2020

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