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Calcium in PDB 1qle: Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

Enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment

All present enzymatic activity of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment:
1.9.3.1;

Protein crystallography data

The structure of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle was solved by A.Harrenga, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 3.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 205.200, 205.200, 81.100, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 30.9

Other elements in 1qle:

The structure of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Iron (Fe) 2 atoms
Copper (Cu) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment (pdb code 1qle). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment, PDB code: 1qle:

Calcium binding site 1 out of 1 in 1qle

Go back to Calcium Binding Sites List in 1qle
Calcium binding site 1 out of 1 in the Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Structure of the Paracoccus Denitrificans Four-Subunit Cytochrome C Oxidase in the Completely Oxidized State Complexed with An Antibody Fv Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:22.2
occ:1.00
 O A:HIS59 2.3 31.8 1.0
O A:GLY61 2.3 40.0 1.0
OE1 A:GLN63 2.3 52.2 1.0
O A:GLU56 2.4 37.6 1.0
OE1 A:GLU56 2.4 45.0 1.0
CD A:GLN63 3.1 52.3 1.0
O A:PRO60 3.2 18.6 1.0
NE2 A:GLN63 3.3 52.7 1.0
C A:GLU56 3.4 37.3 1.0
C A:HIS59 3.4 32.1 1.0
C A:GLY61 3.5 41.4 1.0
C A:PRO60 3.5 25.2 1.0
CD A:GLU56 3.6 44.4 1.0
CA A:GLU56 3.7 36.8 1.0
N A:GLY61 4.0 30.6 1.0
CA A:PRO60 4.1 27.4 1.0
N A:PRO60 4.1 29.9 1.0
CB A:GLU56 4.2 37.5 1.0
CA A:GLY61 4.3 37.4 1.0
N A:GLN63 4.3 44.1 1.0
CG A:GLU56 4.4 39.5 1.0
CA A:HIS59 4.5 31.8 1.0
N A:VAL62 4.5 43.2 1.0
CG A:GLN63 4.5 49.5 1.0
N A:HIS59 4.5 35.7 1.0
OE2 A:GLU56 4.5 44.5 1.0
N A:LEU57 4.6 38.0 1.0
CA A:VAL62 4.6 45.1 1.0
CB A:GLN63 4.8 46.7 1.0
CB A:HIS59 4.8 32.3 1.0
O A:MET55 4.9 47.8 1.0
C A:VAL62 4.9 46.6 1.0

Reference:

A.Harrenga, H.Michel. The Cytochrome C Oxidase From Paracoccus Denitrificans Does Not Change the Metal Center Ligation Upon Reduction J.Biol.Chem. V. 274 33296 1999.
ISSN: ISSN 0021-9258
PubMed: 10559205
DOI: 10.1074/JBC.274.47.33296
Page generated: Sat Dec 12 03:16:47 2020

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