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Calcium in PDB 3ehb: A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate

Enzymatic activity of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate

All present enzymatic activity of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate:
1.9.3.1;

Protein crystallography data

The structure of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate, PDB code: 3ehb was solved by J.Koepke, H.Mueller, G.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.69 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.461, 151.332, 157.487, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 3ehb:

The structure of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 2 atoms
Copper (Cu) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate (pdb code 3ehb). 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 A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate, PDB code: 3ehb:

Calcium binding site 1 out of 1 in 3ehb

Go back to Calcium Binding Sites List in 3ehb
Calcium binding site 1 out of 1 in the A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome C Oxidase By Altering the Side Chain Orientation of A Distant, Conserved Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca563

b:53.9
occ:1.00
O A:HIS59 2.3 40.8 1.0
OE1 A:GLN63 2.3 58.5 1.0
OE2 A:GLU56 2.3 46.5 1.0
O A:GLY61 2.3 58.1 1.0
O A:GLU56 2.4 51.4 1.0
O A:HOH669 2.4 46.4 1.0
CD A:GLN63 3.4 62.1 1.0
CD A:GLU56 3.4 54.9 1.0
C A:GLU56 3.5 49.7 1.0
C A:GLY61 3.5 60.2 1.0
C A:HIS59 3.5 44.9 1.0
CA A:VAL62 3.9 54.9 1.0
CA A:GLU56 4.0 45.4 1.0
NE2 A:GLN63 4.0 57.4 1.0
CG A:GLU56 4.0 52.1 1.0
N A:VAL62 4.1 54.3 1.0
C A:PRO60 4.1 52.5 1.0
N A:HIS59 4.1 52.4 1.0
O A:PRO60 4.1 48.9 1.0
N A:GLN63 4.2 62.4 1.0
CA A:HIS59 4.3 50.3 1.0
N A:GLY61 4.4 53.9 1.0
CA A:PRO60 4.4 52.6 1.0
N A:PRO60 4.5 46.5 1.0
C A:VAL62 4.5 62.6 1.0
OE1 A:GLU56 4.5 51.1 1.0
CB A:HIS59 4.5 52.6 1.0
O A:HOH658 4.5 62.5 1.0
CB A:GLU56 4.6 46.9 1.0
CG A:GLN63 4.6 63.1 1.0
OD1 A:ASP477 4.6 53.0 1.0
N A:LEU57 4.6 45.5 1.0
CA A:GLY61 4.7 50.9 1.0
N A:GLN58 4.9 43.9 1.0
CA A:LEU57 4.9 42.5 1.0

Reference:

K.L.Durr, J.Koepke, P.Hellwig, H.Muller, H.Angerer, G.Peng, E.Olkhova, O.-M.H.Richter, B.Ludwig, H.Michel. A D-Pathway Mutation Decouples the Paracoccusdenitrificans Cytochrome C Oxidase By Altering the Side-Chain Orientation of A Distant Conserved Glutamate J.Mol.Biol. V. 384 865 2008.
ISSN: ISSN 0022-2836
PubMed: 18930738
DOI: 10.1016/J.JMB.2008.09.074
Page generated: Sat Dec 12 04:10:08 2020

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