Calcium in PDB 2w0q: E. Coli Copper Amine Oxidase in Complex with Xenon

All present enzymatic activity of E. Coli Copper Amine Oxidase in Complex with Xenon:
1.4.3.4;

The structure of E. Coli Copper Amine Oxidase in Complex with Xenon, PDB code: 2w0q was solved by P.Pirrat, M.A.Smith, A.R.Pearson, M.J.Mcpherson, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 2.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.588, 166.871, 80.330, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 21.9

The structure of E. Coli Copper Amine Oxidase in Complex with Xenon also contains other interesting chemical elements:

Xenon	(Xe)	11 atoms
Copper	(Cu)	2 atoms

The binding sites of Calcium atom in the E. Coli Copper Amine Oxidase in Complex with Xenon (pdb code 2w0q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the E. Coli Copper Amine Oxidase in Complex with Xenon, PDB code: 2w0q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:27.3 occ:1.00 OD1 A:ASP535 2.2 28.4 1.0 OD1 A:ASP533 2.3 24.3 1.0 OD1 A:ASP678 2.3 33.0 1.0 O A:HOH2254 2.3 27.0 1.0 O A:LEU534 2.3 29.4 1.0 O A:ALA679 2.4 28.8 1.0 C A:LEU534 3.4 29.4 1.0 C A:ALA679 3.5 30.3 1.0 CG A:ASP535 3.5 28.5 1.0 N A:ALA679 3.5 32.1 1.0 CG A:ASP678 3.5 35.7 1.0 CG A:ASP533 3.6 27.9 1.0 NZ A:LYS133 3.7 27.1 1.0 C A:ASP533 4.0 28.3 1.0 CA A:ALA679 4.1 30.9 1.0 CA A:ASP535 4.1 28.2 1.0 N A:ASP535 4.1 28.9 1.0 C A:ASP678 4.2 33.3 1.0 N A:LEU534 4.2 28.7 1.0 OD2 A:ASP678 4.2 38.5 1.0 O A:ASP533 4.3 29.9 1.0 OD2 A:ASP535 4.3 29.8 1.0 OD2 A:ASP533 4.3 29.0 1.0 CA A:ASP678 4.4 33.9 1.0 CA A:LEU534 4.4 29.2 1.0 CB A:ASP535 4.4 27.2 1.0 CA A:ASP533 4.4 27.7 1.0 O A:GLU539 4.5 32.3 1.0 N A:VAL680 4.6 29.8 1.0 CB A:ASP678 4.6 33.6 1.0 CB A:ASP533 4.6 26.9 1.0 ND2 A:ASN541 4.7 28.3 1.0 CB A:ALA679 4.9 29.8 1.0 CA A:VAL680 5.0 29.2 1.0 O A:ASP678 5.0 33.1 1.0

Calcium binding site 2 out of 4 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:69.8 occ:1.00 O A:HOH2290 2.2 40.9 1.0 O A:TYR667 2.5 41.9 1.0 O A:HOH2294 2.6 39.1 1.0 OE2 A:GLU573 2.6 36.1 1.0 OE1 A:GLU672 2.8 53.9 1.0 O A:HOH2268 3.2 55.6 1.0 OE1 A:GLU573 3.3 37.7 1.0 CD A:GLU573 3.3 38.7 1.0 O A:HOH2307 3.4 53.0 1.0 C A:TYR667 3.7 42.0 1.0 CD A:GLU672 3.9 52.8 1.0 OE1 A:GLU647 4.0 38.9 1.0 N A:ARG642 4.2 33.5 1.0 OE2 A:GLU647 4.4 38.5 1.0 CG A:GLU672 4.4 47.1 1.0 CA A:TYR667 4.4 41.7 1.0 O A:ARG642 4.5 32.9 1.0 CB A:THR641 4.5 32.7 1.0 CD A:GLU647 4.6 40.3 1.0 CB A:ARG642 4.6 33.9 1.0 N A:SER668 4.7 43.2 1.0 CB A:TYR667 4.7 42.0 1.0 CA A:SER668 4.8 44.1 1.0 CG A:GLU573 4.8 37.2 1.0 CG2 A:THR641 4.9 32.6 1.0 CA A:ARG642 4.9 34.3 1.0

Calcium binding site 3 out of 4 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:31.2 occ:1.00 OD1 B:ASP535 2.3 30.0 1.0 OD1 B:ASP533 2.3 26.5 1.0 OD1 B:ASP678 2.4 33.5 1.0 O B:HOH2204 2.4 25.5 1.0 O B:ALA679 2.4 34.6 1.0 O B:LEU534 2.4 32.7 1.0 C B:LEU534 3.4 31.4 1.0 CG B:ASP535 3.5 30.6 1.0 C B:ALA679 3.5 33.4 1.0 CG B:ASP678 3.6 33.4 1.0 CG B:ASP533 3.6 31.8 1.0 NZ B:LYS133 3.6 34.3 1.0 N B:ALA679 3.7 33.6 1.0 C B:ASP533 4.0 30.5 1.0 N B:ASP535 4.1 30.9 1.0 N B:LEU534 4.1 29.5 1.0 CA B:ASP535 4.1 30.2 1.0 O B:ASP533 4.1 31.3 1.0 OD2 B:ASP678 4.3 29.1 1.0 CA B:ALA679 4.3 33.0 1.0 C B:ASP678 4.3 33.7 1.0 OD2 B:ASP535 4.3 32.0 1.0 CA B:LEU534 4.3 30.9 1.0 OD2 B:ASP533 4.4 31.0 1.0 CA B:ASP533 4.4 30.3 1.0 CB B:ASP535 4.4 29.5 1.0 CA B:ASP678 4.5 32.9 1.0 N B:VAL680 4.5 32.7 1.0 CB B:ASP533 4.6 30.2 1.0 ND2 B:ASN541 4.6 31.8 1.0 O B:GLU539 4.6 38.2 1.0 CB B:ASP678 4.7 32.4 1.0 CG2 B:VAL680 4.7 31.9 1.0 CA B:VAL680 4.8 31.3 1.0 CE B:LYS133 4.9 35.1 1.0 CB B:ALA679 5.0 32.8 1.0

Calcium binding site 4 out of 4 in the E. Coli Copper Amine Oxidase in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E. Coli Copper Amine Oxidase in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:77.6 occ:1.00 OE2 B:GLU573 2.4 33.9 1.0 O B:TYR667 2.4 48.0 1.0 OE2 B:GLU672 2.5 58.4 1.0 O B:HOH2232 2.9 56.9 1.0 CD B:GLU573 3.0 39.0 1.0 OE1 B:GLU573 3.1 40.4 1.0 CD B:GLU672 3.4 57.7 1.0 C B:TYR667 3.6 47.9 1.0 CG B:GLU672 3.8 53.2 1.0 N B:ARG642 4.2 37.4 1.0 OE1 B:GLU647 4.2 51.0 1.0 CB B:THR641 4.3 35.5 1.0 CA B:TYR667 4.4 47.3 1.0 CB B:ARG642 4.5 37.2 1.0 OE1 B:GLU672 4.5 62.0 1.0 CG B:GLU573 4.5 40.4 1.0 N B:SER668 4.5 48.7 1.0 CA B:SER668 4.6 49.7 1.0 OE2 B:GLU647 4.6 52.4 1.0 CB B:GLU672 4.6 50.2 1.0 O B:ARG642 4.7 36.5 1.0 CG2 B:THR641 4.7 36.4 1.0 CB B:TYR667 4.8 46.2 1.0 CA B:THR641 4.9 35.4 1.0 CD B:GLU647 4.9 51.5 1.0 CA B:ARG642 4.9 37.6 1.0 CG B:ARG642 4.9 38.0 1.0

P.Pirrat, M.A.Smith, A.R.Pearson, M.J.Mcpherson, S.E.V.Phillips. Structure of A Xenon Derivative of Escherichia Coli Copper Amine Oxidase: Confirmation of the Proposed Oxygen-Entry Pathway. Acta Crystallogr.,Sect.F V. 64 1105 2008.
ISSN: ISSN 1744-3091
PubMed: 19052360
DOI: 10.1107/S1744309108036373