Calcium in PDB 2y73: The Native Structures of Soluble Human Primary Amine Oxidase AOC3

All present enzymatic activity of The Native Structures of Soluble Human Primary Amine Oxidase AOC3:
1.4.3.21;

The structure of The Native Structures of Soluble Human Primary Amine Oxidase AOC3, PDB code: 2y73 was solved by H.Elovaara, H.Kidron, V.Parkash, Y.Nymalm, E.Bligt, P.Ollikka, D.J.Smith, M.Pihlavisto, M.Salmi, S.Jalkanen, T.A.Salminen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	225.755, 225.755, 216.985, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 21.3

The structure of The Native Structures of Soluble Human Primary Amine Oxidase AOC3 also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3 (pdb code 2y73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3, PDB code: 2y73:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Native Structures of Soluble Human Primary Amine Oxidase AOC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:24.9 occ:1.00 OD1 A:ASP529 2.3 23.1 1.0 O A:LEU530 2.3 26.9 1.0 OD1 A:ASP531 2.4 24.4 1.0 OD1 A:ASP673 2.4 26.6 1.0 O A:LEU674 2.4 23.6 1.0 O A:HOH929 2.5 27.1 1.0 C A:LEU530 3.2 23.9 1.0 CG A:ASP529 3.5 22.1 1.0 CG A:ASP531 3.6 27.4 1.0 C A:LEU674 3.6 25.8 1.0 CG A:ASP673 3.6 30.7 1.0 N A:LEU674 3.8 29.8 1.0 NZ A:LYS106 3.8 21.2 1.0 N A:ASP531 3.8 22.6 1.0 CA A:ASP531 3.9 21.1 1.0 C A:ASP529 4.1 21.7 1.0 N A:LEU530 4.1 25.0 1.0 OD2 A:ASP529 4.2 26.6 1.0 O A:ASP529 4.3 21.8 1.0 C A:ASP673 4.3 28.9 1.0 CA A:LEU530 4.3 22.4 1.0 OD2 A:ASP673 4.3 30.7 1.0 CA A:LEU674 4.3 24.1 1.0 CB A:ASP531 4.4 23.4 1.0 CA A:ASP529 4.4 22.2 1.0 OD1 A:ASN537 4.5 25.5 1.0 CA A:ASP673 4.5 26.7 1.0 OD2 A:ASP531 4.5 24.5 1.0 CB A:ASP529 4.6 20.1 1.0 O A:LEU535 4.6 26.9 1.0 N A:VAL675 4.7 24.2 1.0 CB A:ASP673 4.7 26.9 1.0 CA A:VAL675 4.9 20.6 1.0

Calcium binding site 2 out of 4 in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Native Structures of Soluble Human Primary Amine Oxidase AOC3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:29.4 occ:1.00 OE1 A:GLU667 2.2 42.2 1.0 O A:HOH941 2.3 31.9 1.0 O A:PHE663 2.3 26.1 1.0 OE1 A:GLU572 2.5 40.6 1.0 OD1 A:ASN665 2.5 48.4 1.0 OE2 A:GLU572 2.6 35.1 1.0 O A:HOH903 2.6 33.4 1.0 CD A:GLU572 2.9 41.6 1.0 CD A:GLU667 3.2 46.5 1.0 CG A:ASN665 3.5 39.2 1.0 C A:PHE663 3.5 28.3 1.0 CG A:GLU667 3.7 36.2 1.0 ND2 A:ASN665 4.0 41.1 1.0 N A:ASN665 4.1 39.0 1.0 NZ A:LYS638 4.2 39.7 1.0 OE2 A:GLU667 4.2 52.1 1.0 CA A:PHE663 4.3 29.8 1.0 CB A:GLU667 4.3 31.8 1.0 OG1 A:THR635 4.4 32.4 1.0 CG A:GLU572 4.4 30.2 1.0 N A:ILE664 4.5 29.5 1.0 OE1 A:GLU641 4.5 29.6 1.0 CE A:LYS638 4.5 34.8 1.0 CB A:ASN665 4.6 33.8 1.0 OE2 A:GLU641 4.6 39.0 1.0 CA A:ILE664 4.6 34.7 1.0 N A:GLN636 4.7 32.1 1.0 CA A:ASN665 4.8 35.4 1.0 O A:ASP662 4.8 31.2 1.0 C A:ILE664 4.8 38.9 1.0 CB A:GLN636 4.9 32.4 1.0 CB A:PHE663 5.0 29.6 1.0

Calcium binding site 3 out of 4 in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Native Structures of Soluble Human Primary Amine Oxidase AOC3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:29.4 occ:1.00 OD1 B:ASP531 2.3 37.5 1.0 OD1 B:ASP529 2.3 26.4 1.0 O B:LEU530 2.4 31.2 1.0 OD1 B:ASP673 2.4 35.8 1.0 O B:LEU674 2.5 27.1 1.0 O B:HOH925 2.6 29.5 1.0 C B:LEU530 3.4 33.6 1.0 CG B:ASP531 3.4 36.8 1.0 CG B:ASP529 3.5 35.9 1.0 C B:LEU674 3.6 26.8 1.0 NZ B:LYS106 3.6 21.7 1.0 CG B:ASP673 3.6 33.8 1.0 N B:LEU674 3.7 29.9 1.0 C B:ASP529 3.9 28.2 1.0 O B:ASP529 4.0 31.4 1.0 N B:ASP531 4.0 36.8 1.0 CA B:ASP531 4.0 32.2 1.0 N B:LEU530 4.1 27.0 1.0 OD2 B:ASP531 4.2 33.2 1.0 CA B:LEU674 4.2 32.1 1.0 OD2 B:ASP673 4.2 33.9 1.0 CA B:ASP529 4.3 25.7 1.0 OD2 B:ASP529 4.3 35.2 1.0 C B:ASP673 4.3 32.3 1.0 CB B:ASP531 4.4 31.5 1.0 CA B:LEU530 4.4 29.8 1.0 CB B:ASP529 4.5 34.4 1.0 N B:VAL675 4.6 26.7 1.0 OD1 B:ASN537 4.6 39.4 1.0 CA B:ASP673 4.6 30.8 1.0 CB B:ASP673 4.7 23.6 1.0 CA B:VAL675 4.8 26.1 1.0 O B:LEU535 4.9 35.7 1.0

Calcium binding site 4 out of 4 in the The Native Structures of Soluble Human Primary Amine Oxidase AOC3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Native Structures of Soluble Human Primary Amine Oxidase AOC3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:32.7 occ:1.00 O B:HOH903 2.4 37.4 1.0 O B:HOH910 2.4 35.2 1.0 OE1 B:GLU572 2.5 26.3 1.0 O B:PHE663 2.5 31.2 1.0 OD1 B:ASN665 2.6 41.8 1.0 OE1 B:GLU667 2.8 45.3 1.0 OE2 B:GLU572 2.8 37.9 1.0 CD B:GLU572 3.0 30.4 1.0 CD B:GLU667 3.2 45.0 1.0 CG B:ASN665 3.5 43.3 1.0 NZ B:LYS638 3.7 38.5 1.0 CG B:GLU667 3.7 37.5 1.0 C B:PHE663 3.7 31.2 1.0 ND2 B:ASN665 3.9 45.1 1.0 OE2 B:GLU667 3.9 49.4 1.0 CE B:LYS638 4.2 35.2 1.0 OE1 B:GLU641 4.3 35.4 1.0 CA B:PHE663 4.4 31.3 1.0 CB B:GLU667 4.4 36.2 1.0 N B:ASN665 4.4 39.0 1.0 CG B:GLU572 4.5 31.8 1.0 OE2 B:GLU641 4.6 40.3 1.0 CB B:THR635 4.6 26.1 1.0 N B:GLN636 4.6 29.5 1.0 CB B:ASN665 4.7 34.5 1.0 N B:ILE664 4.7 30.5 1.0 CD B:LYS638 4.7 31.5 1.0 CA B:ILE664 4.8 34.6 1.0 CB B:GLN636 4.8 33.4 1.0 CD B:GLU641 4.9 36.4 1.0 CA B:ASN665 5.0 35.6 1.0 O B:GLN636 5.0 24.5 1.0 CB B:PHE663 5.0 32.9 1.0

H.Elovaara, H.Kidron, V.Parkash, Y.Nymalm, E.Bligt, P.Ollikka, D.J.Smith, M.Pihlavisto, M.Salmi, S.Jalkanen, T.A.Salminen. Identification of Two Imidazole Binding Sites and Key Residues For Substrate Specificity in Human Primary Amine Oxidase AOC3. Biochemistry V. 50 5507 2011.
ISSN: ISSN 0006-2960
PubMed: 21585208
DOI: 10.1021/BI200117Z