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Calcium in PDB 2y74: The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation

Enzymatic activity of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation

All present enzymatic activity of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation:
1.4.3.6;

Protein crystallography data

The structure of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation, PDB code: 2y74 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) 38.21 / 2.95
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 225.800, 225.800, 218.700, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.4

Other elements in 2y74:

The structure of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation (pdb code 2y74). 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 Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation, PDB code: 2y74:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2y74

Go back to Calcium Binding Sites List in 2y74
Calcium binding site 1 out of 4 in the The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:30.9
occ:1.00
 OD1 A:ASN665 2.4 45.8 1.0
O A:HOH903 2.5 29.0 1.0
O A:PHE663 2.6 26.2 1.0
OE2 A:GLU572 2.6 35.3 1.0
OE1 A:GLU572 2.8 24.2 1.0
OE1 A:GLU667 2.8 42.3 1.0
CD A:GLU572 3.0 32.1 1.0
CD A:GLU667 3.1 38.0 1.0
CG A:ASN665 3.2 42.7 1.0
ND2 A:ASN665 3.4 47.1 1.0
CG A:GLU667 3.6 29.9 1.0
NZ A:LYS638 3.7 31.5 1.0
OE2 A:GLU667 3.7 41.8 1.0
C A:PHE663 3.8 24.9 1.0
OE2 A:GLU641 4.1 27.3 1.0
CB A:GLU667 4.1 24.3 1.0
CE A:LYS638 4.1 21.2 1.0
N A:ASN665 4.2 27.1 1.0
OE1 A:GLU641 4.4 32.0 1.0
CA A:PHE663 4.5 21.6 1.0
CB A:ASN665 4.5 30.9 1.0
CG A:GLU572 4.5 28.6 1.0
CD A:GLU641 4.7 38.7 1.0
N A:ILE664 4.8 26.9 1.0
CA A:ASN665 4.8 29.2 1.0
CD A:LYS638 4.8 29.4 1.0
CB A:THR635 4.9 25.4 1.0
N A:GLN636 4.9 31.6 1.0
CA A:ILE664 4.9 29.6 1.0
CB A:GLN636 5.0 32.5 1.0

Calcium binding site 2 out of 4 in 2y74

Go back to Calcium Binding Sites List in 2y74
Calcium binding site 2 out of 4 in the The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:22.2
occ:1.00
 OD1 A:ASP531 1.9 29.3 1.0
O A:HOH901 2.1 29.0 1.0
O A:LEU530 2.1 46.2 1.0
OD1 A:ASP529 2.2 19.5 1.0
O A:LEU674 2.3 31.9 1.0
OD1 A:ASP673 2.6 35.6 1.0
C A:LEU530 3.1 32.5 1.0
CG A:ASP531 3.1 40.5 1.0
CG A:ASP529 3.4 34.5 1.0
C A:LEU674 3.5 28.4 1.0
NZ A:LYS106 3.6 21.4 1.0
N A:LEU530 3.6 19.3 1.0
C A:ASP529 3.7 27.2 1.0
CG A:ASP673 3.8 28.9 1.0
OD2 A:ASP531 3.9 42.8 1.0
N A:ASP531 4.0 37.2 1.0
CA A:LEU530 4.0 24.1 1.0
CA A:ASP531 4.0 28.7 1.0
N A:LEU674 4.0 35.2 1.0
O A:ASP529 4.1 30.3 1.0
CA A:ASP529 4.1 24.2 1.0
CB A:ASP531 4.1 36.0 1.0
ND2 A:ASN537 4.3 37.5 1.0
OD2 A:ASP529 4.3 35.0 1.0
OD2 A:ASP673 4.4 30.1 1.0
CB A:ASP529 4.4 30.1 1.0
CA A:LEU674 4.4 29.4 1.0
N A:VAL675 4.5 25.4 1.0
C A:ASP673 4.6 32.9 1.0
CA A:VAL675 4.7 26.0 1.0
CA A:ASP673 4.9 28.9 1.0
CB A:ASP673 4.9 31.4 1.0

Calcium binding site 3 out of 4 in 2y74

Go back to Calcium Binding Sites List in 2y74
Calcium binding site 3 out of 4 in the The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:23.0
occ:1.00
 O B:LEU674 2.5 19.6 1.0
O B:LEU530 2.5 31.9 1.0
O B:HOH901 2.5 29.0 1.0
OD1 B:ASP529 2.5 19.4 1.0
OD1 B:ASP531 2.6 23.1 1.0
OD1 B:ASP673 2.6 21.2 1.0
C B:LEU530 3.4 23.5 1.0
N B:LEU674 3.5 24.1 1.0
C B:LEU674 3.5 23.4 1.0
CG B:ASP673 3.6 22.0 1.0
NZ B:LYS106 3.8 18.0 1.0
CG B:ASP531 3.8 24.2 1.0
CG B:ASP529 3.8 29.2 1.0
C B:ASP673 4.0 29.9 1.0
CA B:ASP531 4.0 16.1 1.0
N B:ASP531 4.0 22.1 1.0
OD1 B:ASN537 4.1 24.7 1.0
CA B:LEU674 4.1 22.2 1.0
CA B:ASP673 4.2 23.0 1.0
N B:LEU530 4.2 19.7 1.0
C B:ASP529 4.3 21.1 1.0
O B:LEU535 4.3 31.4 1.0
OD2 B:ASP673 4.4 31.7 1.0
OD2 B:ASP529 4.4 32.2 1.0
CA B:LEU530 4.5 21.4 1.0
CB B:ASP531 4.5 20.1 1.0
CB B:ASP673 4.6 25.7 1.0
O B:ASP529 4.6 24.6 1.0
OD2 B:ASP531 4.7 20.1 1.0
N B:VAL675 4.7 25.9 1.0
CA B:ASP529 4.7 18.2 1.0
O B:ASP673 4.8 28.7 1.0
CB B:ASP529 4.8 25.3 1.0
CB B:LEU674 4.9 18.9 1.0

Calcium binding site 4 out of 4 in 2y74

Go back to Calcium Binding Sites List in 2y74
Calcium binding site 4 out of 4 in the The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Human Soluble Primary Amine Oxidase AOC3 in the Off-Copper Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:33.8
occ:1.00
 OE2 B:GLU572 2.3 35.9 1.0
OE1 B:GLU572 2.3 32.8 1.0
OE1 B:GLU667 2.5 44.1 1.0
O B:PHE663 2.5 27.4 1.0
OD1 B:ASN665 2.6 48.8 1.0
CD B:GLU572 2.6 36.0 1.0
CD B:GLU667 3.2 41.8 1.0
CG B:ASN665 3.3 46.3 1.0
ND2 B:ASN665 3.5 46.7 1.0
C B:PHE663 3.6 28.8 1.0
OE2 B:GLU667 3.9 32.3 1.0
CG B:GLU667 4.0 37.3 1.0
N B:ASN665 4.1 33.8 1.0
CG B:GLU572 4.1 26.3 1.0
CB B:GLU667 4.2 22.6 1.0
NZ B:LYS638 4.3 36.0 1.0
CA B:PHE663 4.3 27.4 1.0
CE B:LYS638 4.4 25.7 1.0
OE2 B:GLU641 4.5 35.0 1.0
N B:ILE664 4.5 34.0 1.0
N B:GLN636 4.5 35.2 1.0
CB B:THR635 4.5 20.7 1.0
CB B:ASN665 4.5 37.1 1.0
OE1 B:GLU641 4.6 37.7 1.0
CA B:ILE664 4.6 31.6 1.0
CA B:ASN665 4.8 31.1 1.0
CB B:GLN636 4.8 22.6 1.0
C B:ILE664 4.8 32.7 1.0
CG2 B:THR635 4.9 23.2 1.0
O B:GLN636 4.9 28.6 1.0
O B:ASP662 5.0 31.0 1.0
CB B:GLU572 5.0 24.9 1.0

Reference:

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
Page generated: Fri Jul 12 19:25:11 2024

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