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Calcium in PDB 2pnc: Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine

Enzymatic activity of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine

All present enzymatic activity of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine, PDB code: 2pnc was solved by L.Cendron, A.Holt, D.J.Smith, G.Zanotti, A.Rigo, M.L.Di Paolo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.11 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.360, 131.956, 134.159, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 25.2

Other elements in 2pnc:

The structure of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Chlorine (Cl) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine (pdb code 2pnc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine, PDB code: 2pnc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2pnc

Go back to Calcium Binding Sites List in 2pnc
Calcium binding site 1 out of 4 in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:20.1
occ:1.00
 OD1 A:ASP672 2.4 24.4 1.0
OD1 A:ASP530 2.5 24.2 1.0
O A:LEU529 2.6 20.5 1.0
O A:LEU673 2.8 14.8 1.0
N A:LEU673 3.1 23.5 1.0
OD1 A:ASP528 3.2 21.3 1.0
C A:LEU529 3.6 9.2 1.0
CG A:ASP672 3.6 23.8 1.0
C A:LEU673 3.7 17.3 1.0
CG A:ASP530 3.7 18.8 1.0
C A:ASP672 3.8 20.8 1.0
O A:LEU534 3.9 37.4 1.0
CA A:LEU673 3.9 18.8 1.0
CA A:ASP672 3.9 22.5 1.0
OD1 A:ASN536 3.9 25.6 1.0
CA A:ASP530 4.0 15.8 1.0
NZ A:LYS105 4.1 24.1 1.0
N A:ASP530 4.2 12.8 1.0
CG A:ASP528 4.3 16.0 1.0
CB A:ASP672 4.4 20.3 1.0
CB A:ASP530 4.5 15.9 1.0
CB A:LEU673 4.6 19.3 1.0
OD2 A:ASP672 4.6 29.0 1.0
OD2 A:ASP530 4.6 24.0 1.0
N A:LEU529 4.6 15.5 1.0
O A:ASP672 4.7 25.3 1.0
CG A:ASN536 4.7 16.3 1.0
CA A:LEU529 4.7 11.8 1.0
C A:LEU534 4.8 31.0 1.0
C A:ASP528 4.8 14.6 1.0
CA A:LEU534 4.8 28.3 1.0
OD2 A:ASP528 4.8 20.9 1.0
N A:VAL674 4.9 18.3 1.0
O A:LYS671 4.9 22.9 1.0

Calcium binding site 2 out of 4 in 2pnc

Go back to Calcium Binding Sites List in 2pnc
Calcium binding site 2 out of 4 in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca806

b:28.9
occ:1.00
 O A:PHE662 2.5 29.5 1.0
OE1 A:GLU666 2.7 41.3 1.0
OD1 A:ASN664 3.1 21.7 1.0
OE2 A:GLU640 3.3 27.5 1.0
OE1 A:GLU571 3.4 12.5 1.0
OE2 A:GLU571 3.4 12.7 1.0
C A:PHE662 3.5 21.2 1.0
NZ A:LYS637 3.7 33.2 1.0
OE1 A:GLU640 3.7 30.9 1.0
CD A:GLU666 3.8 35.3 1.0
CD A:GLU571 3.8 17.3 1.0
CG A:ASN664 3.8 29.6 1.0
CE A:LYS637 3.9 19.9 1.0
CA A:PHE662 3.9 19.7 1.0
CD A:GLU640 3.9 25.1 1.0
ND2 A:ASN664 4.0 34.9 1.0
CD A:LYS637 4.2 20.0 1.0
CB A:PHE662 4.4 18.5 1.0
OE2 A:GLU666 4.4 39.6 1.0
CG A:GLU666 4.7 30.2 1.0
N A:ILE663 4.7 25.1 1.0
O A:GLN635 4.7 27.7 1.0
CB A:THR634 4.8 14.4 1.0
N A:ASN664 4.9 22.6 1.0

Calcium binding site 3 out of 4 in 2pnc

Go back to Calcium Binding Sites List in 2pnc
Calcium binding site 3 out of 4 in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:20.2
occ:1.00
 O B:HOH979 2.2 36.1 1.0
OD1 B:ASP672 2.3 27.9 1.0
OD1 B:ASP530 2.4 29.8 1.0
O B:LEU529 2.4 15.2 1.0
OD1 B:ASP528 2.5 14.6 1.0
O B:LEU673 2.5 21.8 1.0
N B:LEU673 3.4 26.9 1.0
C B:LEU529 3.5 19.0 1.0
C B:LEU673 3.5 18.4 1.0
CG B:ASP672 3.5 22.8 1.0
CG B:ASP528 3.6 18.2 1.0
CG B:ASP530 3.6 18.8 1.0
NZ B:LYS105 3.8 11.7 1.0
CA B:LEU673 4.0 23.4 1.0
C B:ASP672 4.0 25.9 1.0
C B:ASP528 4.2 17.7 1.0
CA B:ASP530 4.2 13.7 1.0
N B:ASP530 4.2 16.8 1.0
N B:LEU529 4.2 16.5 1.0
OD2 B:ASP528 4.3 8.0 1.0
OD2 B:ASP672 4.3 25.0 1.0
CA B:ASP672 4.3 26.9 1.0
O B:ASP528 4.4 20.0 1.0
OD2 B:ASP530 4.5 15.5 1.0
O B:LEU534 4.5 46.1 1.0
CA B:LEU529 4.5 19.3 1.0
CB B:ASP530 4.5 12.2 1.0
CB B:ASP672 4.5 24.4 1.0
CA B:ASP528 4.6 21.0 1.0
OD1 B:ASN536 4.6 16.9 1.0
N B:VAL674 4.7 18.5 1.0
CB B:ASP528 4.7 17.6 1.0
CB B:LEU673 4.8 22.6 1.0
O B:ASP672 4.8 26.1 1.0

Calcium binding site 4 out of 4 in 2pnc

Go back to Calcium Binding Sites List in 2pnc
Calcium binding site 4 out of 4 in the Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca806

b:29.2
occ:1.00
 O B:PHE662 2.6 27.6 1.0
OE2 B:GLU571 2.8 20.8 1.0
OE1 B:GLU666 2.8 39.1 1.0
OE1 B:GLU640 3.3 25.3 1.0
OD1 B:ASN664 3.3 32.8 1.0
C B:PHE662 3.6 20.1 1.0
CD B:GLU571 3.7 17.0 1.0
OE2 B:GLU640 3.7 27.7 1.0
NZ B:LYS637 3.7 19.0 1.0
CE B:LYS637 3.8 19.1 1.0
O B:GLN635 3.8 24.1 1.0
OE1 B:GLU571 3.9 25.9 1.0
CD B:GLU640 3.9 22.3 1.0
CD B:GLU666 4.0 32.4 1.0
CA B:PHE662 4.1 16.6 1.0
CB B:THR634 4.1 13.8 1.0
CD B:LYS637 4.2 14.6 1.0
N B:GLN635 4.3 18.7 1.0
CG B:ASN664 4.3 34.0 1.0
CB B:PHE662 4.4 15.2 1.0
CB B:GLN635 4.5 18.6 1.0
CG2 B:THR634 4.6 14.9 1.0
OE2 B:GLU666 4.7 37.6 1.0
ND2 B:ASN664 4.7 34.6 1.0
C B:GLN635 4.7 17.6 1.0
CA B:GLN635 4.8 14.8 1.0
N B:ILE663 4.8 22.2 1.0
OG1 B:THR634 4.8 14.9 1.0
O B:HOH992 4.8 31.4 1.0
CG B:LYS637 4.9 10.8 1.0
O B:HOH927 5.0 11.2 1.0

Reference:

A.Holt, D.J.Smith, L.Cendron, G.Zanotti, A.Rigo, M.L.Di Paolo. Multiple Binding Sites For Substrates and Modulators of Semicarbazide-Sensitive Amine Oxidases: Kinetic Consequences Mol.Pharmacol. V. 73 525 2008.
ISSN: ISSN 0026-895X
PubMed: 17989349
DOI: 10.1124/MOL.107.040964
Page generated: Tue Jul 8 07:44:02 2025

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