Calcium in PDB 1pu4: Crystal Structure of Human Vascular Adhesion Protein-1

All present enzymatic activity of Crystal Structure of Human Vascular Adhesion Protein-1:
1.4.3.6;

The structure of Crystal Structure of Human Vascular Adhesion Protein-1, PDB code: 1pu4 was solved by T.A.Salminen, T.T.Airenne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	225.916, 225.916, 218.668, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 25.4

The structure of Crystal Structure of Human Vascular Adhesion Protein-1 also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Vascular Adhesion Protein-1 (pdb code 1pu4). 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 Human Vascular Adhesion Protein-1, PDB code: 1pu4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1


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 Human Vascular Adhesion Protein-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:24.5 occ:1.00 O A:LEU530 2.3 24.1 1.0 OD1 A:ASP673 2.3 24.5 1.0 O A:LEU674 2.3 24.6 1.0 OD1 A:ASP529 2.4 22.5 1.0 OD1 A:ASP531 2.4 25.6 1.0 C A:LEU530 3.3 23.3 1.0 N A:LEU674 3.4 25.9 1.0 C A:LEU674 3.5 24.8 1.0 CG A:ASP673 3.5 25.1 1.0 NZ A:LYS106 3.6 16.9 1.0 CG A:ASP529 3.6 21.4 1.0 CG A:ASP531 3.7 25.6 1.0 N A:ASP531 4.0 24.0 1.0 CA A:LEU674 4.0 25.3 1.0 CA A:ASP531 4.0 24.2 1.0 C A:ASP673 4.1 26.4 1.0 OD2 A:ASP673 4.1 23.9 1.0 ND2 A:ASN537 4.1 23.2 1.0 N A:LEU530 4.1 21.7 1.0 C A:ASP529 4.2 20.9 1.0 CA A:ASP673 4.3 26.6 1.0 CA A:LEU530 4.3 22.4 1.0 OD2 A:ASP529 4.3 22.8 1.0 CB A:ASP531 4.5 24.8 1.0 CB A:ASP673 4.5 26.6 1.0 O A:ASP529 4.5 20.3 1.0 CA A:ASP529 4.5 20.8 1.0 OD2 A:ASP531 4.6 26.1 1.0 O A:LEU535 4.6 29.8 1.0 N A:VAL675 4.6 24.0 1.0 CB A:ASP529 4.7 21.0 1.0 CB A:LEU674 4.8 25.1 1.0 O A:ASP673 4.9 26.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1


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 Human Vascular Adhesion Protein-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:37.6 occ:1.00 OE1 A:GLU667 2.3 37.9 1.0 O A:PHE663 2.3 33.5 1.0 OD1 A:ASN665 2.4 38.8 1.0 NZ A:LYS638 2.8 25.0 1.0 OE2 A:GLU572 3.0 28.7 1.0 OE1 A:GLU572 3.0 28.6 1.0 CG A:ASN665 3.4 37.1 1.0 CD A:GLU572 3.4 30.1 1.0 C A:PHE663 3.4 32.0 1.0 CD A:GLU667 3.5 37.7 1.0 OE2 A:GLU641 3.5 26.8 1.0 ND2 A:ASN665 3.9 37.0 1.0 OE1 A:GLU641 4.0 30.0 1.0 CA A:PHE663 4.1 31.4 1.0 CD A:GLU641 4.2 27.9 1.0 OE2 A:GLU667 4.2 38.0 1.0 CE A:LYS638 4.2 25.6 1.0 CG A:GLU667 4.5 36.6 1.0 O A:GLN636 4.5 26.8 1.0 N A:ASN665 4.5 34.9 1.0 CB A:ASN665 4.5 35.9 1.0 N A:ILE664 4.6 32.8 1.0 CG2 A:THR635 4.6 27.2 1.0 CB A:GLN636 4.6 27.0 1.0 CB A:PHE663 4.7 31.4 1.0 CD A:LYS638 4.7 26.9 1.0 N A:GLN636 4.7 27.0 1.0 OG1 A:THR635 4.8 26.4 1.0 CA A:ILE664 4.9 33.2 1.0 CG A:GLU572 4.9 30.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1


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 Human Vascular Adhesion Protein-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:23.8 occ:1.00 O B:LEU530 2.3 24.3 1.0 O B:LEU674 2.3 25.0 1.0 OD1 B:ASP673 2.3 24.2 1.0 OD1 B:ASP529 2.3 21.8 1.0 OD1 B:ASP531 2.4 25.6 1.0 C B:LEU530 3.4 23.6 1.0 N B:LEU674 3.4 26.1 1.0 C B:LEU674 3.4 25.0 1.0 CG B:ASP673 3.5 25.2 1.0 CG B:ASP529 3.6 21.0 1.0 CG B:ASP531 3.6 24.9 1.0 NZ B:LYS106 3.6 18.4 1.0 ND2 B:ASN537 3.6 24.6 1.0 C B:ASP673 4.0 26.5 1.0 CA B:LEU674 4.0 25.5 1.0 N B:ASP531 4.1 24.2 1.0 CA B:ASP531 4.1 24.2 1.0 OD2 B:ASP529 4.2 20.1 1.0 CA B:ASP673 4.2 26.7 1.0 N B:LEU530 4.3 21.9 1.0 C B:ASP529 4.3 21.2 1.0 OD2 B:ASP673 4.3 24.5 1.0 CB B:ASP531 4.5 24.6 1.0 CA B:LEU530 4.5 22.7 1.0 OD2 B:ASP531 4.5 24.0 1.0 CB B:ASP673 4.5 26.6 1.0 CA B:ASP529 4.6 20.9 1.0 O B:ASP529 4.6 20.7 1.0 N B:VAL675 4.6 24.2 1.0 O B:LEU535 4.6 29.8 1.0 CB B:ASP529 4.7 20.9 1.0 O B:ASP673 4.7 26.4 1.0 CB B:LEU674 4.8 25.6 1.0 CG B:ASN537 5.0 26.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1


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 Human Vascular Adhesion Protein-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:37.7 occ:1.00 OE1 B:GLU667 2.3 38.3 1.0 O B:PHE663 2.3 33.7 1.0 OD1 B:ASN665 2.4 38.1 1.0 OE2 B:GLU572 3.0 28.1 1.0 OE1 B:GLU572 3.0 26.6 1.0 NZ B:LYS638 3.3 27.1 1.0 CD B:GLU667 3.4 37.0 1.0 CG B:ASN665 3.4 36.7 1.0 CD B:GLU572 3.4 29.8 1.0 C B:PHE663 3.5 32.1 1.0 OE2 B:GLU641 3.6 26.6 1.0 OE1 B:GLU641 3.8 29.3 1.0 ND2 B:ASN665 3.8 37.1 1.0 CA B:PHE663 4.0 31.5 1.0 CD B:GLU641 4.1 27.3 1.0 CD B:LYS638 4.1 27.6 1.0 OE2 B:GLU667 4.1 36.1 1.0 O B:GLN636 4.2 26.7 1.0 CE B:LYS638 4.2 27.2 1.0 CG B:GLU667 4.2 36.2 1.0 OG1 B:THR635 4.4 26.0 1.0 CG2 B:THR635 4.5 26.9 1.0 CB B:PHE663 4.5 31.5 1.0 N B:GLN636 4.6 26.9 1.0 CB B:GLN636 4.6 27.0 1.0 N B:ILE664 4.6 32.8 1.0 CB B:ASN665 4.7 35.7 1.0 N B:ASN665 4.7 34.9 1.0 CG B:GLU572 4.9 31.2 1.0 CA B:ILE664 5.0 33.4 1.0 CA B:GLN636 5.0 26.7 1.0

T.T.Airenne, Y.Nymalm, H.Kidron, D.J.Smith, M.Pihlavisto, M.Salmi, S.Jalkanen, M.S.Johnson, T.A.Salminen. Crystal Structure of the Human Vascular Adhesion Protein-1: Unique Structural Features with Functional Implications. Protein Sci. V. 14 1964 2005.
ISSN: ISSN 0961-8368
PubMed: 16046623
DOI: 10.1110/PS.051438105