Calcium in PDB 1us1: 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: 1us1 was solved by T.T.Airenne, Y.Nymalm, H.Kidron, A.Soderholm, M.S.Johnson, T.A.Salminen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	226.099, 226.099, 223.004, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 26.7

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 1us1). 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: 1us1:
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:Ca1763 b:33.1 occ:1.00 O A:LEU674 2.3 36.0 1.0 O A:LEU530 2.3 36.1 1.0 OD1 A:ASP531 2.3 34.0 1.0 OD1 A:ASP529 2.3 31.5 1.0 OD1 A:ASP673 2.3 32.6 1.0 C A:LEU530 3.3 35.9 1.0 N A:LEU674 3.3 38.1 1.0 C A:LEU674 3.3 37.1 1.0 CG A:ASP673 3.5 33.3 1.0 CG A:ASP531 3.6 37.1 1.0 CG A:ASP529 3.6 34.0 1.0 CA A:LEU674 3.9 37.6 1.0 NZ A:LYS106 3.9 25.8 1.0 C A:ASP673 4.0 38.4 1.0 N A:ASP531 4.0 36.5 1.0 N A:LEU530 4.1 34.5 1.0 CA A:ASP531 4.1 36.6 1.0 C A:ASP529 4.1 33.5 1.0 ND2 A:ASN537 4.2 36.2 1.0 OD2 A:ASP673 4.2 27.8 1.0 CA A:ASP673 4.3 38.2 1.0 CA A:LEU530 4.3 35.2 1.0 OD2 A:ASP529 4.3 37.4 1.0 O A:ASP529 4.4 32.5 1.0 OD2 A:ASP531 4.4 38.1 1.0 CB A:ASP673 4.5 38.0 1.0 CB A:ASP531 4.5 36.8 1.0 N A:VAL675 4.5 36.6 1.0 CA A:ASP529 4.5 33.4 1.0 O A:LEU535 4.7 42.5 1.0 CB A:LEU674 4.7 37.3 1.0 CB A:ASP529 4.7 33.1 1.0 O A:ASP673 4.8 38.1 1.0 CA A:VAL675 5.0 36.1 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:Ca1764 b:52.1 occ:1.00 OE1 A:GLU667 2.3 51.1 1.0 O A:PHE663 2.4 46.8 1.0 OD1 A:ASN665 2.4 51.3 1.0 OE2 A:GLU572 2.8 36.8 1.0 NZ A:LYS638 3.0 36.6 1.0 OE1 A:GLU572 3.0 40.5 1.0 CG A:ASN665 3.2 49.3 1.0 CD A:GLU572 3.3 41.2 1.0 C A:PHE663 3.4 45.2 1.0 CD A:GLU667 3.6 50.4 1.0 ND2 A:ASN665 3.7 49.6 1.0 OE2 A:GLU641 3.7 45.7 1.0 OE1 A:GLU641 3.9 45.7 1.0 CA A:PHE663 4.0 44.6 1.0 CD A:GLU641 4.2 44.2 1.0 OE2 A:GLU667 4.3 51.1 1.0 CE A:LYS638 4.4 36.9 1.0 O A:GLN636 4.4 39.0 1.0 CB A:ASN665 4.5 48.5 1.0 N A:ILE664 4.6 45.9 1.0 N A:ASN665 4.6 47.7 1.0 CG A:GLU667 4.6 49.5 1.0 CB A:PHE663 4.7 44.5 1.0 CG2 A:THR635 4.7 40.9 1.0 CB A:GLN636 4.7 38.9 1.0 CD A:LYS638 4.8 38.4 1.0 OG1 A:THR635 4.9 37.6 1.0 CG A:GLU572 4.9 43.1 1.0 N A:GLN636 4.9 39.7 1.0 CA A:ILE664 4.9 46.2 1.0 O A:ASP662 4.9 43.6 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:Ca1763 b:35.9 occ:1.00 OD1 B:ASP673 2.3 35.5 1.0 O B:LEU674 2.3 36.6 1.0 O B:LEU530 2.3 37.0 1.0 OD1 B:ASP529 2.4 35.5 1.0 OD1 B:ASP531 2.4 37.3 1.0 C B:LEU530 3.4 36.5 1.0 N B:LEU674 3.4 38.3 1.0 C B:LEU674 3.5 37.3 1.0 CG B:ASP673 3.5 35.6 1.0 CG B:ASP531 3.6 37.9 1.0 CG B:ASP529 3.6 34.4 1.0 NZ B:LYS106 3.8 30.9 1.0 ND2 B:ASN537 3.8 39.6 1.0 C B:ASP673 4.0 38.5 1.0 CA B:LEU674 4.0 37.8 1.0 N B:ASP531 4.1 36.9 1.0 CA B:ASP531 4.2 37.0 1.0 OD2 B:ASP673 4.2 33.3 1.0 N B:LEU530 4.2 35.1 1.0 C B:ASP529 4.3 34.2 1.0 OD2 B:ASP529 4.3 33.2 1.0 CA B:ASP673 4.3 38.5 1.0 CA B:LEU530 4.4 35.8 1.0 CB B:ASP673 4.5 38.0 1.0 OD2 B:ASP531 4.5 39.3 1.0 CB B:ASP531 4.5 36.9 1.0 O B:LEU535 4.6 42.6 1.0 CA B:ASP529 4.6 33.6 1.0 N B:VAL675 4.6 36.8 1.0 O B:ASP529 4.7 33.5 1.0 O B:ASP673 4.7 38.6 1.0 CB B:ASP529 4.7 33.7 1.0 CB B:LEU674 4.9 37.8 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:Ca1764 b:48.0 occ:1.00 OE1 B:GLU667 2.3 50.0 1.0 OD1 B:ASN665 2.3 49.1 1.0 O B:PHE663 2.3 46.1 1.0 OE2 B:GLU572 2.7 42.2 1.0 OE1 B:GLU572 3.2 40.5 1.0 NZ B:LYS638 3.3 39.8 1.0 CD B:GLU572 3.4 42.8 1.0 CD B:GLU667 3.4 50.4 1.0 CG B:ASN665 3.4 48.3 1.0 C B:PHE663 3.5 45.0 1.0 OE2 B:GLU641 3.7 44.4 1.0 OE1 B:GLU641 3.9 43.8 1.0 ND2 B:ASN665 4.0 47.4 1.0 CA B:PHE663 4.1 44.4 1.0 CE B:LYS638 4.2 38.9 1.0 OE2 B:GLU667 4.2 49.1 1.0 O B:GLN636 4.2 39.5 1.0 CD B:GLU641 4.2 43.4 1.0 CD B:LYS638 4.3 39.0 1.0 CG B:GLU667 4.3 49.1 1.0 CB B:PHE663 4.5 44.1 1.0 N B:GLN636 4.5 39.6 1.0 N B:ILE664 4.6 45.8 1.0 CB B:GLN636 4.6 39.5 1.0 CG2 B:THR635 4.6 39.2 1.0 OG1 B:THR635 4.6 38.0 1.0 N B:ASN665 4.7 47.6 1.0 CB B:ASN665 4.7 48.5 1.0 CG B:GLU572 4.9 43.4 1.0 CA B:ILE664 4.9 46.4 1.0 CA B:GLN636 5.0 39.3 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