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Calcium in PDB 4bty: Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors

Enzymatic activity of Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors

All present enzymatic activity of Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors, PDB code: 4bty was solved by E.Bligt-Linden, M.Pihlavisto, I.Szatmari, Z.Otwinowski, D.J.Smith, L.Lazar, F.Fulop, T.A.Salminen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 3.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 226.736, 226.736, 218.160, 90.00, 90.00, 120.00
R / Rfree (%) 18.42 / 24.638

Other elements in 4bty:

The structure of Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors also contains other interesting chemical elements:

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

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 4bty

Go back to Calcium Binding Sites List in 4bty
Calcium binding site 1 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors


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 in Complex with Pyridazinone Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1763

b:71.6
occ:1.00
 O A:LEU530 2.3 79.0 1.0
OD1 A:ASP673 2.3 62.7 1.0
OD1 A:ASP531 2.3 76.0 1.0
O A:LEU674 2.3 74.6 1.0
OD1 A:ASP529 2.4 75.9 1.0
N A:LEU674 3.2 75.5 1.0
C A:LEU530 3.3 81.1 1.0
C A:LEU674 3.3 72.5 1.0
CG A:ASP673 3.5 70.1 1.0
CG A:ASP531 3.5 83.6 1.0
CG A:ASP529 3.7 78.4 1.0
ND2 A:ASN537 3.8 70.7 1.0
C A:ASP673 3.8 79.3 1.0
CA A:LEU674 3.9 74.9 1.0
NZ A:LYS106 3.9 77.1 1.0
CA A:ASP673 4.0 77.9 1.0
N A:ASP531 4.0 81.2 1.0
CA A:ASP531 4.0 83.5 1.0
C A:ASP529 4.1 74.4 1.0
N A:LEU530 4.2 75.8 1.0
O A:LEU535 4.2 89.0 1.0
O A:ASP529 4.3 77.6 1.0
CA A:LEU530 4.4 77.7 1.0
CB A:ASP673 4.4 75.5 1.0
CB A:ASP531 4.4 85.5 1.0
OD2 A:ASP673 4.4 65.8 1.0
N A:VAL675 4.4 68.2 1.0
OD2 A:ASP531 4.5 80.2 1.0
OD2 A:ASP529 4.5 78.5 1.0
CA A:ASP529 4.5 72.8 1.0
O A:ASP673 4.7 78.6 1.0
CB A:ASP529 4.7 72.7 1.0
CB A:LEU674 4.8 79.3 1.0
CA A:VAL675 4.9 69.1 1.0
CD2 A:LEU535 4.9 73.1 1.0

Calcium binding site 2 out of 4 in 4bty

Go back to Calcium Binding Sites List in 4bty
Calcium binding site 2 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors


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 in Complex with Pyridazinone Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1764

b:94.5
occ:1.00
 OE2 A:GLU667 2.3 0.2 1.0
O A:PHE663 2.3 89.2 1.0
OE2 A:GLU572 2.4 89.0 1.0
OD1 A:ASN665 2.5 0.0 1.0
OE1 A:GLU572 3.1 0.9 1.0
CD A:GLU572 3.1 86.5 1.0
CG A:ASN665 3.3 92.0 1.0
CD A:GLU667 3.3 0.7 1.0
C A:PHE663 3.4 81.1 1.0
OE1 A:GLU641 3.5 87.7 1.0
ND2 A:ASN665 3.5 91.4 1.0
NZ A:LYS638 3.7 95.2 1.0
OE2 A:GLU641 4.0 85.8 1.0
CA A:PHE663 4.1 79.6 1.0
OG1 A:THR635 4.1 68.7 1.0
OE1 A:GLU667 4.1 90.3 1.0
CG A:GLU667 4.1 95.5 1.0
CD A:GLU641 4.2 90.5 1.0
CG2 A:THR635 4.3 80.0 1.0
N A:GLN636 4.4 81.9 1.0
O A:GLN636 4.5 85.2 1.0
N A:ILE664 4.5 82.6 1.0
N A:ASN665 4.6 86.1 1.0
CG A:GLU572 4.7 84.8 1.0
CB A:THR635 4.7 74.0 1.0
CB A:ASN665 4.7 91.1 1.0
CB A:GLN636 4.7 83.6 1.0
CA A:ILE664 4.7 82.0 1.0
CB A:PHE663 4.7 82.1 1.0
CE A:LYS638 4.8 87.5 1.0
CD A:LYS638 4.9 87.5 1.0

Calcium binding site 3 out of 4 in 4bty

Go back to Calcium Binding Sites List in 4bty
Calcium binding site 3 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors


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 in Complex with Pyridazinone Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1763

b:72.1
occ:1.00
 OD1 B:ASP673 2.3 74.2 1.0
O B:LEU530 2.3 86.1 1.0
O B:LEU674 2.3 84.1 1.0
OD1 B:ASP531 2.3 80.6 1.0
OD1 B:ASP529 2.4 70.1 1.0
N B:LEU674 3.2 81.4 1.0
C B:LEU530 3.3 79.2 1.0
C B:LEU674 3.3 79.5 1.0
CG B:ASP673 3.5 77.1 1.0
CG B:ASP531 3.6 72.0 1.0
CG B:ASP529 3.7 80.9 1.0
NZ B:LYS106 3.8 67.9 1.0
CA B:LEU674 3.8 79.2 1.0
C B:ASP673 3.8 77.0 1.0
ND2 B:ASN537 3.9 88.5 1.0
N B:ASP531 4.0 80.2 1.0
CA B:ASP531 4.0 75.8 1.0
CA B:ASP673 4.1 73.0 1.0
N B:LEU530 4.1 72.3 1.0
C B:ASP529 4.2 75.5 1.0
CA B:LEU530 4.3 72.4 1.0
OD2 B:ASP673 4.4 69.9 1.0
CB B:ASP531 4.4 73.6 1.0
CB B:ASP673 4.4 77.9 1.0
OD2 B:ASP529 4.4 86.2 1.0
O B:LEU535 4.4 91.2 1.0
N B:VAL675 4.5 75.3 1.0
OD2 B:ASP531 4.5 66.7 1.0
CA B:ASP529 4.6 80.3 1.0
CB B:LEU674 4.6 75.3 1.0
O B:ASP529 4.6 72.3 1.0
O B:ASP673 4.7 79.7 1.0
CB B:ASP529 4.7 81.2 1.0
CD2 B:LEU535 4.7 1.0 1.0
CA B:VAL675 4.9 73.6 1.0

Calcium binding site 4 out of 4 in 4bty

Go back to Calcium Binding Sites List in 4bty
Calcium binding site 4 out of 4 in the Crystal Structure of Human Vascular Adhesion Protein-1 in Complex with Pyridazinone Inhibitors


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 in Complex with Pyridazinone Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1764

b:81.1
occ:1.00
 OE1 B:GLU667 2.3 0.2 1.0
O B:PHE663 2.3 83.0 1.0
OE2 B:GLU572 2.4 79.8 1.0
OD1 B:ASN665 2.4 94.1 1.0
OE1 B:GLU572 3.1 73.6 1.0
CD B:GLU572 3.1 77.2 1.0
NZ B:LYS638 3.2 98.1 1.0
C B:PHE663 3.3 76.5 1.0
CD B:GLU667 3.4 0.8 1.0
CG B:ASN665 3.5 86.6 1.0
OE1 B:GLU641 3.6 84.3 1.0
OE2 B:GLU641 3.7 73.0 1.0
ND2 B:ASN665 3.9 87.1 1.0
OE2 B:GLU667 3.9 0.9 1.0
CA B:PHE663 4.0 80.7 1.0
CD B:GLU641 4.1 81.9 1.0
CG2 B:THR635 4.3 81.8 1.0
N B:ILE664 4.4 76.8 1.0
CE B:LYS638 4.4 93.2 1.0
CD B:LYS638 4.4 89.7 1.0
N B:GLN636 4.5 71.8 1.0
OG1 B:THR635 4.5 75.5 1.0
O B:GLN636 4.5 82.0 1.0
CB B:GLN636 4.6 88.2 1.0
CG B:GLU667 4.6 88.0 1.0
CG B:GLU572 4.6 79.0 1.0
CB B:PHE663 4.7 85.0 1.0
CA B:ILE664 4.7 84.0 1.0
CB B:GLU667 4.8 83.5 1.0
O B:ASP662 4.8 0.9 1.0
CB B:THR635 4.9 78.8 1.0
N B:ASN665 4.9 83.4 1.0
CB B:ASN665 5.0 77.0 1.0

Reference:

E.Bligt-Linden, M.Pihlavisto, I.Szatmari, Z.Otwinowski, D.J.Smith, L.Lazar, F.Fulop, T.A.Salminen. Novel Pyridazinone Inhibitors For Vascular Adhesion Protein- 1 (Vap-1): Old Target - New Inhibition Mode. J.Med.Chem. V. 56 9837 2013.
ISSN: ISSN 0022-2623
PubMed: 24304424
DOI: 10.1021/JM401372D
Page generated: Sat Jul 13 22:50:37 2024

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