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Calcium in PDB 4btx: 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: 4btx 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) 49.05 / 2.78
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 226.350, 226.350, 217.226, 90.00, 90.00, 120.00
R / Rfree (%) 18.065 / 23.679

Other elements in 4btx:

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

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 4btx). 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: 4btx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4btx

Go back to Calcium Binding Sites List in 4btx
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:33.4
occ:1.00
 O A:LEU530 2.1 26.2 1.0
OD1 A:ASP673 2.2 28.6 1.0
OD1 A:ASP531 2.3 27.2 1.0
O A:LEU674 2.4 32.9 1.0
OD1 A:ASP529 2.5 23.9 1.0
N A:LEU674 3.2 31.9 1.0
C A:LEU530 3.3 27.3 1.0
C A:LEU674 3.4 31.0 1.0
CG A:ASP673 3.5 30.5 1.0
CG A:ASP531 3.6 27.6 1.0
ND2 A:ASN537 3.6 36.1 1.0
CG A:ASP529 3.8 24.0 1.0
CA A:LEU674 3.8 31.2 1.0
C A:ASP673 3.9 33.9 1.0
CA A:ASP531 4.0 28.8 1.0
NZ A:LYS106 4.0 37.2 1.0
N A:ASP531 4.1 27.4 1.0
CA A:ASP673 4.1 35.0 1.0
O A:LEU535 4.1 33.0 1.0
OD2 A:ASP673 4.3 29.1 1.0
CB A:ASP531 4.4 28.1 1.0
N A:LEU530 4.4 27.4 1.0
CB A:ASP673 4.4 33.2 1.0
OD2 A:ASP529 4.4 23.1 1.0
CA A:LEU530 4.4 27.8 1.0
OD2 A:ASP531 4.5 25.5 1.0
C A:ASP529 4.5 25.4 1.0
N A:VAL675 4.6 29.3 1.0
CB A:LEU674 4.6 29.9 1.0
CA A:ASP529 4.8 25.0 1.0
O A:ASP673 4.9 33.3 1.0
O A:ASP529 4.9 23.4 1.0
CB A:ASP529 4.9 24.7 1.0
CG A:ASN537 4.9 35.2 1.0

Calcium binding site 2 out of 4 in 4btx

Go back to Calcium Binding Sites List in 4btx
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:46.3
occ:1.00
 OE1 A:GLU667 2.4 57.2 1.0
O A:PHE663 2.4 38.7 1.0
OD1 A:ASN665 2.5 47.5 1.0
OE2 A:GLU572 2.6 34.9 1.0
OE1 A:GLU572 3.1 38.3 1.0
CD A:GLU572 3.2 38.9 1.0
CG A:ASN665 3.4 52.0 1.0
CD A:GLU667 3.4 52.4 1.0
C A:PHE663 3.4 36.0 1.0
NZ A:LYS638 3.7 39.1 1.0
ND2 A:ASN665 3.7 55.6 1.0
OE1 A:GLU641 3.7 37.1 1.0
OE2 A:GLU641 3.9 37.3 1.0
CA A:PHE663 3.9 32.2 1.0
OE2 A:GLU667 4.0 46.0 1.0
CG2 A:THR635 4.1 44.8 1.0
CD A:GLU641 4.2 35.7 1.0
OG1 A:THR635 4.4 43.3 1.0
CE A:LYS638 4.4 36.7 1.0
CG A:GLU667 4.5 50.3 1.0
O A:GLN636 4.5 32.4 1.0
N A:ILE664 4.6 39.3 1.0
CB A:PHE663 4.6 30.2 1.0
CB A:ASN665 4.7 48.7 1.0
CB A:GLN636 4.7 34.9 1.0
N A:GLN636 4.7 35.4 1.0
CG A:GLU572 4.8 39.0 1.0
N A:ASN665 4.8 42.6 1.0
O A:ASP662 4.8 37.0 1.0
CB A:THR635 4.8 41.4 1.0
CD A:LYS638 4.9 34.5 1.0
CA A:ILE664 5.0 37.3 1.0

Calcium binding site 3 out of 4 in 4btx

Go back to Calcium Binding Sites List in 4btx
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:30.1
occ:1.00
 O B:HOH2100 2.1 17.3 1.0
OD1 B:ASP529 2.1 29.6 1.0
O B:LEU674 2.3 28.1 1.0
OD1 B:ASP531 2.4 28.5 1.0
OD1 B:ASP673 2.5 28.2 1.0
O B:LEU530 2.7 37.3 1.0
CG B:ASP529 3.2 33.6 1.0
NZ B:LYS106 3.3 26.4 1.0
C B:LEU530 3.4 34.7 1.0
C B:LEU674 3.5 27.9 1.0
CG B:ASP531 3.6 29.9 1.0
CG B:ASP673 3.7 27.6 1.0
C B:ASP529 3.8 30.8 1.0
N B:LEU530 3.9 30.8 1.0
N B:LEU674 3.9 28.7 1.0
OD2 B:ASP529 4.0 34.5 1.0
CA B:ASP529 4.0 31.5 1.0
N B:ASP531 4.0 34.1 1.0
O B:ASP529 4.0 28.1 1.0
CB B:ASP529 4.2 33.2 1.0
OD2 B:ASP673 4.3 25.5 1.0
CA B:LEU530 4.3 33.2 1.0
CA B:ASP531 4.3 31.7 1.0
CA B:LEU674 4.3 27.8 1.0
OD2 B:ASP531 4.4 28.7 1.0
C B:ASP673 4.4 28.6 1.0
N B:VAL675 4.5 26.7 1.0
CB B:ASP531 4.6 30.9 1.0
CA B:VAL675 4.6 27.1 1.0
ND2 B:ASN537 4.7 38.6 1.0
CE B:LYS106 4.8 26.2 1.0
CA B:ASP673 4.8 28.4 1.0
CB B:ASP673 4.9 27.7 1.0
O B:ASP673 4.9 29.7 1.0
CB B:VAL675 5.0 26.6 1.0

Calcium binding site 4 out of 4 in 4btx

Go back to Calcium Binding Sites List in 4btx
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:40.6
occ:1.00
 O B:PHE663 2.2 34.7 1.0
OE1 B:GLU667 2.2 43.2 1.0
O B:HOH2108 2.4 29.3 1.0
OE2 B:GLU572 2.8 31.9 1.0
OE1 B:GLU572 2.8 28.4 1.0
OD1 B:ASN665 2.9 45.6 1.0
CD B:GLU572 3.2 32.0 1.0
CD B:GLU667 3.2 37.9 1.0
C B:PHE663 3.3 33.5 1.0
CG B:ASN665 3.4 44.0 1.0
ND2 B:ASN665 3.5 45.0 1.0
NZ B:LYS638 3.6 35.1 1.0
OE2 B:GLU641 3.8 30.5 1.0
OE2 B:GLU667 3.9 36.7 1.0
CA B:PHE663 4.0 33.6 1.0
OE1 B:GLU641 4.2 33.9 1.0
CG B:GLU667 4.2 36.5 1.0
N B:ASN665 4.4 44.3 1.0
N B:ILE664 4.4 33.7 1.0
CD B:GLU641 4.4 31.3 1.0
CA B:ILE664 4.6 36.8 1.0
CB B:ASN665 4.6 42.7 1.0
O B:ASP662 4.7 44.2 1.0
CG B:GLU572 4.7 32.3 1.0
CB B:PHE663 4.7 31.6 1.0
CD B:LYS638 4.7 33.2 1.0
CB B:GLU667 4.8 37.4 1.0
CE B:LYS638 4.8 34.4 1.0
C B:ILE664 4.9 40.5 1.0
N B:GLN636 4.9 32.5 1.0
CG2 B:THR635 4.9 27.0 1.0
OG1 B:THR635 4.9 27.8 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 22:50:14 2024

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