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Calcium in PDB 4btw: 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: 4btw 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) 49.39 / 2.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 226.473, 226.473, 219.250, 90.00, 90.00, 120.00
R / Rfree (%) 20.504 / 26.032

Other elements in 4btw:

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

Calcium binding site 1 out of 4 in 4btw

Go back to Calcium Binding Sites List in 4btw
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:52.0
occ:1.00
 O A:LEU530 2.3 42.1 1.0
OD1 A:ASP531 2.3 49.3 1.0
OD1 A:ASP673 2.3 48.5 1.0
N A:LEU674 2.3 57.0 1.0
O A:LEU674 2.3 53.9 1.0
OD1 A:ASP529 2.4 56.4 1.0
C A:LEU674 3.1 49.8 1.0
C A:ASP673 3.2 60.0 1.0
CA A:LEU674 3.2 52.1 1.0
CG A:ASP673 3.4 52.6 1.0
C A:LEU530 3.5 49.5 1.0
CA A:ASP673 3.5 58.6 1.0
CG A:ASP531 3.5 49.5 1.0
CG A:ASP529 3.7 56.0 1.0
ND2 A:ASN537 3.9 45.2 1.0
CB A:ASP673 4.0 56.6 1.0
NZ A:LYS106 4.1 48.2 1.0
O A:LEU535 4.1 58.5 1.0
CB A:LEU674 4.1 52.9 1.0
CA A:ASP531 4.2 48.5 1.0
N A:VAL675 4.2 48.7 1.0
O A:ASP673 4.3 55.6 1.0
N A:ASP531 4.3 51.1 1.0
OD2 A:ASP531 4.4 44.4 1.0
OD2 A:ASP529 4.4 53.1 1.0
OD2 A:ASP673 4.4 51.9 1.0
CB A:ASP531 4.5 50.3 1.0
N A:LEU530 4.5 51.1 1.0
C A:ASP529 4.5 50.2 1.0
CA A:LEU530 4.7 50.1 1.0
O A:LYS672 4.7 61.2 1.0
CA A:ASP529 4.7 51.6 1.0
CB A:ASP529 4.8 53.9 1.0
N A:ASP673 4.8 55.8 1.0
CA A:VAL675 4.9 49.4 1.0
CB A:ARG637 4.9 56.5 1.0
O A:ASP529 4.9 53.2 1.0

Calcium binding site 2 out of 4 in 4btw

Go back to Calcium Binding Sites List in 4btw
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:59.8
occ:1.00
 OE1 A:GLU667 2.3 62.6 1.0
O A:PHE663 2.3 61.3 1.0
OD1 A:ASN665 2.4 59.1 1.0
OE2 A:GLU572 2.4 54.0 1.0
OE1 A:GLU572 2.4 51.4 1.0
CD A:GLU572 2.8 50.3 1.0
C A:PHE663 3.4 54.4 1.0
CG A:ASN665 3.5 59.5 1.0
CD A:GLU667 3.5 65.0 1.0
OE1 A:GLU641 3.7 50.9 1.0
NZ A:LYS638 3.7 56.8 1.0
ND2 A:ASN665 3.9 62.3 1.0
CA A:PHE663 4.1 53.0 1.0
OE2 A:GLU667 4.2 61.5 1.0
OE2 A:GLU641 4.3 54.6 1.0
CG A:GLU572 4.3 48.8 1.0
CG2 A:THR635 4.3 53.7 1.0
CB A:THR635 4.4 53.6 1.0
O A:GLN636 4.4 68.5 1.0
CD A:GLU641 4.4 53.1 1.0
N A:ILE664 4.4 57.0 1.0
N A:GLN636 4.5 65.2 1.0
N A:ASN665 4.5 63.4 1.0
CB A:GLN636 4.5 59.8 1.0
CG A:GLU667 4.5 68.9 1.0
CB A:GLU667 4.6 68.5 1.0
CA A:ILE664 4.7 56.2 1.0
CB A:PHE663 4.8 53.8 1.0
CB A:ASN665 4.8 57.7 1.0
O A:ASP662 4.9 49.5 1.0
O A:ASN665 4.9 70.3 1.0
CA A:GLN636 5.0 63.9 1.0

Calcium binding site 3 out of 4 in 4btw

Go back to Calcium Binding Sites List in 4btw
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:51.0
occ:1.00
 O B:LEU674 2.3 47.5 1.0
OD1 B:ASP673 2.3 43.8 1.0
OD1 B:ASP531 2.3 48.9 1.0
O B:LEU530 2.3 56.9 1.0
OD1 B:ASP529 2.3 48.2 1.0
C B:LEU530 3.4 56.3 1.0
N B:LEU674 3.4 46.5 1.0
C B:LEU674 3.4 47.2 1.0
CG B:ASP673 3.5 40.8 1.0
CG B:ASP531 3.5 51.1 1.0
CG B:ASP529 3.6 56.3 1.0
ND2 B:ASN537 3.6 62.2 1.0
NZ B:LYS106 3.7 37.2 1.0
C B:ASP673 3.9 43.0 1.0
CA B:LEU674 3.9 44.4 1.0
N B:ASP531 4.0 56.6 1.0
CA B:ASP531 4.1 50.8 1.0
CA B:ASP673 4.2 44.1 1.0
OD2 B:ASP529 4.2 55.7 1.0
OD2 B:ASP673 4.2 40.8 1.0
C B:ASP529 4.3 50.5 1.0
N B:LEU530 4.3 49.7 1.0
CB B:ASP531 4.4 49.9 1.0
O B:LEU535 4.4 57.8 1.0
CB B:ASP673 4.4 42.7 1.0
CA B:LEU530 4.5 52.4 1.0
OD2 B:ASP531 4.5 54.2 1.0
N B:VAL675 4.6 47.0 1.0
CA B:ASP529 4.6 50.4 1.0
O B:ASP673 4.6 43.4 1.0
O B:ASP529 4.7 51.1 1.0
CB B:ASP529 4.7 56.2 1.0
CB B:LEU674 4.8 43.8 1.0
CA B:VAL675 5.0 48.8 1.0
CG B:ASN537 5.0 57.2 1.0

Calcium binding site 4 out of 4 in 4btw

Go back to Calcium Binding Sites List in 4btw
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:60.5
occ:1.00
 OE1 B:GLU667 2.3 55.6 1.0
O B:PHE663 2.3 55.5 1.0
OE2 B:GLU572 2.4 58.7 1.0
OD1 B:ASN665 2.4 67.4 1.0
OE2 B:GLU641 2.4 65.7 1.0
OE1 B:GLU572 2.4 49.8 1.0
CD B:GLU572 2.8 52.6 1.0
NZ B:LYS638 3.3 49.1 1.0
CD B:GLU641 3.4 65.6 1.0
CG B:ASN665 3.4 56.6 1.0
C B:PHE663 3.5 50.7 1.0
CD B:GLU667 3.5 50.1 1.0
OE1 B:GLU641 3.5 73.6 1.0
ND2 B:ASN665 3.9 56.9 1.0
OE2 B:GLU667 4.0 49.1 1.0
CA B:PHE663 4.1 53.6 1.0
CG B:GLU572 4.3 47.4 1.0
CB B:THR635 4.5 50.1 1.0
N B:ASN665 4.5 58.6 1.0
N B:ILE664 4.5 50.6 1.0
CE B:LYS638 4.6 52.9 1.0
CG B:GLU667 4.6 47.9 1.0
N B:GLN636 4.6 50.9 1.0
CD B:LYS638 4.7 55.1 1.0
O B:GLN636 4.7 55.8 1.0
CB B:ASN665 4.7 52.1 1.0
CA B:ILE664 4.8 55.2 1.0
CB B:GLU667 4.8 46.5 1.0
O B:ASP662 4.8 76.7 1.0
CB B:PHE663 4.9 53.5 1.0
CG B:GLU641 4.9 52.0 1.0
C B:ILE664 5.0 59.2 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 22:49:42 2024

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