Atomistry » Calcium » PDB 8bd8-8c5h » 8c3p
Atomistry »
  Calcium »
    PDB 8bd8-8c5h »
      8c3p »

Calcium in PDB 8c3p: Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1

Enzymatic activity of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1

All present enzymatic activity of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p was solved by M.C.Eymery, A.A.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.88 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.94, 57.22, 287.926, 90, 92.72, 90
R / Rfree (%) 22.2 / 28

Other elements in 8c3p:

The structure of Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 also contains other interesting chemical elements:

Iodine (I) 17 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1 (pdb code 8c3p). 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 Autotaxin Gamma in Complex with Lpa 18:1, PDB code: 8c3p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8c3p

Go back to Calcium Binding Sites List in 8c3p
Calcium binding site 1 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:34.4
occ:1.00
OD1 A:ASP773 2.2 35.7 1.0
OD1 A:ASP769 2.3 38.0 1.0
OD1 A:ASP767 2.3 38.8 1.0
OD1 A:ASP765 2.4 38.4 1.0
O A:LEU771 2.4 31.1 1.0
O A:HOH1118 2.5 37.8 1.0
CG A:ASP767 3.3 40.9 1.0
CG A:ASP769 3.3 37.5 1.0
CG A:ASP773 3.5 39.7 1.0
C A:LEU771 3.5 33.6 1.0
CG A:ASP765 3.5 34.7 1.0
OD2 A:ASP767 3.5 44.5 1.0
OD2 A:ASP769 3.7 32.8 1.0
N A:LEU771 3.9 30.6 1.0
CA A:ASP765 4.0 37.2 1.0
N A:ASP773 4.1 28.5 1.0
CA A:LEU771 4.1 34.0 1.0
OD2 A:ASP773 4.2 39.8 1.0
CB A:ASP765 4.2 39.8 1.0
C A:HIS772 4.2 39.8 1.0
CA A:ASP773 4.3 38.4 1.0
CB A:LEU771 4.4 28.3 1.0
N A:ASP769 4.4 32.9 1.0
OD2 A:ASP765 4.4 41.4 1.0
O A:PHE764 4.4 35.5 1.0
CB A:ASP773 4.5 38.2 1.0
N A:HIS772 4.5 28.3 1.0
O A:HIS772 4.5 32.1 1.0
CB A:ASP769 4.6 29.8 1.0
C A:ASP765 4.7 35.9 1.0
N A:ASP767 4.7 35.2 1.0
CB A:ASP767 4.7 35.2 1.0
N A:GLY770 4.8 41.5 1.0
CA A:HIS772 4.8 36.1 1.0
N A:TYR768 4.8 37.5 1.0
N A:TYR766 4.9 37.3 1.0
CA A:ASP769 4.9 33.1 1.0
C A:ASP769 5.0 32.6 1.0
C A:ASP767 5.0 38.4 1.0

Calcium binding site 2 out of 4 in 8c3p

Go back to Calcium Binding Sites List in 8c3p
Calcium binding site 2 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:60.9
occ:1.00
OG A:SER833 2.4 43.0 1.0
O A:HOH1128 2.5 32.2 1.0
O A:SER830 2.7 39.3 1.0
O A:ASN827 3.3 35.1 1.0
O A:HOH1003 3.6 30.1 1.0
CB A:SER833 3.6 33.9 1.0
C A:SER830 3.8 40.2 1.0
O A:CYS831 3.8 40.6 1.0
CA A:CYS831 3.9 45.3 1.0
C A:CYS831 3.9 43.8 1.0
N A:SER833 3.9 42.8 1.0
C A:ASN827 4.3 34.0 1.0
CA A:SER833 4.3 36.4 1.0
N A:CYS831 4.3 37.9 1.0
O A:HOH1157 4.3 30.7 1.0
OE2 A:GLU828 4.6 62.3 1.0
CA A:GLU828 4.6 32.3 1.0
N A:SER834 4.6 39.3 1.0
N A:ASN832 4.7 43.6 1.0
C A:SER833 4.7 31.5 1.0
N A:GLU828 4.8 31.5 1.0
C A:GLU828 5.0 36.5 1.0

Calcium binding site 3 out of 4 in 8c3p

Go back to Calcium Binding Sites List in 8c3p
Calcium binding site 3 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:37.3
occ:1.00
OD1 B:ASP773 2.3 40.8 1.0
OD1 B:ASP769 2.3 35.1 1.0
OD1 B:ASP767 2.3 36.0 1.0
O B:LEU771 2.4 29.4 1.0
OD1 B:ASP765 2.5 37.6 1.0
CG B:ASP769 3.3 33.6 1.0
CG B:ASP767 3.4 38.5 1.0
CG B:ASP773 3.4 44.0 1.0
C B:LEU771 3.5 35.2 1.0
OD2 B:ASP769 3.6 29.8 1.0
CG B:ASP765 3.6 35.0 1.0
OD2 B:ASP767 3.7 43.4 1.0
CA B:ASP765 3.9 33.4 1.0
N B:ASP773 3.9 28.8 1.0
N B:LEU771 4.0 31.1 1.0
OD2 B:ASP773 4.1 38.4 1.0
CA B:ASP773 4.1 31.9 1.0
C B:HIS772 4.2 34.6 1.0
CA B:LEU771 4.2 36.0 1.0
CB B:ASP765 4.2 27.4 1.0
CB B:ASP773 4.3 42.1 1.0
O B:PHE764 4.3 30.7 1.0
N B:ASP769 4.4 35.7 1.0
C B:ASP765 4.5 33.4 1.0
O B:HIS772 4.5 37.9 1.0
N B:HIS772 4.5 33.0 1.0
CB B:LEU771 4.5 31.2 1.0
N B:ASP767 4.5 36.8 1.0
CB B:ASP769 4.6 29.3 1.0
OD2 B:ASP765 4.6 40.1 1.0
N B:TYR766 4.6 34.9 1.0
CB B:ASP767 4.7 26.6 1.0
N B:TYR768 4.7 34.6 1.0
CA B:HIS772 4.7 27.3 1.0
N B:GLY770 4.8 28.5 1.0
CA B:ASP769 4.9 29.8 1.0
C B:ASP767 4.9 37.2 1.0
N B:ASP765 4.9 34.6 1.0
CD B:LYS777 5.0 48.1 1.0
CA B:ASP767 5.0 33.2 1.0

Calcium binding site 4 out of 4 in 8c3p

Go back to Calcium Binding Sites List in 8c3p
Calcium binding site 4 out of 4 in the Crystal Structure of Autotaxin Gamma in Complex with Lpa 18:1


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 Autotaxin Gamma in Complex with Lpa 18:1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca907

b:41.8
occ:0.51
O B:SER830 2.4 34.5 1.0
O B:ASN827 2.4 30.7 1.0
O B:HOH1177 2.5 40.4 1.0
OG B:SER833 2.5 43.7 1.0
O B:HOH1178 2.8 34.8 1.0
C B:ASN827 3.4 39.4 1.0
C B:SER830 3.4 41.1 1.0
CB B:SER833 3.5 31.1 1.0
CA B:GLU828 3.8 39.8 1.0
N B:GLU828 4.0 38.8 1.0
CA B:CYS831 4.1 40.5 1.0
C B:GLU828 4.2 39.6 1.0
N B:CYS831 4.2 43.1 1.0
OE1 B:GLU828 4.2 56.7 1.0
N B:SER833 4.2 39.0 1.0
O B:GLU828 4.3 35.1 1.0
CB B:ASN827 4.4 29.2 1.0
C B:CYS831 4.4 47.6 1.0
N B:SER830 4.4 41.4 1.0
O B:HOH1001 4.4 44.5 1.0
CA B:SER830 4.4 29.6 1.0
O B:HOH1049 4.4 32.3 1.0
CA B:ASN827 4.5 35.2 1.0
CA B:SER833 4.5 37.4 1.0
O B:CYS831 4.6 42.4 1.0
N B:ASN832 4.9 44.6 1.0
CB B:SER830 4.9 34.4 1.0
N B:GLU829 4.9 34.5 1.0
SG B:CYS414 4.9 41.2 1.0

Reference:

M.C.Eymery, K.A.Nguyen, S.Basu, J.Hausmann, V.K.T.Nguyen, H.P.Seidel, L.Gutierrez, A.Boumendjel, A.A.Mccarthy. Discovery of Potent Chromone-Based Autotaxin Inhibitors Inspired By Cannabinoids Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115944
Page generated: Thu Dec 28 01:35:58 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy