Calcium in PDB 7ju8: X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine

The structure of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine, PDB code: 7ju8 was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.74 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.764, 35.987, 95.724, 90, 130.55, 90
R / Rfree (%)	19.8 / 26.4

The structure of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine (pdb code 7ju8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine, PDB code: 7ju8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:41.2 occ:1.00 O A:GLY180 2.1 27.8 1.0 OD2 A:ASP202 2.2 13.8 1.0 O A:LEU184 2.4 27.2 1.0 O A:SER182 2.4 31.6 1.0 OE2 A:GLU205 2.4 32.7 1.0 OD1 A:ASP179 2.5 36.0 1.0 CG A:ASP202 3.3 18.3 1.0 C A:GLY180 3.4 30.6 1.0 C A:LEU184 3.5 28.6 1.0 C A:SER182 3.5 33.5 1.0 CD A:GLU205 3.6 28.9 1.0 CG A:ASP179 3.6 38.6 1.0 N A:SER182 3.8 33.3 1.0 C A:PRO181 4.0 32.4 1.0 N A:LEU184 4.0 33.4 1.0 N A:GLY180 4.0 31.4 1.0 CG A:GLU205 4.1 24.7 1.0 OD1 A:ASP202 4.1 22.5 1.0 CB A:ASP202 4.2 20.2 1.0 CA A:PRO181 4.2 32.0 1.0 CA A:LEU184 4.2 32.6 1.0 N A:ASP179 4.2 31.2 1.0 C A:GLY183 4.2 32.6 1.0 CA A:SER182 4.3 34.1 1.0 C A:ASP179 4.3 32.1 1.0 N A:PRO181 4.3 31.5 1.0 OD2 A:ASP179 4.3 40.0 1.0 CA A:GLY180 4.3 30.7 1.0 N A:GLY183 4.5 33.5 1.0 N A:LEU185 4.6 24.8 1.0 O A:PRO181 4.6 29.8 1.0 CA A:ASP179 4.6 33.2 1.0 OE1 A:GLU205 4.6 28.8 1.0 O A:GLY183 4.6 31.2 1.0 CB A:LEU184 4.6 33.8 1.0 CB A:ASP179 4.7 33.4 1.0 CA A:GLY183 4.7 32.6 1.0 O A:ASP179 4.8 32.4 1.0 CB A:ASP204 4.8 18.2 1.0 O A:HOH422 4.8 10.0 1.0 CA A:LEU185 5.0 20.8 1.0

Calcium binding site 2 out of 4 in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:48.7 occ:1.00 O A:ASP162 2.4 17.3 1.0 OD1 A:ASP198 2.5 14.4 1.0 O A:HOH416 2.6 31.0 1.0 O A:GLY196 2.6 22.3 1.0 O A:ASN194 2.8 22.4 1.0 O A:HOH536 3.0 27.0 1.0 O A:ALA161 3.3 22.1 1.0 C A:ASP162 3.4 15.7 1.0 CG A:ASP198 3.4 21.2 1.0 C A:GLY196 3.8 18.9 1.0 OD2 A:ASP198 3.8 17.2 1.0 O2 A:FMT307 3.9 82.6 1.0 C A:ASN194 4.0 23.6 1.0 C A:TYR195 4.0 22.5 1.0 O A:HOH426 4.0 20.6 1.0 CA A:ASP162 4.0 18.4 1.0 O A:TYR195 4.2 24.4 1.0 CA A:TYR195 4.2 23.7 1.0 N A:GLY196 4.2 20.8 1.0 N A:ILE163 4.3 15.1 1.0 C A:ALA161 4.4 22.6 1.0 N A:ASP198 4.4 17.3 1.0 CG A:MET164 4.4 15.1 1.0 N A:MET164 4.5 13.1 1.0 N A:TYR195 4.5 23.1 1.0 CA A:ILE163 4.6 16.6 1.0 CA A:GLY196 4.6 19.8 1.0 CB A:ASP198 4.7 15.9 1.0 N A:ASP162 4.7 19.7 1.0 C A:FMT307 4.7 83.4 1.0 O A:HOH474 4.7 26.2 1.0 N A:GLY197 4.7 17.0 1.0 O A:HOH505 4.8 50.8 1.0 C A:GLY197 4.8 17.2 1.0 CA A:GLY197 4.8 17.2 1.0 CA A:ASP198 4.9 16.7 1.0 O A:HOH591 4.9 43.4 1.0

Calcium binding site 3 out of 4 in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:53.9 occ:1.00 OD2 B:ASP202 2.6 21.0 1.0 O B:LEU184 2.7 36.5 1.0 OE2 B:GLU205 2.7 34.9 1.0 O B:SER182 2.7 51.2 1.0 O B:GLY180 2.8 47.8 1.0 OD1 B:ASP179 3.3 48.8 1.0 C B:SER182 3.5 52.2 1.0 C B:LEU184 3.5 34.5 1.0 CD B:GLU205 3.6 35.3 1.0 CG B:GLU205 3.7 28.0 1.0 CG B:ASP202 3.7 24.9 1.0 N B:LEU184 3.8 42.5 1.0 C B:GLY183 4.0 45.4 1.0 C B:GLY180 4.0 49.0 1.0 N B:SER182 4.1 53.1 1.0 CB B:ASP202 4.2 23.9 1.0 N B:GLY183 4.2 50.9 1.0 CA B:SER182 4.3 53.4 1.0 CA B:LEU184 4.3 39.9 1.0 C B:PRO181 4.3 52.5 1.0 N B:LEU185 4.3 29.4 1.0 CA B:GLY183 4.3 48.8 1.0 CA B:LEU185 4.4 25.5 1.0 O B:GLY183 4.4 44.6 1.0 CG B:ASP179 4.4 47.6 1.0 N B:ASP179 4.6 36.7 1.0 C B:ASP179 4.7 44.7 1.0 OE1 B:GLU205 4.7 29.5 1.0 CA B:PRO181 4.7 50.9 1.0 O B:ASP179 4.7 44.9 1.0 O B:PRO181 4.8 53.4 1.0 N B:GLY180 4.8 47.1 1.0 OD1 B:ASP202 4.8 21.4 1.0 N B:PRO181 4.9 49.8 1.0

Calcium binding site 4 out of 4 in the X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Mmp-13 in Complex with 4-(1,2,3-Thiadiazol-4-Yl) Pyridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:54.1 occ:1.00 O B:GLY196 2.6 26.6 1.0 OD1 B:ASP198 2.6 15.2 1.0 O B:ASP162 2.6 19.9 1.0 O B:ASN194 2.7 40.0 1.0 O B:HOH465 2.8 29.0 1.0 O B:HOH458 3.2 33.6 1.0 CG B:ASP198 3.4 20.6 1.0 C B:ASP162 3.6 18.6 1.0 C B:GLY196 3.7 26.3 1.0 OD2 B:ASP198 3.8 20.2 1.0 O B:ALA161 3.8 21.3 1.0 C B:TYR195 3.9 34.1 1.0 C B:ASN194 3.9 40.6 1.0 O B:TYR195 3.9 33.1 1.0 O B:HOH418 4.1 15.9 1.0 N B:GLY196 4.2 29.6 1.0 N B:ASP198 4.2 19.8 1.0 CG B:MET164 4.3 22.8 1.0 CA B:TYR195 4.3 38.0 1.0 N B:ILE163 4.4 17.3 1.0 CA B:ASP162 4.5 20.1 1.0 N B:MET164 4.5 14.5 1.0 CA B:GLY196 4.5 28.6 1.0 CA B:ILE163 4.5 17.8 1.0 N B:GLY197 4.5 24.5 1.0 O B:HOH533 4.6 45.3 1.0 N B:TYR195 4.6 38.7 1.0 CA B:GLY197 4.6 23.4 1.0 CB B:ASP198 4.7 18.4 1.0 C B:GLY197 4.8 22.7 1.0 CA B:ASP198 4.9 18.0 1.0 C B:ALA161 4.9 20.7 1.0 C B:ILE163 4.9 16.2 1.0 CB B:MET164 5.0 18.1 1.0

S.J.Taylor, A.Abeywardane, S.Liang, Z.Xiong, J.R.Proudfoot, B.S.Farmer, D.A.Gao, A.Heim-Riether, L.L.Smith-Keenan, I.Muegge, Y.Yu, Q.Zhang, D.Souza, M.Panzenbeck, D.Goldberg, M.Hill-Drzewi, M.Margarit, B.Collins, J.X.Li, L.Zuvela-Jelaska, J.Li, N.A.Farrow. Indole Inhibitors of Mmp-13 For Arthritic Disorders Acs Omega V. 6 18635 2021.
ISSN: ESSN 2470-1343
DOI: 10.1021/ACSOMEGA.1C01320