Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:18.2 occ:1.00 O2 A:FMT312 1.8 26.8 1.0 NE2 A:HIS232 2.1 14.2 1.0 NE2 A:HIS222 2.1 9.2 1.0 NE2 A:HIS226 2.1 15.5 1.0 C A:FMT312 2.6 25.3 1.0 O1 A:FMT312 2.7 22.1 1.0 CD2 A:HIS222 2.9 15.9 1.0 CD2 A:HIS232 2.9 22.9 1.0 CD2 A:HIS226 3.0 14.8 1.0 CE1 A:HIS232 3.1 18.5 1.0 CE1 A:HIS222 3.2 12.9 1.0 CE1 A:HIS226 3.2 21.9 1.0 CG A:HIS232 4.1 16.0 1.0 CG A:HIS222 4.1 15.2 1.0 ND1 A:HIS232 4.2 19.5 1.0 CG A:HIS226 4.2 17.3 1.0 ND1 A:HIS222 4.2 16.9 1.0 ND1 A:HIS226 4.3 17.8 1.0 OE2 A:GLU223 4.3 17.9 1.0 C9 A:9DY305 4.3 30.4 1.0 O A:HOH525 4.3 19.8 1.0 OE1 A:GLU223 4.7 16.4 1.0 CE A:MET240 4.7 12.8 1.0 N7 A:9DY305 4.8 31.9 1.0 O A:HOH556 4.8 36.4 1.0 C11 A:9DY305 4.8 30.7 1.0 CD A:GLU223 4.9 16.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:17.0 occ:1.00 OD2 A:ASP174 2.0 15.1 1.0 ND1 A:HIS200 2.0 15.5 1.0 NE2 A:HIS187 2.0 18.8 1.0 NE2 A:HIS172 2.1 19.9 1.0 CD2 A:HIS172 2.9 9.7 1.0 CE1 A:HIS187 2.9 15.6 1.0 CE1 A:HIS200 3.0 15.8 1.0 CG A:ASP174 3.0 21.5 1.0 CG A:HIS200 3.1 19.4 1.0 CD2 A:HIS187 3.1 17.2 1.0 CE1 A:HIS172 3.2 16.2 1.0 OD1 A:ASP174 3.4 20.0 1.0 CB A:HIS200 3.4 19.6 1.0 ND1 A:HIS187 4.1 19.6 1.0 CG A:HIS172 4.1 16.9 1.0 NE2 A:HIS200 4.1 18.0 1.0 O A:TYR176 4.1 18.0 1.0 CD2 A:HIS200 4.2 18.4 1.0 CG A:HIS187 4.2 14.9 1.0 ND1 A:HIS172 4.2 11.3 1.0 CB A:ASP174 4.3 20.8 1.0 CE1 A:PHE189 4.6 24.2 1.0 CB A:TYR176 4.6 22.0 1.0 CZ A:PHE178 4.7 21.8 1.0 CZ A:PHE189 4.7 25.7 1.0 CE2 A:PHE178 4.8 17.9 1.0 C A:TYR176 4.9 18.3 1.0 O A:HOH544 4.9 28.8 1.0 CA A:HIS200 4.9 18.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:26.5 occ:1.00 NE2 B:HIS232 2.0 26.8 1.0 NE2 B:HIS222 2.0 17.6 1.0 O1 B:FMT306 2.1 31.5 1.0 NE2 B:HIS226 2.2 18.5 1.0 O B:HOH452 2.3 36.7 1.0 C B:FMT306 2.8 34.1 1.0 CD2 B:HIS222 2.9 19.6 1.0 CE1 B:HIS232 2.9 26.9 1.0 O2 B:FMT306 3.0 34.4 1.0 CD2 B:HIS232 3.0 22.3 1.0 CE1 B:HIS222 3.1 20.8 1.0 CE1 B:HIS226 3.1 18.8 1.0 CD2 B:HIS226 3.1 18.0 1.0 ND1 B:HIS232 4.0 23.3 1.0 CG B:HIS222 4.1 19.0 1.0 CG B:HIS232 4.1 24.9 1.0 ND1 B:HIS222 4.2 17.3 1.0 ND1 B:HIS226 4.2 20.3 1.0 CG B:HIS226 4.3 19.2 1.0 OE2 B:GLU223 4.4 20.1 1.0 C9 B:9DY305 4.5 37.8 1.0 O B:HOH406 4.5 41.4 1.0 O B:HOH463 4.7 37.5 1.0 CE B:MET240 4.7 21.9 1.0 O B:HOH530 4.9 33.5 1.0 OE1 B:GLU223 4.9 16.2 1.0 CD B:GLU223 5.0 19.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:20.1 occ:1.00 OD2 B:ASP174 1.9 22.1 1.0 NE2 B:HIS172 1.9 18.3 1.0 NE2 B:HIS187 2.1 15.7 1.0 ND1 B:HIS200 2.1 17.8 1.0 CG B:ASP174 2.8 20.6 1.0 CD2 B:HIS172 2.9 17.1 1.0 CE1 B:HIS172 2.9 9.6 1.0 CE1 B:HIS187 3.0 12.9 1.0 CE1 B:HIS200 3.1 21.0 1.0 OD1 B:ASP174 3.1 16.4 1.0 CG B:HIS200 3.1 13.5 1.0 CD2 B:HIS187 3.1 20.9 1.0 CB B:HIS200 3.5 16.5 1.0 ND1 B:HIS172 4.0 18.4 1.0 CG B:HIS172 4.0 20.8 1.0 ND1 B:HIS187 4.1 14.3 1.0 NE2 B:HIS200 4.2 19.4 1.0 CB B:ASP174 4.2 15.0 1.0 CG B:HIS187 4.2 18.6 1.0 CD2 B:HIS200 4.2 17.8 1.0 O B:TYR176 4.3 20.1 1.0 CB B:TYR176 4.6 23.2 1.0 CE1 B:PHE189 4.7 24.0 1.0 O B:HOH440 4.8 13.1 1.0 CZ B:PHE178 4.8 18.5 1.0 CE2 B:PHE178 4.8 19.5 1.0 O B:HOH446 4.9 35.1 1.0 CA B:HIS200 5.0 16.6 1.0 CZ B:PHE189 5.0 28.2 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