Calcium in PDB 4jp4: MMP13 in Complex with A Reverse Hydroxamate Zn-Binder

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4 was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.16 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.616, 36.130, 95.755, 90.00, 131.02, 90.00
R / Rfree (%)	15.1 / 17.5

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Zinc	(Zn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder (pdb code 4jp4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:7.5 occ:1.00 O A:GLY196 2.3 7.1 1.0 O A:ASN194 2.3 11.2 1.0 O A:ASP162 2.3 8.2 1.0 O A:HOH607 2.3 9.6 1.0 O A:HOH606 2.4 8.2 1.0 OD1 A:ASP198 2.4 6.3 1.0 CG A:ASP198 3.4 6.8 1.0 C A:GLY196 3.5 7.3 1.0 C A:ASP162 3.5 7.2 1.0 C A:ASN194 3.5 10.9 1.0 OD2 A:ASP198 3.9 7.5 1.0 C A:TYR195 3.9 9.2 1.0 N A:GLY196 4.0 8.8 1.0 O A:TYR195 4.1 9.2 1.0 O A:ALA161 4.1 8.5 1.0 N A:ASP198 4.2 5.9 1.0 CA A:ASP162 4.3 8.3 1.0 CA A:GLY196 4.3 8.0 1.0 CA A:TYR195 4.3 10.3 1.0 N A:ASN194 4.4 11.9 1.0 O A:HOH615 4.4 14.3 1.0 N A:TYR195 4.4 10.7 1.0 O A:GLY192 4.4 11.7 1.0 CA A:ASN194 4.4 12.3 1.0 N A:GLY197 4.4 5.3 1.0 N A:ILE163 4.5 6.9 1.0 O A:HOH629 4.5 20.8 1.0 CA A:GLY197 4.6 5.7 1.0 CB A:ASP198 4.6 5.4 1.0 C A:GLY197 4.6 5.5 1.0 O A:HOH617 4.7 11.9 1.0 N A:MET164 4.7 6.5 1.0 CA A:ILE163 4.7 6.8 1.0 CG A:MET164 4.7 6.5 1.0 CA A:ASP198 4.8 5.9 1.0 C A:PRO193 4.8 11.2 1.0 CH2 A:TRP113 4.8 10.5 1.0

Calcium binding site 2 out of 4 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:7.4 occ:1.00 OE2 A:GLU205 2.2 10.8 1.0 O A:GLY180 2.3 8.2 1.0 OD1 A:ASP179 2.3 8.6 1.0 O A:LEU184 2.3 8.6 1.0 OD2 A:ASP202 2.3 6.5 1.0 O A:SER182 2.4 11.3 1.0 CG A:ASP202 3.4 6.4 1.0 C A:LEU184 3.5 8.7 1.0 CD A:GLU205 3.5 9.1 1.0 C A:SER182 3.5 11.5 1.0 C A:GLY180 3.5 9.2 1.0 CG A:ASP179 3.5 10.2 1.0 N A:SER182 3.9 11.8 1.0 N A:LEU184 3.9 9.3 1.0 C A:PRO181 4.0 11.9 1.0 CB A:ASP202 4.1 5.5 1.0 N A:GLY180 4.1 8.2 1.0 OD2 A:ASP179 4.1 12.5 1.0 CA A:LEU184 4.2 8.6 1.0 OE1 A:GLU205 4.2 10.1 1.0 C A:ASP179 4.2 9.4 1.0 N A:ASP179 4.2 7.8 1.0 CA A:SER182 4.2 12.8 1.0 C A:GLY183 4.3 10.4 1.0 OD1 A:ASP202 4.3 6.4 1.0 CA A:GLY180 4.4 8.6 1.0 O A:PRO181 4.4 13.3 1.0 N A:PRO181 4.4 10.4 1.0 CA A:PRO181 4.4 11.0 1.0 N A:LEU185 4.4 7.5 1.0 CG A:GLU205 4.5 8.8 1.0 N A:GLY183 4.5 11.8 1.0 CA A:GLY183 4.6 10.5 1.0 CA A:ASP179 4.6 8.6 1.0 CB A:LEU184 4.6 9.0 1.0 CA A:LEU185 4.6 7.0 1.0 CB A:ASP179 4.7 8.8 1.0 O A:HOH453 4.7 22.5 1.0 O A:ASP179 4.7 11.0 1.0 O A:GLY183 4.8 11.4 1.0 CD2 A:LEU185 4.9 10.2 1.0

Calcium binding site 3 out of 4 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:6.5 occ:1.00 O B:GLY196 2.3 6.3 1.0 O B:ASN194 2.3 9.0 1.0 O B:HOH587 2.3 7.8 1.0 O B:ASP162 2.4 5.7 1.0 O B:HOH588 2.4 7.7 1.0 OD1 B:ASP198 2.4 6.2 1.0 CG B:ASP198 3.4 6.7 1.0 C B:GLY196 3.5 6.6 1.0 C B:ASP162 3.5 6.6 1.0 C B:ASN194 3.5 9.2 1.0 C B:TYR195 3.9 8.0 1.0 OD2 B:ASP198 3.9 6.8 1.0 N B:GLY196 4.0 7.8 1.0 O B:TYR195 4.1 7.3 1.0 O B:HOH591 4.1 13.2 1.0 O B:ALA161 4.1 6.4 1.0 N B:ASP198 4.2 6.2 1.0 CA B:ASP162 4.2 6.6 1.0 O B:HOH607 4.2 20.8 1.0 CA B:GLY196 4.3 7.4 1.0 CA B:TYR195 4.3 9.3 1.0 N B:TYR195 4.4 9.2 1.0 O B:GLY192 4.4 8.6 1.0 CA B:ASN194 4.5 9.7 1.0 N B:ASN194 4.5 9.4 1.0 N B:GLY197 4.5 6.5 1.0 N B:ILE163 4.5 5.3 1.0 CB B:ASP198 4.6 6.0 1.0 CA B:GLY197 4.6 6.4 1.0 C B:GLY197 4.6 5.9 1.0 O B:HOH594 4.6 12.6 1.0 N B:MET164 4.7 5.6 1.0 CA B:ILE163 4.7 5.8 1.0 CA B:ASP198 4.8 5.9 1.0 C B:PRO193 4.8 9.2 1.0 CG B:MET164 4.8 5.9 1.0 CH2 B:TRP113 4.9 8.6 1.0 O B:PRO193 5.0 9.3 1.0

Calcium binding site 4 out of 4 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:8.6 occ:1.00 OE2 B:GLU205 2.2 12.8 1.0 O B:GLY180 2.3 12.0 1.0 O B:SER182 2.3 12.2 1.0 O B:LEU184 2.3 9.0 1.0 OD2 B:ASP202 2.3 8.3 1.0 OD1 B:ASP179 2.3 8.3 1.0 CG B:ASP202 3.4 7.0 1.0 C B:SER182 3.4 13.2 1.0 C B:LEU184 3.5 9.0 1.0 C B:GLY180 3.5 12.1 1.0 CD B:GLU205 3.5 11.1 1.0 CG B:ASP179 3.5 11.3 1.0 N B:SER182 3.8 13.8 1.0 N B:LEU184 3.9 9.9 1.0 C B:PRO181 4.0 13.6 1.0 N B:GLY180 4.0 10.8 1.0 OD2 B:ASP179 4.1 12.6 1.0 CB B:ASP202 4.1 5.9 1.0 CA B:SER182 4.2 13.9 1.0 C B:ASP179 4.2 11.0 1.0 CA B:LEU184 4.2 9.8 1.0 N B:ASP179 4.3 9.6 1.0 OE1 B:GLU205 4.3 11.8 1.0 C B:GLY183 4.3 11.2 1.0 OD1 B:ASP202 4.4 7.5 1.0 CA B:PRO181 4.4 13.3 1.0 CA B:GLY180 4.4 11.4 1.0 O B:PRO181 4.4 14.7 1.0 N B:PRO181 4.4 13.0 1.0 CG B:GLU205 4.4 9.3 1.0 N B:LEU185 4.4 7.2 1.0 N B:GLY183 4.5 12.2 1.0 CA B:ASP179 4.6 9.9 1.0 CA B:LEU185 4.6 7.4 1.0 CA B:GLY183 4.6 11.5 1.0 CB B:ASP179 4.6 9.7 1.0 CB B:LEU184 4.6 10.1 1.0 O B:ASP179 4.7 11.9 1.0 O B:GLY183 4.8 11.7 1.0 CD2 B:LEU185 4.9 9.7 1.0

C.De Savi, D.Waterson, A.Pape, S.Lamont, E.Hadley, M.Mills, K.M.Page, J.Bowyer, R.A.Maciewicz. Hydantoin Based Inhibitors of MMP13--Discovery of AZD6605. Bioorg.Med.Chem.Lett. V. 23 4705 2013.
ISSN: ISSN 0960-894X
PubMed: 23810497
DOI: 10.1016/J.BMCL.2013.05.089