Zinc 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
Calcium	(Ca)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:6.6 occ:1.00 O1 A:AZ4306 2.0 6.2 1.0 NE2 A:HIS232 2.1 6.4 1.0 NE2 A:HIS222 2.1 5.8 1.0 NE2 A:HIS226 2.1 5.9 1.0 O2 A:AZ4306 2.2 6.6 1.0 C1 A:AZ4306 2.8 7.3 1.0 N1 A:AZ4306 2.8 6.4 1.0 CE1 A:HIS232 3.0 7.4 1.0 CD2 A:HIS222 3.0 7.2 1.0 CD2 A:HIS226 3.1 6.2 1.0 CE1 A:HIS226 3.1 6.3 1.0 CE1 A:HIS222 3.1 6.5 1.0 CD2 A:HIS232 3.1 6.3 1.0 O A:HOH620 4.1 14.6 1.0 ND1 A:HIS232 4.1 8.6 1.0 CG A:HIS222 4.2 4.5 1.0 ND1 A:HIS222 4.2 4.9 1.0 C2 A:AZ4306 4.2 5.5 1.0 ND1 A:HIS226 4.2 6.2 1.0 CG A:HIS232 4.2 6.5 1.0 CG A:HIS226 4.2 5.2 1.0 N2 A:AZ4306 4.3 8.9 1.0 C6 A:AZ4306 4.3 8.5 1.0 C5 A:AZ4306 4.4 7.8 1.0 OE2 A:GLU223 4.4 7.7 1.0 C11 A:AZ4306 4.5 11.4 1.0 C7 A:AZ4306 4.5 10.0 1.0 N3 A:AZ4306 4.5 9.3 1.0 N4 A:AZ4306 4.6 8.6 1.0 C8 A:AZ4306 4.6 9.3 1.0 C12 A:AZ4306 4.7 9.3 1.0 C3 A:AZ4306 4.7 7.8 1.0 CE A:MET240 4.8 7.8 1.0 N5 A:AZ4306 4.9 10.0 1.0 C9 A:AZ4306 4.9 7.7 1.0 C10 A:AZ4306 5.0 11.4 1.0 C4 A:AZ4306 5.0 9.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn303 b:7.3 occ:1.00 OD2 A:ASP174 2.0 7.3 1.0 NE2 A:HIS187 2.0 9.1 1.0 NE2 A:HIS172 2.0 5.0 1.0 ND1 A:HIS200 2.0 7.1 1.0 CE1 A:HIS187 2.7 12.8 1.0 CG A:ASP174 2.9 7.1 1.0 CD2 A:HIS172 2.9 6.2 1.0 CE1 A:HIS200 2.9 7.1 1.0 CE1 A:HIS172 3.0 5.6 1.0 CG A:HIS200 3.1 6.0 1.0 OD1 A:ASP174 3.2 8.6 1.0 CD2 A:HIS187 3.2 15.0 1.0 CB A:HIS200 3.5 4.8 1.0 ND1 A:HIS187 3.9 14.3 1.0 CG A:HIS172 4.1 6.1 1.0 O A:TYR176 4.1 9.8 1.0 NE2 A:HIS200 4.1 8.0 1.0 ND1 A:HIS172 4.1 6.6 1.0 CG A:HIS187 4.1 8.3 1.0 CD2 A:HIS200 4.2 8.6 1.0 CB A:ASP174 4.2 8.0 1.0 CE1 A:PHE189 4.6 14.1 1.0 CZ A:PHE178 4.7 7.7 1.0 CB A:TYR176 4.7 14.0 1.0 CZ A:PHE189 4.8 14.7 1.0 CE2 A:PHE178 4.8 6.4 1.0 C A:TYR176 4.9 11.0 1.0 O A:HOH402 4.9 7.5 1.0 CA A:HIS200 5.0 4.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:7.0 occ:1.00 O1 B:AZ4306 2.0 7.6 1.0 NE2 B:HIS222 2.1 6.4 1.0 NE2 B:HIS232 2.1 5.9 1.0 NE2 B:HIS226 2.1 7.2 1.0 O2 B:AZ4306 2.2 6.4 1.0 C1 B:AZ4306 2.8 7.6 1.0 N1 B:AZ4306 2.9 6.3 1.0 CD2 B:HIS222 3.0 7.7 1.0 CD2 B:HIS226 3.0 6.6 1.0 CD2 B:HIS232 3.0 6.5 1.0 CE1 B:HIS232 3.1 9.0 1.0 CE1 B:HIS222 3.1 5.3 1.0 CE1 B:HIS226 3.1 8.1 1.0 CG B:HIS222 4.1 3.9 1.0 ND1 B:HIS232 4.2 9.1 1.0 ND1 B:HIS222 4.2 5.1 1.0 N2 B:AZ4306 4.2 7.5 1.0 CG B:HIS232 4.2 8.3 1.0 CG B:HIS226 4.2 5.3 1.0 ND1 B:HIS226 4.2 6.3 1.0 C6 B:AZ4306 4.2 7.2 1.0 C2 B:AZ4306 4.2 7.7 1.0 C13 B:AZ4306 4.3 7.9 1.0 C5 B:AZ4306 4.4 7.5 1.0 C7 B:AZ4306 4.4 7.2 1.0 OE2 B:GLU223 4.5 7.4 1.0 C10 B:AZ4306 4.5 9.2 1.0 C8 B:AZ4306 4.6 9.2 1.0 N3 B:AZ4306 4.6 7.0 1.0 N4 B:AZ4306 4.6 8.8 1.0 C3 B:AZ4306 4.7 7.8 1.0 C9 B:AZ4306 4.8 8.0 1.0 CE B:MET240 4.8 7.2 1.0 N5 B:AZ4306 4.9 8.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:6.5 occ:1.00 OD2 B:ASP174 2.0 5.5 1.0 NE2 B:HIS187 2.0 7.8 1.0 NE2 B:HIS172 2.0 6.3 1.0 ND1 B:HIS200 2.0 5.9 1.0 CG B:ASP174 2.9 8.3 1.0 CE1 B:HIS187 2.9 8.2 1.0 CD2 B:HIS172 2.9 5.5 1.0 CE1 B:HIS200 2.9 7.4 1.0 CE1 B:HIS172 3.1 6.5 1.0 CD2 B:HIS187 3.1 9.2 1.0 CG B:HIS200 3.1 5.7 1.0 OD1 B:ASP174 3.2 8.0 1.0 CB B:HIS200 3.5 5.4 1.0 ND1 B:HIS187 4.1 8.6 1.0 NE2 B:HIS200 4.1 5.8 1.0 CG B:HIS172 4.1 6.2 1.0 ND1 B:HIS172 4.1 6.3 1.0 CG B:HIS187 4.2 5.8 1.0 CD2 B:HIS200 4.2 6.9 1.0 CB B:ASP174 4.3 7.3 1.0 O B:TYR176 4.3 8.7 1.0 CZ B:PHE178 4.6 8.0 1.0 CZ B:PHE189 4.6 14.2 1.0 CE1 B:PHE189 4.7 12.7 1.0 CE2 B:PHE178 4.7 7.3 1.0 O B:HOH429 4.8 8.5 1.0 CB B:TYR176 4.9 11.3 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