Zinc in PDB 456c: Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid

The structure of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid, PDB code: 456c was solved by B.Lovejoy, A.Welch, S.Carr, C.Luong, C.Broka, R.T.Hendricks, J.Campbell, K.Walker, R.Martin, H.Van Wart, M.F.Browner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.004, 35.622, 94.875, 90.00, 131.19, 90.00
R / Rfree (%)	21.6 / 33.8

The structure of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid (pdb code 456c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid, PDB code: 456c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn272 b:15.2 occ:1.00 O4 A:CBP1 1.9 17.9 1.0 NE2 A:HIS222 1.9 9.2 1.0 O1 A:CBP1 2.0 17.5 1.0 NE2 A:HIS232 2.0 7.4 1.0 NE2 A:HIS226 2.1 2.9 1.0 C3 A:CBP1 2.7 16.9 1.0 N2 A:CBP1 2.7 16.5 1.0 HO1I A:CBP1 2.8 0.0 1.0 CE1 A:HIS232 2.8 8.5 1.0 CD2 A:HIS222 2.9 5.2 1.0 CE1 A:HIS222 3.0 5.0 1.0 CE1 A:HIS226 3.1 5.0 1.0 CD2 A:HIS226 3.2 2.9 1.0 CD2 A:HIS232 3.2 5.7 1.0 HN21 A:CBP1 3.7 0.0 1.0 OE2 A:GLU223 4.0 3.9 1.0 ND1 A:HIS232 4.0 8.9 1.0 HC72 A:CBP1 4.1 0.0 1.0 CG A:HIS222 4.1 3.3 1.0 ND1 A:HIS222 4.1 4.1 1.0 C5 A:CBP1 4.2 14.2 1.0 CG A:HIS232 4.2 7.5 1.0 ND1 A:HIS226 4.3 4.3 1.0 CG A:HIS226 4.3 3.2 1.0 HC52 A:CBP1 4.4 0.0 1.0 O A:HOH46 4.5 2.0 1.0 C16 A:CBP1 4.6 8.2 1.0 OE1 A:GLU223 4.6 6.5 1.0 CD A:GLU223 4.7 3.2 1.0 C17 A:CBP1 4.7 7.5 1.0 H161 A:CBP1 4.7 0.0 1.0 HC51 A:CBP1 4.8 0.0 1.0 HC81 A:CBP1 4.9 0.0 1.0 H171 A:CBP1 4.9 0.0 1.0 HD1 A:HIS232 4.9 0.0 1.0 C15 A:CBP1 4.9 11.0 1.0 CE A:MET240 4.9 9.2 1.0 C7 A:CBP1 4.9 13.3 1.0 H1 A:HOH46 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn273 b:14.7 occ:1.00 OD2 A:ASP174 1.7 15.9 1.0 NE2 A:HIS172 1.8 11.8 1.0 ND1 A:HIS200 1.8 16.2 1.0 NE2 A:HIS187 2.1 16.0 1.0 CE1 A:HIS187 2.4 18.2 1.0 CD2 A:HIS172 2.7 10.9 1.0 CG A:ASP174 2.7 12.6 1.0 CE1 A:HIS200 2.8 16.2 1.0 CE1 A:HIS172 2.9 14.2 1.0 CG A:HIS200 2.9 18.7 1.0 OD1 A:ASP174 3.1 14.6 1.0 CB A:HIS200 3.3 16.4 1.0 CD2 A:HIS187 3.5 14.0 1.0 ND1 A:HIS187 3.7 16.7 1.0 CG A:HIS172 3.8 10.5 1.0 ND1 A:HIS172 3.9 11.5 1.0 NE2 A:HIS200 3.9 16.4 1.0 CD2 A:HIS200 4.0 15.2 1.0 O A:TYR176 4.1 19.0 1.0 CB A:ASP174 4.1 12.2 1.0 CG A:HIS187 4.3 14.1 1.0 CE2 A:PHE178 4.5 14.3 1.0 HD1 A:HIS187 4.5 0.0 1.0 CE1 A:PHE189 4.5 11.7 1.0 CB A:TYR176 4.7 18.6 1.0 CZ A:PHE178 4.7 14.3 1.0 H A:TYR176 4.8 0.0 1.0 HD1 A:HIS172 4.8 0.0 1.0 HE2 A:HIS200 4.8 0.0 1.0 CA A:HIS200 4.8 8.5 1.0 C A:TYR176 4.9 2.0 1.0 CZ A:PHE189 4.9 11.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn272 b:11.8 occ:1.00 O4 B:CBP1 1.7 16.0 1.0 NE2 B:HIS222 1.8 7.2 1.0 NE2 B:HIS226 2.0 5.4 1.0 NE2 B:HIS232 2.4 11.3 1.0 O1 B:CBP1 2.6 14.0 1.0 C3 B:CBP1 2.7 15.8 1.0 CD2 B:HIS222 2.7 6.9 1.0 CE1 B:HIS222 2.9 8.9 1.0 CD2 B:HIS226 3.0 8.3 1.0 CE1 B:HIS226 3.0 7.9 1.0 N2 B:CBP1 3.1 13.2 1.0 CD2 B:HIS232 3.2 8.5 1.0 HO1I B:CBP1 3.4 0.0 1.0 CE1 B:HIS232 3.4 5.7 1.0 OE2 B:GLU223 3.8 6.3 1.0 CG B:HIS222 3.9 9.3 1.0 ND1 B:HIS222 3.9 8.9 1.0 HN21 B:CBP1 4.1 0.0 1.0 C5 B:CBP1 4.1 14.5 1.0 HC72 B:CBP1 4.2 0.0 1.0 ND1 B:HIS226 4.2 9.9 1.0 CG B:HIS226 4.2 7.8 1.0 HC52 B:CBP1 4.3 0.0 1.0 H161 B:CBP1 4.3 0.0 1.0 C16 B:CBP1 4.4 8.8 1.0 CG B:HIS232 4.4 9.3 1.0 ND1 B:HIS232 4.5 5.9 1.0 C17 B:CBP1 4.6 6.0 1.0 H171 B:CBP1 4.6 0.0 1.0 CE B:MET240 4.7 8.0 1.0 HC51 B:CBP1 4.8 0.0 1.0 CD B:GLU223 4.8 6.0 1.0 HD1 B:HIS222 4.9 0.0 1.0 C15 B:CBP1 4.9 8.0 1.0 C7 B:CBP1 5.0 15.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Collagenase-3 (Mmp-13) Complexed to A Diphenyl- Ether Sulphone Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn273 b:17.4 occ:1.00 OD2 B:ASP174 1.6 20.8 1.0 NE2 B:HIS187 1.8 4.6 1.0 NE2 B:HIS172 1.8 17.6 1.0 ND1 B:HIS200 1.8 3.8 1.0 CG B:ASP174 2.6 15.3 1.0 CE1 B:HIS200 2.7 2.6 1.0 CD2 B:HIS172 2.7 13.4 1.0 CE1 B:HIS187 2.7 4.9 1.0 OD1 B:ASP174 3.0 12.6 1.0 CE1 B:HIS172 3.0 17.7 1.0 CD2 B:HIS187 3.0 5.4 1.0 CG B:HIS200 3.0 4.8 1.0 CB B:HIS200 3.6 9.2 1.0 NE2 B:HIS200 3.9 3.4 1.0 ND1 B:HIS187 3.9 3.1 1.0 CG B:HIS172 3.9 15.5 1.0 CB B:ASP174 4.0 14.0 1.0 ND1 B:HIS172 4.0 14.6 1.0 CG B:HIS187 4.1 5.7 1.0 CD2 B:HIS200 4.1 5.0 1.0 O B:TYR176 4.3 9.2 1.0 CE1 B:PHE189 4.4 9.3 1.0 O B:HOH277 4.5 12.0 1.0 CZ B:PHE189 4.5 10.6 1.0 CZ B:PHE178 4.5 5.4 1.0 O B:HOH323 4.5 11.2 1.0 CE2 B:PHE178 4.7 7.5 1.0 H B:ASP174 4.7 0.0 1.0 HE2 B:HIS200 4.8 0.0 1.0 HD1 B:HIS187 4.8 0.0 1.0 HD1 B:HIS172 4.9 0.0 1.0 H2 B:HOH277 5.0 0.0 1.0

B.Lovejoy, A.R.Welch, S.Carr, C.Luong, C.Broka, R.T.Hendricks, J.A.Campbell, K.A.Walker, R.Martin, H.Van Wart, M.F.Browner. Crystal Structures of Mmp-1 and -13 Reveal the Structural Basis For Selectivity of Collagenase Inhibitors. Nat.Struct.Biol. V. 6 217 1999.
ISSN: ISSN 1072-8368
PubMed: 10074939
DOI: 10.1038/6657