Zinc in PDB 830c: Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid

The structure of Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid, PDB code: 830c 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.072, 36.098, 96.368, 90.00, 131.06, 90.00
R / Rfree (%)	20.8 / 26.6

The structure of Collagenase-3 (Mmp-13) Complexed to A 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 Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid (pdb code 830c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid, PDB code: 830c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A 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 Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn272 b:11.1 occ:1.00 O43 A:RS11 1.8 18.4 1.0 NE2 A:HIS222 1.9 6.7 1.0 NE2 A:HIS226 2.0 11.6 1.0 O42 A:RS11 2.0 19.7 1.0 NE2 A:HIS232 2.1 13.5 1.0 HO A:RS11 2.7 0.0 1.0 N41 A:RS11 2.8 17.8 1.0 C40 A:RS11 2.8 17.5 1.0 CE1 A:HIS222 2.9 5.7 1.0 CD2 A:HIS222 2.9 7.2 1.0 CE1 A:HIS226 3.0 11.5 1.0 CD2 A:HIS232 3.0 12.6 1.0 CD2 A:HIS226 3.0 11.0 1.0 CE1 A:HIS232 3.1 13.6 1.0 HN A:RS11 3.8 0.0 1.0 OE2 A:GLU223 4.0 11.9 1.0 ND1 A:HIS222 4.0 7.0 1.0 CG A:HIS222 4.1 7.5 1.0 ND1 A:HIS226 4.1 11.3 1.0 H321 A:RS11 4.2 0.0 1.0 CG A:HIS226 4.2 11.4 1.0 CG A:HIS232 4.2 12.4 1.0 ND1 A:HIS232 4.2 12.9 1.0 H2 A:HOH289 4.2 0.0 1.0 C26 A:RS11 4.3 17.2 1.0 H332 A:RS11 4.3 0.0 1.0 O A:HOH289 4.3 13.3 1.0 C33 A:RS11 4.7 16.7 1.0 OE1 A:GLU223 4.7 11.6 1.0 O A:HOH369 4.7 24.1 1.0 CD A:GLU223 4.7 11.9 1.0 H1 A:HOH289 4.8 0.0 1.0 H252 A:RS11 4.8 0.0 1.0 C14 A:RS11 4.8 13.5 1.0 H14 A:RS11 4.8 0.0 1.0 C32 A:RS11 4.9 17.0 1.0 CE A:MET240 4.9 4.6 1.0 H302 A:RS11 4.9 0.0 1.0 HD1 A:HIS222 5.0 0.0 1.0 C13 A:RS11 5.0 14.1 1.0

Zinc binding site 2 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A 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 Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn273 b:11.6 occ:1.00 OD2 A:ASP174 1.7 9.8 1.0 NE2 A:HIS187 1.9 18.1 1.0 NE2 A:HIS172 1.9 8.3 1.0 ND1 A:HIS200 1.9 8.8 1.0 CE1 A:HIS187 2.7 18.4 1.0 CG A:ASP174 2.8 9.0 1.0 CD2 A:HIS172 2.9 8.8 1.0 CE1 A:HIS200 2.9 9.0 1.0 CE1 A:HIS172 3.0 8.2 1.0 CG A:HIS200 3.0 7.0 1.0 CD2 A:HIS187 3.1 16.4 1.0 OD1 A:ASP174 3.2 10.1 1.0 CB A:HIS200 3.5 7.8 1.0 ND1 A:HIS187 3.9 18.1 1.0 CG A:HIS172 4.0 9.0 1.0 NE2 A:HIS200 4.1 9.9 1.0 ND1 A:HIS172 4.1 8.2 1.0 O A:TYR176 4.1 11.0 1.0 CG A:HIS187 4.1 13.3 1.0 CD2 A:HIS200 4.1 9.6 1.0 CB A:ASP174 4.2 9.8 1.0 CE1 A:PHE189 4.5 15.4 1.0 HD1 A:HIS187 4.7 0.0 1.0 CZ A:PHE178 4.7 8.5 1.0 CE2 A:PHE178 4.8 9.9 1.0 H A:TYR176 4.8 0.0 1.0 CZ A:PHE189 4.8 14.8 1.0 CB A:TYR176 4.9 12.9 1.0 HE2 A:HIS200 4.9 0.0 1.0 C A:TYR176 5.0 9.2 1.0 CA A:HIS200 5.0 6.3 1.0 O A:HOH275 5.0 6.1 1.0 HD1 A:HIS172 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A 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 Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn272 b:11.8 occ:1.00 O42 B:RS11 1.9 20.0 1.0 O43 B:RS11 1.9 19.6 1.0 NE2 B:HIS222 1.9 8.9 1.0 NE2 B:HIS232 2.0 11.1 1.0 NE2 B:HIS226 2.1 16.1 1.0 HO B:RS11 2.7 0.0 1.0 C40 B:RS11 2.8 18.2 1.0 N41 B:RS11 2.8 18.2 1.0 CD2 B:HIS222 2.9 8.8 1.0 CE1 B:HIS232 3.0 11.5 1.0 CE1 B:HIS222 3.0 8.4 1.0 CD2 B:HIS232 3.0 10.7 1.0 CD2 B:HIS226 3.0 15.0 1.0 CE1 B:HIS226 3.1 16.0 1.0 HN B:RS11 3.8 0.0 1.0 CG B:HIS222 4.1 9.0 1.0 H321 B:RS11 4.1 0.0 1.0 ND1 B:HIS222 4.1 8.5 1.0 ND1 B:HIS232 4.1 11.4 1.0 H332 B:RS11 4.1 0.0 1.0 CG B:HIS232 4.1 11.2 1.0 OE2 B:GLU223 4.2 15.2 1.0 O B:HOH452 4.2 28.9 1.0 C26 B:RS11 4.2 16.6 1.0 CG B:HIS226 4.2 14.3 1.0 ND1 B:HIS226 4.2 15.5 1.0 O B:HOH297 4.4 13.8 1.0 C33 B:RS11 4.5 15.7 1.0 H1 B:HOH297 4.6 0.0 1.0 H14 B:RS11 4.6 0.0 1.0 H252 B:RS11 4.7 0.0 1.0 C14 B:RS11 4.7 12.4 1.0 H1 B:HOH452 4.7 0.0 1.0 OE1 B:GLU223 4.8 15.6 1.0 C32 B:RS11 4.8 15.4 1.0 CD B:GLU223 4.8 14.1 1.0 H2 B:HOH297 4.9 0.0 1.0 C13 B:RS11 4.9 10.7 1.0 H2 B:HOH452 4.9 0.0 1.0 O B:HOH329 4.9 30.3 1.0 C25 B:RS11 5.0 17.0 1.0 HD1 B:HIS232 5.0 0.0 1.0 H13 B:RS11 5.0 0.0 1.0

Zinc binding site 4 out of 4 in the Collagenase-3 (Mmp-13) Complexed to A 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 Collagenase-3 (Mmp-13) Complexed to A Sulphone-Based Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn273 b:10.5 occ:1.00 OD2 B:ASP174 1.7 13.9 1.0 ND1 B:HIS200 1.9 7.3 1.0 NE2 B:HIS172 1.9 10.5 1.0 NE2 B:HIS187 2.0 10.3 1.0 CG B:ASP174 2.7 13.1 1.0 CE1 B:HIS187 2.8 9.6 1.0 CE1 B:HIS200 2.9 6.9 1.0 CD2 B:HIS172 2.9 8.6 1.0 CE1 B:HIS172 3.0 10.0 1.0 CG B:HIS200 3.0 6.3 1.0 OD1 B:ASP174 3.1 12.7 1.0 CD2 B:HIS187 3.1 10.0 1.0 CB B:HIS200 3.4 6.7 1.0 NE2 B:HIS200 4.0 7.7 1.0 ND1 B:HIS187 4.0 10.7 1.0 CG B:HIS172 4.1 10.2 1.0 ND1 B:HIS172 4.1 9.6 1.0 CD2 B:HIS200 4.1 6.3 1.0 CB B:ASP174 4.1 14.2 1.0 CG B:HIS187 4.2 9.6 1.0 O B:TYR176 4.3 14.8 1.0 O B:HOH412 4.3 26.6 1.0 O B:HOH436 4.5 20.8 1.0 H B:ASP174 4.6 0.0 1.0 CZ B:PHE178 4.6 8.9 1.0 CZ B:PHE189 4.7 18.0 1.0 CE1 B:PHE189 4.7 18.6 1.0 H2 B:HOH412 4.7 0.0 1.0 O B:HOH360 4.8 8.3 1.0 CE2 B:PHE178 4.8 8.5 1.0 HD1 B:HIS187 4.9 0.0 1.0 CA B:HIS200 4.9 7.0 1.0 HE2 B:HIS200 4.9 0.0 1.0 H B:TYR176 4.9 0.0 1.0 CB B:TYR176 4.9 15.6 1.0 HD1 B:HIS172 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