Calcium 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
Zinc	(Zn)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca274 b:12.6 occ:1.00 O A:GLY180 1.9 29.3 1.0 OE2 A:GLU205 1.9 13.2 1.0 OD1 A:ASP179 1.9 2.6 1.0 O A:SER182 2.0 27.0 1.0 OD2 A:ASP202 2.5 7.8 1.0 O A:LEU184 2.7 14.5 1.0 CD A:GLU205 3.1 13.3 1.0 C A:GLY180 3.2 20.5 1.0 CG A:ASP179 3.2 2.8 1.0 C A:SER182 3.3 18.8 1.0 CG A:ASP202 3.6 7.1 1.0 N A:GLY180 3.7 20.6 1.0 C A:LEU184 3.7 15.8 1.0 C A:PRO181 3.8 13.6 1.0 N A:SER182 3.8 18.9 1.0 H A:GLY180 3.8 0.0 1.0 OE1 A:GLU205 3.8 7.7 1.0 OD2 A:ASP179 3.9 5.0 1.0 O A:PRO181 4.0 15.4 1.0 C A:ASP179 4.0 19.3 1.0 H A:ASP179 4.0 0.0 1.0 CB A:ASP202 4.0 8.8 1.0 CA A:GLY180 4.1 19.7 1.0 H A:SER182 4.1 0.0 1.0 N A:LEU184 4.1 20.1 1.0 N A:PRO181 4.1 13.3 1.0 C A:GLY183 4.1 12.1 1.0 CA A:SER182 4.1 19.4 1.0 CG A:GLU205 4.2 14.2 1.0 CA A:PRO181 4.2 11.9 1.0 N A:GLY183 4.3 12.3 1.0 N A:ASP179 4.3 20.6 1.0 H A:LEU184 4.3 0.0 1.0 CB A:ASP179 4.3 7.9 1.0 CA A:ASP179 4.4 18.0 1.0 O A:GLY183 4.4 19.7 1.0 CA A:GLY183 4.4 10.1 1.0 CA A:LEU184 4.5 18.5 1.0 O A:ASP179 4.5 12.7 1.0 N A:LEU185 4.6 7.8 1.0 OD1 A:ASP202 4.7 3.9 1.0 CA A:LEU185 4.8 7.5 1.0 CB A:LEU184 4.9 14.5 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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 B:Ca274 b:24.6 occ:1.00 O B:GLY180 1.8 38.1 1.0 OE2 B:GLU205 1.8 10.5 1.0 O B:SER182 2.0 21.3 1.0 OD2 B:ASP202 2.1 13.7 1.0 O B:LEU184 2.2 26.8 1.0 OD1 B:ASP179 2.2 14.5 1.0 C B:GLY180 3.0 7.1 1.0 CD B:GLU205 3.1 10.2 1.0 C B:SER182 3.2 18.6 1.0 CG B:ASP179 3.2 12.3 1.0 CG B:ASP202 3.3 15.1 1.0 C B:LEU184 3.4 9.9 1.0 H B:GLY180 3.6 0.0 1.0 N B:GLY180 3.7 6.5 1.0 OD2 B:ASP179 3.7 16.6 1.0 N B:SER182 3.7 19.2 1.0 C B:PRO181 3.7 13.2 1.0 H B:LEU184 3.8 0.0 1.0 N B:LEU184 3.8 8.6 1.0 OE1 B:GLU205 3.9 7.3 1.0 CA B:GLY180 3.9 5.5 1.0 N B:PRO181 4.0 12.2 1.0 CG B:GLU205 4.0 10.4 1.0 O B:PRO181 4.0 18.2 1.0 H B:SER182 4.0 0.0 1.0 CA B:SER182 4.0 19.4 1.0 H B:ASP179 4.0 0.0 1.0 CB B:ASP202 4.1 15.2 1.0 C B:GLY183 4.1 11.4 1.0 C B:ASP179 4.1 14.5 1.0 CA B:LEU184 4.2 8.8 1.0 CA B:PRO181 4.2 12.5 1.0 OD1 B:ASP202 4.2 12.2 1.0 N B:GLY183 4.3 14.3 1.0 N B:LEU185 4.4 28.0 1.0 N B:ASP179 4.5 15.0 1.0 CB B:ASP179 4.5 13.4 1.0 CA B:GLY183 4.5 12.7 1.0 CA B:ASP179 4.6 13.3 1.0 CB B:LEU184 4.6 27.3 1.0 O B:GLY183 4.6 8.0 1.0 CA B:LEU185 4.6 26.4 1.0 CD2 B:LEU185 4.7 3.4 1.0 O B:ASP179 4.7 16.5 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