Calcium in PDB 3f19: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide, PDB code: 3f19 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.80 / 1.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.411, 60.686, 53.900, 90.00, 114.57, 90.00
R / Rfree (%)	16.4 / 18.2

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide (pdb code 3f19). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide, PDB code: 3f19:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide


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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca266 b:14.6 occ:1.00 O A:GLY192 2.3 9.2 1.0 O A:GLY190 2.5 13.9 1.0 O A:HOH10 2.5 10.0 1.0 O A:ASP158 2.5 9.9 1.0 OD2 A:ASP194 2.6 10.1 1.0 O A:HOH432 3.3 22.1 1.0 CG A:ASP194 3.5 8.6 1.0 C A:GLY192 3.5 8.8 1.0 C A:ASP158 3.5 8.9 1.0 C A:GLY190 3.6 13.2 1.0 C A:ILE191 3.8 10.9 1.0 OD1 A:ASP194 3.9 9.4 1.0 O A:ALA157 3.9 12.1 1.0 N A:GLY192 4.0 10.1 1.0 O A:ILE191 4.0 10.0 1.0 O A:HOH463 4.1 23.2 1.0 CA A:ILE191 4.1 12.3 1.0 O A:HOH60 4.2 15.6 1.0 N A:ASP194 4.3 7.5 1.0 N A:ILE191 4.3 12.6 1.0 CA A:GLY192 4.3 9.4 1.0 CA A:ASP158 4.3 9.5 1.0 N A:ILE159 4.4 8.3 1.0 N A:GLY193 4.5 8.3 1.0 O A:GLY188 4.5 12.1 1.0 CA A:ILE159 4.6 8.3 1.0 CA A:GLY193 4.6 8.1 1.0 N A:LEU160 4.7 8.2 1.0 CB A:ASP194 4.7 7.8 1.0 C A:GLY193 4.7 7.7 1.0 CA A:GLY190 4.7 13.7 1.0 N A:GLY190 4.8 13.6 1.0 C A:ALA157 4.9 11.6 1.0 CA A:ASP194 4.9 7.6 1.0 O A:HOH30 4.9 11.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide


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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca267 b:7.8 occ:1.00 O A:HOH27 2.3 11.2 1.0 O A:GLU199 2.3 7.6 1.0 OE2 A:GLU199 2.4 8.1 1.0 O A:HOH24 2.4 9.9 1.0 OD2 A:ASP124 2.4 7.8 1.0 O A:GLU201 2.4 8.0 1.0 OD1 A:ASP124 2.6 8.2 1.0 CG A:ASP124 2.8 7.7 1.0 C A:GLU199 3.5 7.5 1.0 CD A:GLU199 3.5 7.7 1.0 C A:GLU201 3.6 8.0 1.0 CG A:GLU199 3.9 7.9 1.0 CA A:GLU199 4.1 7.5 1.0 OG1 A:THR122 4.1 8.2 1.0 CA A:PHE202 4.3 8.4 1.0 CB A:ASP124 4.3 7.7 1.0 N A:PHE202 4.4 8.2 1.0 CD1 A:TRP203 4.4 7.6 1.0 N A:GLU201 4.4 7.8 1.0 N A:ASP200 4.5 7.7 1.0 C A:ASP200 4.6 8.2 1.0 OE1 A:GLU199 4.6 8.6 1.0 CB A:GLU199 4.6 7.8 1.0 NH2 A:ARG165 4.7 12.1 1.0 CA A:ASP200 4.7 8.1 1.0 CA A:GLU201 4.7 8.0 1.0 O A:HOH31 4.7 11.9 1.0 CD1 A:PHE202 4.9 10.3 1.0 NE1 A:TRP203 4.9 7.6 1.0 N A:TRP203 4.9 8.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor 4-Fluoro-N-(2-Nitroso-2- Oxoethyl)Benzenesulfonamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca268 b:8.6 occ:1.00 OE2 A:GLU201 2.3 11.7 1.0 O A:GLY176 2.3 9.4 1.0 O A:ILE180 2.3 9.8 1.0 O A:GLY178 2.3 10.2 1.0 OD2 A:ASP175 2.4 9.4 1.0 OD1 A:ASP198 2.4 8.3 1.0 C A:ILE180 3.4 9.0 1.0 CG A:ASP198 3.4 7.6 1.0 CD A:GLU201 3.5 10.2 1.0 C A:GLY176 3.5 9.2 1.0 C A:GLY178 3.5 10.2 1.0 CG A:ASP175 3.5 9.1 1.0 N A:GLY178 3.9 10.4 1.0 N A:ILE180 3.9 9.6 1.0 CB A:ASP198 4.0 7.4 1.0 N A:GLY176 4.1 8.9 1.0 OE1 A:GLU201 4.1 10.6 1.0 C A:LYS177 4.2 10.3 1.0 OD1 A:ASP175 4.2 10.2 1.0 CA A:ILE180 4.2 9.7 1.0 C A:ASP175 4.2 9.0 1.0 N A:ASP175 4.2 8.9 1.0 C A:GLY179 4.3 9.7 1.0 CA A:GLY178 4.3 10.5 1.0 OD2 A:ASP198 4.4 7.6 1.0 N A:LEU181 4.4 8.3 1.0 CA A:GLY176 4.4 9.0 1.0 N A:LYS177 4.4 9.7 1.0 CA A:LYS177 4.4 10.2 1.0 N A:GLY179 4.5 10.1 1.0 CG A:GLU201 4.5 8.7 1.0 CA A:LEU181 4.6 7.9 1.0 CA A:ASP175 4.6 9.0 1.0 CB A:ASP175 4.7 9.3 1.0 CB A:ILE180 4.7 9.8 1.0 CA A:GLY179 4.7 9.9 1.0 O A:ASP175 4.7 9.4 1.0 O A:LYS177 4.7 10.7 1.0 O A:GLY179 4.8 10.1 1.0 CD2 A:LEU181 5.0 9.9 1.0

I.Bertini, V.Calderone, M.Fragai, A.Giachetti, M.Loconte, C.Luchinat, M.Maletta, C.Nativi, K.J.Yeo. Exploring the Subtleties of Drug-Receptor Interactions: the Case of Matrix Metalloproteinases. J.Am.Chem.Soc. V. 129 2466 2007.
ISSN: ISSN 0002-7863
PubMed: 17269766
DOI: 10.1021/JA065156Z