Calcium in PDB 1os2: Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12

All present enzymatic activity of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12:
3.4.24.65;

The structure of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12, PDB code: 1os2 was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.01 / 2.15
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	123.839, 123.839, 69.730, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 27.1

The structure of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 (pdb code 1os2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12, PDB code: 1os2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca871 b:44.1 occ:1.00 O A:GLY178 2.1 46.5 1.0 O A:GLY176 2.2 51.7 1.0 O A:ILE180 2.3 39.1 1.0 OD1 A:ASP198 2.3 39.9 1.0 OD2 A:ASP175 2.4 45.0 1.0 OE2 A:GLU201 2.4 43.8 1.0 C A:GLY178 3.3 45.9 1.0 C A:GLY176 3.4 50.2 1.0 C A:ILE180 3.4 39.8 1.0 CG A:ASP198 3.4 39.4 1.0 CG A:ASP175 3.6 46.1 1.0 CD A:GLU201 3.6 40.5 1.0 N A:GLY178 3.7 50.2 1.0 N A:ILE180 3.9 42.5 1.0 C A:LYS177 4.0 51.0 1.0 C A:GLY179 4.0 43.7 1.0 CB A:ASP198 4.1 37.2 1.0 OD1 A:ASP175 4.1 44.4 1.0 CA A:GLY178 4.1 47.2 1.0 N A:GLY176 4.2 50.1 1.0 OE1 A:GLU201 4.2 42.2 1.0 C A:ASP175 4.2 49.3 1.0 CA A:GLY176 4.2 50.2 1.0 N A:GLY179 4.2 44.4 1.0 CA A:ILE180 4.2 40.1 1.0 N A:LEU181 4.3 37.2 1.0 CA A:GLY179 4.3 44.0 1.0 N A:LYS177 4.3 49.4 1.0 CA A:LYS177 4.3 50.4 1.0 N A:ASP175 4.3 49.4 1.0 O A:ASP175 4.4 49.9 1.0 OD2 A:ASP198 4.4 39.9 1.0 O A:LYS177 4.4 52.6 1.0 CA A:LEU181 4.6 34.6 1.0 O A:GLY179 4.6 43.2 1.0 CA A:ASP175 4.7 48.9 1.0 CG A:GLU201 4.7 40.2 1.0 CB A:ASP175 4.7 48.8 1.0

Calcium binding site 2 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca872 b:39.6 occ:1.00 O A:ASP158 2.2 35.6 1.0 O A:GLY192 2.3 37.8 1.0 O A:GLY190 2.4 45.0 1.0 OD2 A:ASP194 2.5 33.9 1.0 C A:ASP158 3.4 37.5 1.0 C A:GLY192 3.5 39.5 1.0 C A:GLY190 3.5 46.2 1.0 CG A:ASP194 3.7 40.4 1.0 N A:GLY192 3.9 41.4 1.0 C A:ILE191 4.0 43.1 1.0 O A:ALA157 4.1 41.5 1.0 CA A:ASP158 4.2 38.1 1.0 CA A:GLY192 4.2 40.5 1.0 OD1 A:ASP194 4.2 45.2 1.0 O A:ILE191 4.2 42.6 1.0 N A:ASP194 4.3 33.5 1.0 N A:GLY190 4.3 45.4 1.0 O A:GLY188 4.3 39.9 1.0 N A:ILE159 4.4 37.0 1.0 CA A:GLY190 4.4 45.5 1.0 CA A:ILE159 4.5 33.5 1.0 N A:ILE191 4.5 44.7 1.0 N A:GLY193 4.5 38.1 1.0 CA A:ILE191 4.6 44.8 1.0 O A:HOH892 4.6 40.9 1.0 C A:SER189 4.6 44.3 1.0 C A:GLY193 4.7 35.7 1.0 CA A:GLY193 4.7 35.2 1.0 N A:LEU160 4.8 33.4 1.0 CB A:ASP194 4.8 32.9 1.0 CH2 A:TRP109 4.9 39.4 1.0 CA A:ASP194 4.9 33.5 1.0 O A:SER189 5.0 45.6 1.0 C A:ALA157 5.0 40.8 1.0

Calcium binding site 3 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca873 b:47.4 occ:1.00 OD2 A:ASP124 2.3 39.3 1.0 OE2 A:GLU199 2.3 41.4 1.0 O A:GLU201 2.4 37.3 1.0 O A:GLU199 2.5 43.5 1.0 OD1 A:ASP124 2.6 45.3 1.0 CG A:ASP124 2.9 39.2 1.0 CD A:GLU199 3.3 39.5 1.0 C A:GLU201 3.6 36.9 1.0 C A:GLU199 3.7 42.0 1.0 CG A:GLU199 3.7 41.2 1.0 OG1 A:THR122 4.1 38.8 1.0 CA A:PHE202 4.1 34.6 1.0 N A:PHE202 4.3 35.7 1.0 CA A:GLU199 4.3 40.1 1.0 CB A:ASP124 4.4 38.8 1.0 OE1 A:GLU199 4.4 42.0 1.0 CD1 A:TRP203 4.5 34.3 1.0 CD1 A:PHE202 4.6 44.0 1.0 CB A:GLU199 4.6 39.6 1.0 N A:ASP200 4.7 42.5 1.0 CA A:GLU201 4.8 37.9 1.0 N A:GLU201 4.8 39.2 1.0 C A:ASP200 4.8 41.2 1.0 N A:TRP203 4.8 33.3 1.0 CA A:ASP200 4.9 41.8 1.0 CB A:PHE202 5.0 34.5 1.0 N A:ASP124 5.0 39.0 1.0 NE1 A:TRP203 5.0 35.4 1.0

Calcium binding site 4 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca371 b:26.9 occ:1.00 O B:ILE180 2.1 26.6 1.0 O B:GLY178 2.1 27.4 1.0 O B:GLY176 2.2 24.9 1.0 OE2 B:GLU201 2.2 25.7 1.0 OD2 B:ASP175 2.4 28.1 1.0 OD1 B:ASP198 2.5 32.1 1.0 C B:ILE180 3.3 27.5 1.0 C B:GLY178 3.3 28.6 1.0 C B:GLY176 3.4 22.4 1.0 CD B:GLU201 3.4 23.5 1.0 CG B:ASP198 3.5 31.8 1.0 CG B:ASP175 3.6 32.7 1.0 N B:GLY178 3.8 28.1 1.0 N B:ILE180 4.0 24.6 1.0 CB B:ASP198 4.0 24.2 1.0 C B:LYS177 4.0 27.8 1.0 OD1 B:ASP175 4.0 26.4 1.0 OE1 B:GLU201 4.1 24.2 1.0 CA B:GLY178 4.1 26.8 1.0 N B:GLY176 4.2 28.0 1.0 CA B:ILE180 4.2 27.3 1.0 N B:LEU181 4.2 28.1 1.0 N B:LYS177 4.3 22.6 1.0 C B:ASP175 4.3 30.2 1.0 C B:GLY179 4.3 25.9 1.0 CA B:LYS177 4.3 26.5 1.0 CA B:GLY176 4.3 22.5 1.0 N B:ASP175 4.4 31.0 1.0 N B:GLY179 4.4 27.9 1.0 OD2 B:ASP198 4.4 29.9 1.0 CA B:LEU181 4.4 28.6 1.0 O B:LYS177 4.6 26.3 1.0 CG B:GLU201 4.6 16.2 1.0 O B:ASP175 4.6 33.5 1.0 CA B:GLY179 4.6 24.8 1.0 CB B:ILE180 4.7 24.6 1.0 CA B:ASP175 4.7 30.6 1.0 CB B:ASP175 4.8 31.4 1.0 O B:GLY179 4.9 23.4 1.0 CD2 B:LEU181 4.9 20.9 0.9

Calcium binding site 5 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca372 b:35.7 occ:1.00 O B:GLY190 2.3 36.2 1.0 OD2 B:ASP194 2.4 32.5 1.0 O B:GLY192 2.4 30.7 1.0 O B:ASP158 2.4 26.7 1.0 O B:HOH397 2.5 31.2 1.0 C B:GLY190 3.4 37.6 1.0 CG B:ASP194 3.5 28.0 1.0 C B:ASP158 3.5 29.8 1.0 C B:GLY192 3.6 31.4 1.0 OD1 B:ASP194 3.9 35.7 1.0 N B:GLY192 3.9 28.3 1.0 C B:ILE191 3.9 28.5 1.0 O B:ILE191 4.1 30.3 1.0 CA B:GLY190 4.3 38.1 1.0 N B:ILE191 4.3 34.1 1.0 N B:GLY190 4.4 40.3 1.0 CA B:GLY192 4.4 28.2 1.0 N B:ASP194 4.4 25.4 1.0 CA B:ASP158 4.4 30.8 1.0 N B:ILE159 4.4 26.8 1.0 CA B:ILE191 4.4 30.2 1.0 CA B:ILE159 4.4 26.0 1.0 O B:ALA157 4.4 34.2 1.0 O B:GLY188 4.5 37.0 1.0 N B:LEU160 4.5 25.9 1.0 N B:GLY193 4.6 28.7 1.0 O B:HOH384 4.7 28.2 1.0 CA B:GLY193 4.7 24.7 1.0 CB B:ASP194 4.7 25.6 1.0 C B:GLY193 4.7 24.9 1.0 CH2 B:TRP109 4.8 21.2 1.0 C B:SER189 4.9 42.3 1.0 CA B:ASP194 4.9 25.8 1.0

Calcium binding site 6 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca373 b:28.7 occ:1.00 OE2 B:GLU199 2.0 26.1 1.0 O B:HOH430 2.1 30.7 1.0 O B:GLU201 2.3 23.3 1.0 OD2 B:ASP124 2.4 31.3 1.0 O B:GLU199 2.4 24.4 1.0 O B:HOH393 2.5 27.8 1.0 OD1 B:ASP124 2.6 31.8 1.0 CG B:ASP124 2.9 32.4 1.0 CD B:GLU199 3.2 29.6 1.0 C B:GLU201 3.5 25.1 1.0 C B:GLU199 3.6 24.0 1.0 CG B:GLU199 3.9 28.6 1.0 CA B:PHE202 4.1 27.7 1.0 CA B:GLU199 4.2 22.0 1.0 OE1 B:GLU199 4.2 24.6 1.0 N B:PHE202 4.3 24.6 1.0 OG1 B:THR122 4.3 28.6 1.0 N B:GLU201 4.4 20.9 1.0 CB B:ASP124 4.4 32.2 1.0 CD1 B:TRP203 4.4 27.5 1.0 C B:ASP200 4.5 22.5 1.0 NH2 B:ARG165 4.6 25.4 0.8 N B:ASP200 4.6 22.7 1.0 CB B:GLU199 4.6 25.7 1.0 CA B:GLU201 4.7 21.9 1.0 O B:HOH436 4.7 34.9 1.0 CA B:ASP200 4.7 20.7 1.0 N B:TRP203 4.9 25.9 1.0 O B:HOH377 4.9 24.6 1.0 NE1 B:TRP203 4.9 25.1 1.0 CD1 B:PHE202 4.9 36.1 1.0 O B:ASP200 4.9 21.5 1.0

Calcium binding site 7 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca471 b:28.3 occ:1.00 OD2 C:ASP175 2.0 32.6 1.0 OE2 C:GLU201 2.0 31.8 1.0 O C:GLY178 2.3 35.9 1.0 O C:ILE180 2.3 27.5 1.0 O C:GLY176 2.4 34.5 1.0 OD1 C:ASP198 2.6 28.1 1.0 CD C:GLU201 3.3 33.6 1.0 CG C:ASP175 3.3 33.5 1.0 C C:ILE180 3.4 27.8 1.0 CG C:ASP198 3.5 28.8 1.0 C C:GLY178 3.5 31.3 1.0 C C:GLY176 3.6 36.7 1.0 OD1 C:ASP175 3.8 37.6 1.0 N C:GLY178 3.8 32.6 1.0 N C:ILE180 3.8 30.4 1.0 CB C:ASP198 4.0 29.2 1.0 OE1 C:GLU201 4.1 32.0 1.0 C C:LYS177 4.1 33.2 1.0 CA C:ILE180 4.2 29.8 1.0 CA C:GLY178 4.2 33.5 1.0 C C:GLY179 4.3 31.3 1.0 N C:LEU181 4.3 25.8 1.0 N C:GLY176 4.3 36.2 1.0 CG C:GLU201 4.3 35.9 1.0 N C:ASP175 4.3 37.8 1.0 OD2 C:ASP198 4.3 34.6 1.0 CA C:LEU181 4.4 26.0 1.0 C C:ASP175 4.4 36.5 1.0 N C:LYS177 4.4 34.9 1.0 CA C:LYS177 4.5 35.0 1.0 N C:GLY179 4.5 30.6 1.0 CA C:GLY176 4.5 37.6 1.0 CB C:ASP175 4.5 36.1 1.0 O C:LYS177 4.6 33.5 1.0 CA C:ASP175 4.7 35.7 1.0 CA C:GLY179 4.7 29.6 1.0 CB C:ILE180 4.7 32.0 1.0 O C:ASP175 4.8 35.3 1.0 O C:GLY179 4.8 31.6 1.0 CD2 C:LEU181 4.8 22.6 0.9

Calcium binding site 8 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca472 b:31.9 occ:1.00 O C:HOH520 2.2 45.0 1.0 O C:GLY192 2.2 23.8 1.0 O C:ASP158 2.2 23.2 1.0 O C:GLY190 2.4 31.4 1.0 O C:HOH494 2.4 28.4 1.0 OD2 C:ASP194 2.5 28.3 1.0 C C:ASP158 3.4 27.1 1.0 CG C:ASP194 3.4 31.3 1.0 C C:GLY192 3.5 27.1 1.0 C C:GLY190 3.6 29.6 1.0 OD1 C:ASP194 3.7 34.3 1.0 C C:ILE191 4.0 28.9 1.0 O C:GLY188 4.0 32.7 1.0 O C:ILE191 4.1 30.4 1.0 N C:GLY192 4.1 27.8 1.0 CA C:ASP158 4.2 29.2 1.0 N C:ASP194 4.3 23.4 1.0 O C:ALA157 4.3 33.7 1.0 CA C:ILE191 4.3 31.1 1.0 CA C:GLY192 4.4 26.8 1.0 N C:ILE159 4.4 27.2 1.0 N C:ILE191 4.4 29.0 1.0 N C:GLY193 4.4 27.3 1.0 N C:GLY190 4.5 32.2 1.0 CA C:GLY193 4.5 24.0 1.0 CA C:ILE159 4.5 27.1 1.0 CA C:GLY190 4.5 32.4 1.0 N C:LEU160 4.6 27.6 1.0 CB C:ASP194 4.6 26.9 1.0 C C:GLY193 4.7 24.3 1.0 CH2 C:TRP109 4.7 20.4 1.0 C C:SER189 4.7 35.5 1.0 O C:HOH497 4.8 33.9 1.0 CA C:ASP194 4.8 25.9 1.0 O C:SER189 5.0 36.6 1.0

Calcium binding site 9 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca473 b:38.5 occ:1.00 O C:GLU199 2.1 31.1 1.0 OD1 C:ASP124 2.2 36.2 1.0 O C:GLU201 2.2 33.0 1.0 O C:HOH506 2.3 50.2 1.0 OE2 C:GLU199 2.5 34.7 1.0 OD2 C:ASP124 2.9 42.1 1.0 CG C:ASP124 3.0 42.4 1.0 C C:GLU199 3.2 29.9 1.0 C C:GLU201 3.4 35.0 1.0 CD C:GLU199 3.6 37.5 1.0 CG C:GLU199 3.9 29.4 1.0 CA C:GLU199 3.9 28.9 1.0 CA C:PHE202 4.0 35.9 1.0 N C:GLU201 4.1 34.8 1.0 OG1 C:THR122 4.1 39.0 1.0 N C:PHE202 4.2 35.1 1.0 C C:ASP200 4.2 35.9 1.0 CD1 C:TRP203 4.3 27.8 1.0 N C:ASP200 4.3 30.1 1.0 CB C:ASP124 4.5 41.0 1.0 CA C:GLU201 4.5 34.6 1.0 CA C:ASP200 4.6 35.7 1.0 CB C:GLU199 4.6 29.3 1.0 N C:TRP203 4.6 34.7 1.0 O C:ASP200 4.7 37.6 1.0 OE1 C:GLU199 4.7 39.1 1.0 NE1 C:TRP203 4.7 25.9 1.0 CB C:PHE202 4.9 36.6 1.0 CD1 C:PHE202 4.9 40.3 1.0 C C:PHE202 4.9 35.7 1.0

Calcium binding site 10 out of 18 in the Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Ternary Enzyme-Product-Inhibitor Complexes of Human MMP12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca571 b:43.4 occ:1.00 O D:GLY178 2.2 41.1 1.0 O D:GLY176 2.2 50.5 1.0 O D:ILE180 2.3 36.5 1.0 OD1 D:ASP198 2.3 46.9 1.0 OD2 D:ASP175 2.5 42.4 1.0 OE2 D:GLU201 2.5 38.1 1.0 C D:GLY178 3.4 41.8 1.0 CG D:ASP198 3.4 39.8 1.0 C D:GLY176 3.4 49.4 1.0 C D:ILE180 3.4 36.7 1.0 CD D:GLU201 3.6 41.4 1.0 CG D:ASP175 3.7 46.0 1.0 N D:GLY178 3.7 47.8 1.0 N D:ILE180 3.9 39.0 1.0 CB D:ASP198 4.0 38.0 1.0 C D:LYS177 4.1 48.6 1.0 C D:GLY179 4.1 40.3 1.0 N D:GLY176 4.1 50.4 1.0 CA D:GLY178 4.2 42.6 1.0 OE1 D:GLU201 4.2 42.3 1.0 N D:ASP175 4.2 49.5 1.0 OD1 D:ASP175 4.3 41.5 1.0 CA D:GLY176 4.3 49.2 1.0 CA D:GLY179 4.3 39.7 1.0 C D:ASP175 4.3 50.1 1.0 N D:GLY179 4.3 38.5 1.0 OD2 D:ASP198 4.3 42.5 1.0 N D:LYS177 4.3 47.7 1.0 CA D:LYS177 4.3 49.2 1.0 CA D:ILE180 4.3 36.8 1.0 N D:LEU181 4.3 34.7 1.0 CA D:LEU181 4.6 32.8 1.0 O D:ASP175 4.6 51.6 1.0 O D:GLY179 4.7 40.0 1.0 CG D:GLU201 4.7 40.5 1.0 CA D:ASP175 4.7 49.0 1.0 O D:LYS177 4.7 50.5 1.0 CB D:ASP175 4.8 48.2 1.0

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni. X-Ray Structures of Binary and Ternary Enzyme-Product-Inhibitor Complexes of Matrix Metalloproteinases Angew.Chem.Int.Ed.Engl. V. 42 2673 2003.
ISSN: ISSN 1433-7851
PubMed: 12813751
DOI: 10.1002/ANIE.200350957