Calcium in PDB 2oxu: Uninhibited Form of Human Mmp-12

All present enzymatic activity of Uninhibited Form of Human Mmp-12:
3.4.24.65;

The structure of Uninhibited Form of Human Mmp-12, PDB code: 2oxu was solved by V.Calderone, I.Bertini, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.64 / 1.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.545, 60.751, 54.264, 90.00, 115.64, 90.00
R / Rfree (%)	19.7 / 21.6

The structure of Uninhibited Form of Human Mmp-12 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Uninhibited Form of Human Mmp-12 (pdb code 2oxu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Uninhibited Form of Human Mmp-12, PDB code: 2oxu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Uninhibited Form of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Uninhibited Form of Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca266 b:8.5 occ:1.00 O A:GLY192 2.3 7.2 1.0 O A:GLY190 2.3 10.8 1.0 O A:HOH350 2.4 14.6 1.0 O A:ASP158 2.4 6.4 1.0 O A:HOH292 2.5 9.5 1.0 OD2 A:ASP194 2.5 6.7 1.0 CG A:ASP194 3.5 6.2 1.0 C A:ASP158 3.5 6.0 1.0 C A:GLY192 3.5 6.7 1.0 C A:GLY190 3.5 10.6 1.0 C A:ILE191 3.8 8.8 1.0 OD1 A:ASP194 3.9 7.5 1.0 N A:GLY192 4.0 8.0 1.0 O A:ILE191 4.0 8.0 1.0 O A:ALA157 4.1 8.9 1.0 N A:ASP194 4.2 5.0 1.0 CA A:ILE191 4.2 10.2 1.0 CA A:GLY192 4.3 7.5 1.0 N A:ILE191 4.3 10.3 1.0 CA A:ASP158 4.3 6.2 1.0 N A:ILE159 4.4 5.8 1.0 O A:GLY188 4.4 10.7 1.0 N A:GLY193 4.5 6.2 1.0 O A:HOH275 4.5 20.0 1.0 CA A:ILE159 4.5 5.6 1.0 CA A:GLY190 4.6 11.0 1.0 CA A:GLY193 4.6 5.7 1.0 N A:GLY190 4.6 11.2 1.0 CB A:ASP194 4.7 5.4 1.0 C A:GLY193 4.7 5.4 1.0 N A:LEU160 4.7 5.7 1.0 CA A:ASP194 4.8 4.7 1.0 O A:HOH337 4.9 10.0 1.0 C A:SER189 4.9 11.4 1.0

Calcium binding site 2 out of 3 in the Uninhibited Form of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Uninhibited Form of Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca267 b:5.4 occ:1.00 O A:GLU199 2.4 5.4 1.0 OD2 A:ASP124 2.4 5.8 1.0 OE2 A:GLU199 2.4 4.9 1.0 O A:HOH289 2.4 7.0 1.0 O A:HOH287 2.4 7.0 1.0 O A:GLU201 2.4 5.8 1.0 OD1 A:ASP124 2.6 5.9 1.0 CG A:ASP124 2.8 5.1 1.0 C A:GLU199 3.5 5.2 1.0 CD A:GLU199 3.5 4.8 1.0 C A:GLU201 3.6 5.5 1.0 CG A:GLU199 3.9 6.2 1.0 CA A:GLU199 4.1 5.5 1.0 OG1 A:THR122 4.1 5.4 1.0 CA A:PHE202 4.3 6.0 1.0 CB A:ASP124 4.3 5.5 1.0 N A:PHE202 4.4 5.8 1.0 CD1 A:TRP203 4.4 5.3 1.0 N A:GLU201 4.5 5.9 1.0 N A:ASP200 4.5 5.7 1.0 C A:ASP200 4.6 6.5 1.0 OE1 A:GLU199 4.6 6.4 1.0 CB A:GLU199 4.6 5.9 1.0 CA A:ASP200 4.7 6.0 1.0 CA A:GLU201 4.7 5.8 1.0 NH2 A:ARG165 4.7 9.2 1.0 O A:HOH288 4.8 9.0 1.0 NE1 A:TRP203 4.8 5.1 1.0 CD1 A:PHE202 4.8 7.2 1.0 N A:TRP203 4.9 5.5 1.0 O A:HOH280 4.9 10.7 1.0

Calcium binding site 3 out of 3 in the Uninhibited Form of Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Uninhibited Form of Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca268 b:7.9 occ:1.00 OE2 A:GLU201 2.2 10.7 1.0 O A:GLY176 2.3 9.2 1.0 OD2 A:ASP175 2.3 8.4 1.0 O A:ILE180 2.3 7.9 1.0 OD1 A:ASP198 2.4 7.6 1.0 O A:GLY178 2.4 9.3 1.0 CG A:ASP198 3.4 5.2 1.0 C A:ILE180 3.5 8.1 1.0 CD A:GLU201 3.5 9.0 1.0 CG A:ASP175 3.5 9.3 1.0 C A:GLY176 3.5 9.2 1.0 C A:GLY178 3.5 9.6 1.0 N A:GLY178 3.9 10.3 1.0 N A:ILE180 4.0 9.5 1.0 CB A:ASP198 4.0 4.8 1.0 OD1 A:ASP175 4.1 11.7 1.0 N A:GLY176 4.1 8.5 1.0 C A:LYS177 4.2 10.4 1.0 OE1 A:GLU201 4.2 9.6 1.0 N A:ASP175 4.2 8.0 1.0 C A:ASP175 4.2 8.6 1.0 CA A:ILE180 4.3 8.9 1.0 CA A:GLY178 4.3 10.0 1.0 C A:GLY179 4.4 10.0 1.0 OD2 A:ASP198 4.4 5.4 1.0 N A:LEU181 4.4 6.8 1.0 CA A:GLY176 4.4 8.9 1.0 N A:LYS177 4.4 9.7 1.0 CA A:LYS177 4.5 10.5 1.0 CG A:GLU201 4.5 6.4 1.0 CA A:LEU181 4.5 6.4 1.0 N A:GLY179 4.6 9.9 1.0 CA A:ASP175 4.6 8.8 1.0 CB A:ASP175 4.6 9.2 1.0 O A:ASP175 4.7 8.9 1.0 O A:LYS177 4.7 10.6 1.0 CA A:GLY179 4.7 9.9 1.0 CB A:ILE180 4.8 9.4 1.0 O A:GLY179 4.9 10.9 1.0

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo. Snapshots of the Reaction Mechanism of Matrix Metalloproteinases. Angew.Chem.Int.Ed.Engl. V. 45 7952 2006.
ISSN: ESSN 0570-0833
PubMed: 17096442
DOI: 10.1002/ANIE.200603100