Calcium in PDB 2oxz: Human Mmp-12 in Complex with Two Peptides Pqg and Iag

All present enzymatic activity of Human Mmp-12 in Complex with Two Peptides Pqg and Iag:
3.4.24.65;

The structure of Human Mmp-12 in Complex with Two Peptides Pqg and Iag, PDB code: 2oxz 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)	30.19 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.546, 60.378, 54.449, 90.00, 115.41, 90.00
R / Rfree (%)	20.7 / 28.8

The structure of Human Mmp-12 in Complex with Two Peptides Pqg and Iag also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag (pdb code 2oxz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag, PDB code: 2oxz:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mmp-12 in Complex with Two Peptides Pqg and Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca266 b:0.7 occ:1.00 O A:HOH361 1.9 8.4 1.0 O A:ASP158 2.3 8.3 1.0 O A:GLY190 2.4 7.3 1.0 O A:GLY192 2.5 7.9 1.0 O A:HOH299 2.6 5.8 1.0 OD2 A:ASP194 2.7 2.0 1.0 C A:ASP158 3.4 8.0 1.0 CG A:ASP194 3.6 6.2 1.0 C A:GLY190 3.6 9.4 1.0 O A:ALA157 3.7 13.0 1.0 C A:GLY192 3.7 8.0 1.0 OD1 A:ASP194 4.0 2.9 1.0 C A:ILE191 4.1 8.9 1.0 CA A:ASP158 4.1 7.6 1.0 N A:GLY192 4.3 8.6 1.0 CA A:ILE191 4.3 9.1 1.0 N A:ILE191 4.4 9.7 1.0 N A:ILE159 4.4 6.1 1.0 O A:HOH295 4.4 8.6 1.0 N A:ASP194 4.4 3.2 1.0 O A:ILE191 4.5 8.8 1.0 O A:GLY188 4.5 10.5 1.0 N A:LEU160 4.5 5.8 1.0 CA A:GLY190 4.6 10.0 1.0 CA A:ILE159 4.6 5.6 1.0 N A:GLY190 4.6 9.9 1.0 CA A:GLY192 4.6 7.8 1.0 N A:GLY193 4.6 7.2 1.0 C A:ALA157 4.6 11.3 1.0 CA A:GLY193 4.7 6.2 1.0 C A:GLY193 4.8 5.7 1.0 CB A:ASP194 4.8 2.0 1.0 N A:ASP158 4.9 9.5 1.0 C A:SER189 4.9 12.0 1.0 CA A:ASP194 5.0 3.2 1.0

Calcium binding site 2 out of 3 in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mmp-12 in Complex with Two Peptides Pqg and Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca267 b:1.7 occ:1.00 O A:GLU199 2.2 3.4 1.0 OE2 A:GLU199 2.3 9.1 1.0 OD2 A:ASP124 2.3 6.3 1.0 O A:GLU201 2.4 5.5 1.0 OD1 A:ASP124 2.6 2.0 1.0 O A:HOH302 2.6 14.5 1.0 O A:HOH288 2.7 5.3 1.0 CG A:ASP124 2.8 3.9 1.0 C A:GLU199 3.4 5.8 1.0 CD A:GLU199 3.5 11.4 1.0 C A:GLU201 3.5 5.1 1.0 OG1 A:THR122 4.0 2.0 1.0 CG A:GLU199 4.1 5.4 1.0 CA A:GLU199 4.1 4.5 1.0 CA A:PHE202 4.2 6.2 1.0 CB A:ASP124 4.3 3.1 1.0 CD1 A:TRP203 4.3 3.6 1.0 N A:PHE202 4.3 4.5 1.0 N A:GLU201 4.5 6.5 1.0 N A:ASP200 4.5 5.8 1.0 OE1 A:GLU199 4.5 14.8 1.0 C A:ASP200 4.5 7.6 1.0 O A:HOH321 4.6 8.6 1.0 CA A:GLU201 4.6 5.7 1.0 N A:TRP203 4.6 4.1 1.0 CB A:GLU199 4.7 6.5 1.0 CA A:ASP200 4.7 7.0 1.0 NE1 A:TRP203 4.8 3.4 1.0 NH2 A:ARG165 4.8 16.6 1.0 O A:HOH335 4.9 17.8 1.0

Calcium binding site 3 out of 3 in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Mmp-12 in Complex with Two Peptides Pqg and Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca268 b:2.9 occ:1.00 OE2 A:GLU201 2.2 12.7 1.0 OD1 A:ASP198 2.2 3.8 1.0 O A:GLY178 2.4 13.5 1.0 O A:GLY176 2.5 8.4 1.0 O A:ILE180 2.5 5.5 1.0 OD2 A:ASP175 2.5 7.3 1.0 CG A:ASP198 3.4 5.7 1.0 CD A:GLU201 3.4 4.5 1.0 C A:ILE180 3.5 6.1 1.0 C A:GLY178 3.6 12.0 1.0 CG A:ASP175 3.6 8.9 1.0 C A:GLY176 3.7 8.7 1.0 N A:ILE180 3.8 9.4 1.0 N A:GLY178 3.9 11.1 1.0 CB A:ASP198 4.0 2.9 1.0 OE1 A:GLU201 4.1 4.7 1.0 OD1 A:ASP175 4.2 5.9 1.0 C A:LYS177 4.2 11.1 1.0 N A:GLY176 4.2 9.2 1.0 CA A:ILE180 4.3 7.6 1.0 CA A:GLY178 4.3 12.2 1.0 C A:ASP175 4.3 8.3 1.0 OD2 A:ASP198 4.3 2.6 1.0 C A:GLY179 4.4 10.4 1.0 N A:ASP175 4.4 7.1 1.0 CG A:GLU201 4.4 3.3 1.0 CA A:LYS177 4.4 11.5 1.0 N A:LEU181 4.5 4.8 1.0 CA A:GLY176 4.5 8.8 1.0 N A:LYS177 4.5 9.2 1.0 N A:GLY179 4.6 11.4 1.0 CA A:LEU181 4.6 4.8 1.0 O A:ASP175 4.6 8.7 1.0 O A:LYS177 4.7 10.5 1.0 CB A:ILE180 4.7 7.4 1.0 CA A:ASP175 4.8 7.8 1.0 CA A:GLY179 4.8 11.4 1.0 CB A:ASP175 4.8 8.0 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: ISSN 1433-7851
PubMed: 17096442
DOI: 10.1002/ANIE.200603100