Calcium in PDB 2oxw: Human Mmp-12 Complexed with the Peptide Iag

All present enzymatic activity of Human Mmp-12 Complexed with the Peptide Iag:
3.4.24.65;

The structure of Human Mmp-12 Complexed with the Peptide Iag, PDB code: 2oxw 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)	36.96 / 1.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.888, 60.358, 54.521, 90.00, 115.73, 90.00
R / Rfree (%)	19.7 / 22.3

The structure of Human Mmp-12 Complexed with the Peptide Iag also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human Mmp-12 Complexed with the Peptide Iag (pdb code 2oxw). 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 Complexed with the Peptide Iag, PDB code: 2oxw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Mmp-12 Complexed with the Peptide 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 Complexed with the Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca266 b:15.7 occ:1.00 O A:HOH321 2.3 23.6 1.0 O A:ASP158 2.3 13.6 1.0 O A:GLY190 2.3 18.2 1.0 O A:GLY192 2.4 14.5 1.0 OD2 A:ASP194 2.5 15.0 1.0 O A:HOH281 2.5 16.2 1.0 C A:ASP158 3.4 12.6 1.0 CG A:ASP194 3.5 13.9 1.0 C A:GLY190 3.6 18.5 1.0 C A:GLY192 3.6 14.3 1.0 OD1 A:ASP194 3.9 15.5 1.0 C A:ILE191 4.0 17.2 1.0 O A:ALA157 4.0 15.5 1.0 N A:GLY192 4.1 16.2 1.0 O A:ILE191 4.2 16.7 1.0 CA A:ASP158 4.2 12.9 1.0 N A:ASP194 4.3 12.3 1.0 CA A:ILE191 4.3 18.4 1.0 N A:ILE159 4.4 12.1 1.0 N A:ILE191 4.4 18.3 1.0 CA A:GLY192 4.4 15.4 1.0 O A:GLY188 4.5 17.6 1.0 N A:GLY193 4.5 13.5 1.0 CA A:GLY190 4.5 18.8 1.0 N A:GLY190 4.6 18.8 1.0 CA A:ILE159 4.6 12.1 1.0 CA A:GLY193 4.6 13.1 1.0 O A:HOH392 4.7 29.8 1.0 N A:LEU160 4.7 12.2 1.0 C A:GLY193 4.7 12.8 1.0 CB A:ASP194 4.7 12.8 1.0 O A:HOH304 4.7 17.4 1.0 O A:HOH399 4.7 28.7 1.0 CA A:ASP194 4.9 12.6 1.0 C A:SER189 4.9 18.9 1.0 C A:ALA157 4.9 14.5 1.0

Calcium binding site 2 out of 3 in the Human Mmp-12 Complexed with the Peptide 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 Complexed with the Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca267 b:11.6 occ:1.00 O A:GLU199 2.3 11.8 1.0 O A:HOH277 2.4 14.1 1.0 OE2 A:GLU199 2.4 12.5 1.0 OD2 A:ASP124 2.4 11.8 1.0 O A:GLU201 2.4 12.1 1.0 O A:HOH278 2.4 14.5 1.0 OD1 A:ASP124 2.6 11.8 1.0 CG A:ASP124 2.8 10.9 1.0 CD A:GLU199 3.5 12.4 1.0 C A:GLU199 3.5 11.6 1.0 C A:GLU201 3.6 11.6 1.0 CG A:GLU199 3.9 13.0 1.0 CA A:GLU199 4.1 11.6 1.0 OG1 A:THR122 4.1 11.6 1.0 CA A:PHE202 4.2 12.1 1.0 CB A:ASP124 4.4 11.5 1.0 N A:PHE202 4.4 12.1 1.0 CD1 A:TRP203 4.4 11.8 1.0 N A:GLU201 4.4 12.0 1.0 N A:ASP200 4.5 11.8 1.0 C A:ASP200 4.5 12.6 1.0 OE1 A:GLU199 4.6 13.3 1.0 CB A:GLU199 4.6 12.0 1.0 CA A:GLU201 4.7 12.0 1.0 CA A:ASP200 4.7 12.4 1.0 O A:HOH286 4.7 16.1 1.0 CD1 A:PHE202 4.8 13.7 1.0 NH2 A:ARG165 4.8 18.7 1.0 N A:TRP203 4.9 11.9 1.0 NE1 A:TRP203 4.9 11.6 1.0

Calcium binding site 3 out of 3 in the Human Mmp-12 Complexed with the Peptide 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 Complexed with the Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca268 b:16.9 occ:1.00 OE2 A:GLU201 2.3 18.7 1.0 OD1 A:ASP198 2.3 14.6 1.0 O A:GLY178 2.3 17.9 1.0 O A:GLY176 2.3 16.4 1.0 O A:ILE180 2.3 16.0 1.0 OD2 A:ASP175 2.4 16.7 1.0 CG A:ASP198 3.4 12.3 1.0 C A:ILE180 3.4 15.5 1.0 C A:GLY178 3.5 18.1 1.0 CD A:GLU201 3.5 16.6 1.0 C A:GLY176 3.5 17.2 1.0 CG A:ASP175 3.6 17.6 1.0 N A:GLY178 3.9 18.5 1.0 N A:ILE180 3.9 16.8 1.0 CB A:ASP198 4.0 11.7 1.0 N A:GLY176 4.1 17.2 1.0 OD1 A:ASP175 4.1 19.4 1.0 C A:LYS177 4.2 18.6 1.0 CA A:ILE180 4.2 16.3 1.0 OE1 A:GLU201 4.2 17.8 1.0 C A:GLY179 4.3 17.3 1.0 CA A:GLY178 4.3 18.3 1.0 C A:ASP175 4.3 17.4 1.0 N A:ASP175 4.3 17.3 1.0 OD2 A:ASP198 4.3 12.7 1.0 N A:LEU181 4.4 14.4 1.0 N A:LYS177 4.4 17.6 1.0 CA A:GLY176 4.4 17.2 1.0 CA A:LYS177 4.5 18.7 1.0 CG A:GLU201 4.5 13.4 1.0 N A:GLY179 4.5 18.0 1.0 CA A:LEU181 4.6 14.0 1.0 O A:HOH427 4.7 27.8 1.0 CA A:ASP175 4.7 17.3 1.0 CA A:GLY179 4.7 17.6 1.0 CB A:ASP175 4.7 17.9 1.0 O A:ASP175 4.7 17.8 1.0 CB A:ILE180 4.7 16.9 1.0 O A:LYS177 4.8 19.5 1.0 O A:GLY179 4.8 18.2 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