Zinc 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:

Calcium

(Ca)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Mmp-12 Complexed with the Peptide Iag, PDB code: 2oxw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Mmp-12 Complexed with the Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn264 b:15.9 occ:1.00 NE2 A:HIS218 2.0 14.2 1.0 NE2 A:HIS228 2.0 15.0 1.0 NE2 A:HIS222 2.1 14.1 1.0 O A:HOH314 2.3 20.3 1.0 CE1 A:HIS228 3.0 14.8 1.0 CD2 A:HIS218 3.0 13.7 1.0 CE1 A:HIS218 3.0 13.7 1.0 CD2 A:HIS228 3.0 15.5 1.0 CD2 A:HIS222 3.0 12.8 1.0 CE1 A:HIS222 3.1 14.8 1.0 ND1 A:HIS228 4.1 15.4 1.0 ND1 A:HIS218 4.1 13.4 1.0 CG A:HIS228 4.2 15.6 1.0 CG A:HIS218 4.2 12.5 1.0 ND1 A:HIS222 4.2 14.4 1.0 CG A:HIS222 4.2 12.5 1.0 CG2 X:ILE207 4.2 20.2 1.0 O A:HOH288 4.3 18.8 1.0 OE1 A:GLU219 4.5 16.9 1.0 O A:HOH444 4.5 35.1 1.0 CA X:ILE207 4.6 19.8 1.0 O A:HOH443 4.7 27.9 1.0 CB X:ILE207 4.8 19.8 1.0 OE2 A:GLU219 4.9 17.0 1.0 CE A:MET236 4.9 14.2 1.0

Zinc binding site 2 out of 2 in the Human Mmp-12 Complexed with the Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn265 b:16.9 occ:1.00 OD1 A:ASP170 1.9 15.9 0.7 NE2 A:HIS168 2.0 17.0 1.0 ND1 A:HIS196 2.0 14.9 1.0 CE1 A:HIS183 2.1 14.4 1.0 NE2 A:HIS183 2.8 18.1 1.0 CG A:ASP170 2.8 18.2 0.7 CD2 A:HIS168 2.9 16.7 1.0 CE1 A:HIS196 3.0 15.0 1.0 CE1 A:HIS168 3.0 15.1 1.0 CG A:HIS196 3.1 13.0 1.0 OD2 A:ASP170 3.1 16.9 0.7 ND1 A:HIS183 3.2 18.2 1.0 CB A:HIS196 3.5 12.5 1.0 CD2 A:HIS183 4.0 16.8 1.0 CG A:HIS168 4.1 17.1 1.0 ND1 A:HIS168 4.1 16.0 1.0 NE2 A:HIS196 4.1 14.2 1.0 CD2 A:HIS196 4.2 13.4 1.0 CB A:ASP170 4.2 20.6 0.7 CG A:HIS183 4.2 15.8 1.0 O A:HIS172 4.3 21.0 1.0 CE2 A:PHE185 4.6 18.4 1.0 CB A:HIS172 4.6 22.6 1.0 CZ A:PHE174 4.7 14.6 1.0 CE1 A:PHE174 4.8 14.0 1.0 CZ A:PHE185 4.8 18.3 1.0 O A:HOH289 5.0 19.8 1.0 CA A:HIS196 5.0 11.8 1.0 C A:HIS172 5.0 21.0 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