Zinc 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:

Calcium

(Ca)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Mmp-12 in Complex with Two Peptides Pqg and Iag, PDB code: 2oxz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Mmp-12 in Complex with Two Peptides Pqg and 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 in Complex with Two Peptides Pqg and Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn264 b:3.5 occ:1.00 NE2 A:HIS222 2.0 2.0 1.0 NE2 A:HIS228 2.0 5.5 1.0 NE2 A:HIS218 2.1 6.8 1.0 OXT Y:GLY206 2.4 33.6 1.0 O Y:HOH120 2.8 18.3 1.0 CE1 A:HIS228 2.9 5.9 1.0 CD2 A:HIS222 3.0 2.0 1.0 CD2 A:HIS228 3.0 4.5 1.0 CE1 A:HIS222 3.0 4.5 1.0 CE1 A:HIS218 3.1 4.8 1.0 CD2 A:HIS218 3.1 5.0 1.0 C Y:GLY206 3.6 34.8 1.0 ND1 A:HIS228 4.0 4.1 1.0 CG A:HIS228 4.1 5.6 1.0 ND1 A:HIS222 4.1 3.4 1.0 CG A:HIS222 4.1 2.0 1.0 ND1 A:HIS218 4.2 2.0 1.0 N X:ILE207 4.2 19.7 1.0 CB Y:GLN205 4.2 36.7 1.0 CG A:HIS218 4.2 2.2 1.0 C Y:GLN205 4.3 36.2 1.0 N Y:GLN205 4.3 35.6 1.0 CA X:ILE207 4.3 17.6 1.0 O Y:GLY206 4.4 34.5 1.0 CA Y:GLN205 4.4 36.3 1.0 N Y:GLY206 4.5 35.7 1.0 CA Y:GLY206 4.5 35.2 1.0 OE1 A:GLU219 4.5 8.4 1.0 O Y:GLN205 4.6 35.5 1.0 OE2 A:GLU219 4.9 4.5 1.0 CE A:MET236 5.0 2.0 1.0

Zinc binding site 2 out of 2 in the Human Mmp-12 in Complex with Two Peptides Pqg and 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 in Complex with Two Peptides Pqg and Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn265 b:3.6 occ:1.00 NE2 A:HIS183 2.0 7.6 1.0 OD1 A:ASP170 2.0 5.6 0.7 NE2 A:HIS168 2.2 8.3 1.0 ND1 A:HIS196 2.2 4.9 1.0 CE1 A:HIS183 2.8 11.5 1.0 CD2 A:HIS168 2.9 10.7 1.0 CG A:ASP170 2.9 9.7 0.7 CD2 A:HIS183 3.1 13.1 1.0 CG A:HIS196 3.2 4.0 1.0 OD2 A:ASP170 3.2 2.0 0.7 CE1 A:HIS196 3.2 4.7 1.0 CE1 A:HIS168 3.4 10.5 1.0 CB A:HIS196 3.4 5.7 1.0 ND1 A:HIS183 4.0 12.3 1.0 CG A:HIS168 4.1 10.8 1.0 CG A:HIS183 4.2 6.9 1.0 NE2 A:HIS196 4.3 6.9 1.0 ND1 A:HIS168 4.3 9.9 1.0 CD2 A:HIS196 4.3 8.5 1.0 CB A:ASP170 4.3 12.7 0.7 CE2 A:PHE185 4.4 11.8 1.0 O A:HIS172 4.4 15.6 1.0 CZ A:PHE185 4.5 13.2 1.0 CZ A:PHE174 4.6 2.0 1.0 CE1 A:PHE174 4.6 2.3 1.0 O A:HOH292 4.8 3.8 1.0 CB A:HIS172 4.9 18.2 1.0 CA A:HIS196 5.0 5.4 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