Zinc in PDB 3dpe: Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor

All present enzymatic activity of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor:
3.4.24.34;

The structure of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dpe was solved by G.Pochetti, R.Montanari, F.Mazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.290, 68.950, 32.750, 90.00, 105.41, 90.00
R / Rfree (%)	21 / 24.2

The structure of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor (pdb code 3dpe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dpe:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:5.2 occ:1.00 OD2 A:ASP149 2.0 5.5 1.0 NE2 A:HIS147 2.1 3.8 1.0 NE2 A:HIS162 2.1 4.9 1.0 CD2 A:HIS175 2.3 6.2 1.0 CD2 A:HIS147 2.9 4.6 1.0 CE1 A:HIS162 2.9 6.3 1.0 CG A:ASP149 2.9 8.5 1.0 OD1 A:ASP149 3.2 7.8 1.0 CG A:HIS175 3.2 7.3 1.0 CE1 A:HIS147 3.2 4.2 1.0 CD2 A:HIS162 3.2 6.0 1.0 NE2 A:HIS175 3.4 9.4 1.0 CB A:HIS175 3.5 6.5 1.0 CG A:HIS147 4.1 5.3 1.0 ND1 A:HIS162 4.1 6.1 1.0 CE1 A:PHE164 4.1 11.7 1.0 O A:SER151 4.2 10.5 1.0 ND1 A:HIS147 4.2 3.9 1.0 CG A:HIS162 4.3 6.0 1.0 CB A:ASP149 4.3 9.9 1.0 ND1 A:HIS175 4.4 8.4 1.0 CE1 A:HIS175 4.5 7.0 1.0 O A:HOH1049 4.5 35.9 1.0 CZ A:PHE164 4.5 12.6 1.0 O A:HOH1147 4.6 34.1 1.0 CZ A:PHE153 4.8 5.6 1.0 CE2 A:PHE153 4.9 7.0 1.0 CB A:SER151 4.9 14.8 1.0 O A:HOH1036 5.0 10.2 1.0 CA A:HIS175 5.0 4.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:5.4 occ:1.00 NE2 A:HIS197 2.1 5.4 1.0 NE2 A:HIS207 2.2 10.0 1.0 NE2 A:HIS201 2.2 7.6 1.0 CD2 A:HIS197 3.0 3.9 1.0 CD2 A:HIS207 3.0 9.2 1.0 CD2 A:HIS201 3.1 6.2 1.0 CE1 A:HIS197 3.2 5.7 1.0 CE1 A:HIS201 3.2 8.6 1.0 CE1 A:HIS207 3.2 9.4 1.0 CG A:HIS197 4.2 3.4 1.0 CG A:HIS207 4.2 8.2 1.0 ND1 A:HIS197 4.2 1.8 1.0 CG A:HIS201 4.2 5.4 1.0 ND1 A:HIS207 4.3 9.0 1.0 ND1 A:HIS201 4.3 5.8 1.0 N1 A:AXB1 4.5 20.8 1.0 OE2 A:GLU198 4.6 4.2 1.0 CE A:MET215 4.6 5.0 1.0 CAP A:AXB1 4.6 13.4 1.0 CAZ A:AXB1 4.6 20.0 1.0 O A:HOH1029 4.7 8.8 1.0 N2 A:AXB1 4.7 15.5 1.0 CBD A:AXB1 4.7 18.8 1.0 CAM A:AXB1 4.8 18.3 1.0 OE1 A:GLU198 4.9 5.5 1.0

G.Pochetti, R.Montanari, C.Gege, C.Chevrier, A.G.Taveras, F.Mazza. Extra Binding Region Induced By Non-Zinc Chelating Inhibitors Into the S(1)' Subsite of Matrix Metalloproteinase 8 (Mmp-8) J.Med.Chem. V. 52 1040 2009.
ISSN: ISSN 0022-2623
PubMed: 19173605
DOI: 10.1021/JM801166J