Zinc in PDB 4qkz: X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115

All present enzymatic activity of X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115:
3.4.24.34;

The structure of X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115, PDB code: 4qkz was solved by G.Pochetti, R.Montanari, D.Capelli, P.Tortorella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.26 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.910, 68.690, 70.690, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.4

The structure of X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115 (pdb code 4qkz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115, PDB code: 4qkz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:7.1 occ:1.00 NE2 A:HIS162 2.0 6.5 1.0 NE2 A:HIS147 2.0 6.2 1.0 OD2 A:ASP149 2.0 7.4 1.0 ND1 A:HIS175 2.1 6.5 1.0 CE1 A:HIS162 2.9 7.0 1.0 CD2 A:HIS147 2.9 6.2 1.0 CG A:ASP149 2.9 8.9 1.0 CE1 A:HIS175 3.0 6.4 1.0 CE1 A:HIS147 3.1 6.3 1.0 CD2 A:HIS162 3.1 6.7 1.0 CG A:HIS175 3.1 5.9 1.0 OD1 A:ASP149 3.2 10.2 1.0 CB A:HIS175 3.5 5.9 1.0 ND1 A:HIS162 4.1 7.1 1.0 CG A:HIS147 4.1 6.1 1.0 ND1 A:HIS147 4.1 6.2 1.0 NE2 A:HIS175 4.1 7.1 1.0 CG A:HIS162 4.2 6.3 1.0 CD2 A:HIS175 4.2 6.4 1.0 CB A:ASP149 4.3 9.7 1.0 O A:SER151 4.3 10.1 1.0 CE1 A:PHE164 4.3 9.0 1.0 CZ A:PHE164 4.6 9.8 1.0 CZ A:PHE153 4.6 7.4 1.0 CE2 A:PHE153 4.7 7.0 1.0 O A:HOH407 4.8 10.6 1.0 CA A:HIS175 4.9 5.6 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:6.9 occ:1.00 OAF A:QZK305 1.9 9.7 1.0 NE2 A:HIS197 2.1 5.7 1.0 CE1 A:HIS207 2.1 6.5 1.0 NE2 A:HIS201 2.1 5.7 1.0 NE2 A:HIS207 3.0 7.8 1.0 CE1 A:HIS197 3.0 5.7 1.0 PAW A:QZK305 3.0 10.0 1.0 CE1 A:HIS201 3.0 6.0 1.0 CD2 A:HIS197 3.1 5.6 1.0 ND1 A:HIS207 3.1 8.8 1.0 CD2 A:HIS201 3.1 5.4 1.0 OAA A:QZK305 3.4 11.2 1.0 OAE A:QZK305 3.5 9.9 1.0 O A:HOH450 3.9 12.4 1.0 ND1 A:HIS197 4.1 5.6 1.0 CD2 A:HIS207 4.1 7.2 1.0 ND1 A:HIS201 4.2 5.9 1.0 CG A:HIS197 4.2 5.4 1.0 CG A:HIS207 4.2 7.8 1.0 CG A:HIS201 4.2 5.5 1.0 OE2 A:GLU198 4.3 9.3 1.0 CAV A:QZK305 4.5 10.2 1.0 CE A:MET215 4.6 7.2 1.0 CAU A:QZK305 4.9 11.2 1.0 CAP A:QZK305 4.9 10.7 1.0 CD A:GLU198 4.9 6.8 1.0 CAN A:QZK305 5.0 10.8 1.0 CAQ A:QZK305 5.0 11.5 1.0

G.Pochetti, R.Montanari, D.Capelli, P.Tortorella. X-Ray Structure of the Complex of the Catalytic Domain of Mmp-8 and A Bis-Phosphonate Inhibitor (ML115) To Be Published.