Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Structure of the Catalytic Domain of Mmp-8 with the Inhibitor ML115, PDB code: 4qkz:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:8.2 occ:1.00 O A:GLY171 2.3 8.0 1.0 O A:GLY169 2.3 9.7 1.0 O A:ASP137 2.3 7.4 1.0 O A:HOH408 2.3 10.5 1.0 O A:HOH412 2.4 10.7 1.0 OD1 A:ASP173 2.4 7.3 1.0 CG A:ASP173 3.4 6.3 1.0 C A:ASP137 3.5 6.8 1.0 C A:GLY171 3.5 7.0 1.0 C A:GLY169 3.5 8.9 1.0 OD2 A:ASP173 3.8 7.3 1.0 C A:ILE170 3.9 8.3 1.0 N A:GLY171 4.0 7.7 1.0 O A:ILE170 4.1 7.9 1.0 CA A:GLY171 4.3 8.2 1.0 N A:ASP173 4.3 5.9 1.0 O A:ALA136 4.3 9.7 1.0 CA A:ASP137 4.3 7.3 1.0 CA A:ILE170 4.3 9.2 1.0 ND2 A:ASN139 4.3 12.5 1.0 N A:ILE170 4.4 9.4 1.0 N A:ILE138 4.4 7.0 1.0 O A:GLY167 4.4 9.0 1.0 CA A:GLY169 4.5 9.6 1.0 N A:GLY169 4.5 10.8 1.0 N A:GLY172 4.5 6.8 1.0 CA A:ILE138 4.5 6.7 1.0 CB A:ASP173 4.6 5.9 1.0 CA A:GLY172 4.7 6.6 1.0 N A:ASN139 4.7 6.7 1.0 C A:GLY172 4.7 5.7 1.0 CH2 A:TRP88 4.8 9.4 1.0 O A:HOH427 4.8 12.3 1.0 CA A:ASP173 4.8 5.9 1.0 C A:GLN168 4.8 11.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca302 b:6.6 occ:1.00 O A:GLY155 2.3 7.7 1.0 O A:ILE159 2.3 7.4 1.0 OE2 A:GLU180 2.3 8.3 1.0 OD2 A:ASP177 2.3 7.0 1.0 OD1 A:ASP154 2.3 6.8 1.0 O A:ASN157 2.4 8.1 1.0 CG A:ASP177 3.4 6.2 1.0 C A:ILE159 3.4 6.5 1.0 CG A:ASP154 3.5 6.8 1.0 C A:GLY155 3.5 7.6 1.0 CD A:GLU180 3.5 7.6 1.0 C A:ASN157 3.5 7.8 1.0 N A:ILE159 3.8 7.1 1.0 N A:ASN157 3.9 8.3 1.0 CB A:ASP177 3.9 5.7 1.0 N A:GLY155 4.0 7.7 1.0 C A:PRO156 4.1 8.4 1.0 OD2 A:ASP154 4.1 7.2 1.0 CA A:ILE159 4.2 7.0 1.0 C A:GLY158 4.2 7.1 1.0 C A:ASP154 4.2 6.9 1.0 OE1 A:GLU180 4.2 8.3 1.0 N A:ASP154 4.3 6.4 1.0 CA A:ASN157 4.3 8.2 1.0 OD1 A:ASP177 4.3 6.6 1.0 CA A:GLY155 4.4 8.0 1.0 N A:LEU160 4.4 5.9 1.0 N A:PRO156 4.4 8.2 1.0 CA A:PRO156 4.4 8.6 1.0 O A:PRO156 4.5 8.6 1.0 N A:GLY158 4.5 8.0 1.0 CG A:GLU180 4.5 7.6 1.0 CB A:ILE159 4.6 7.2 1.0 CA A:ASP154 4.6 6.9 1.0 CA A:GLY158 4.6 7.3 1.0 CB A:ASP154 4.6 7.0 1.0 CA A:LEU160 4.7 5.3 1.0 O A:ASP154 4.7 8.4 1.0 O A:GLY158 4.8 8.0 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.