Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Complex Between Mmp-8 and A Non-Zinc Chelating Inhibitor, PDB code: 3dpe:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca996 b:2.2 occ:1.00 O A:ASP137 2.4 5.0 1.0 O A:GLY171 2.5 6.7 1.0 O A:GLY169 2.5 9.4 1.0 OD1 A:ASP173 2.6 5.0 1.0 O A:HOH1158 2.7 27.4 1.0 CG A:ASP173 3.5 3.9 1.0 C A:ASP137 3.6 5.0 1.0 C A:GLY171 3.6 5.0 1.0 C A:GLY169 3.7 7.8 1.0 OD2 A:ASP173 3.8 3.8 1.0 C A:ILE170 4.0 6.0 1.0 N A:GLY171 4.1 5.2 1.0 O A:ILE170 4.1 5.9 1.0 N A:ASP173 4.2 3.9 1.0 O A:ALA136 4.2 8.3 1.0 O A:GLY167 4.3 4.3 1.0 CA A:ASP137 4.4 4.9 1.0 CA A:GLY171 4.4 5.6 1.0 CA A:ILE170 4.5 6.3 1.0 ND2 A:ASN139 4.5 7.1 1.0 N A:ILE138 4.5 4.6 1.0 N A:ILE170 4.5 6.8 1.0 N A:GLY169 4.5 9.5 1.0 CA A:ILE138 4.5 5.1 1.0 CA A:GLY169 4.6 8.4 1.0 N A:GLY172 4.6 4.4 1.0 CB A:ASP173 4.6 2.4 1.0 C A:GLY172 4.7 3.8 1.0 O A:HOH1008 4.7 6.4 1.0 N A:ASN139 4.7 4.9 1.0 CA A:GLY172 4.7 3.5 1.0 CA A:ASP173 4.8 4.5 1.0 CH2 A:TRP88 4.8 5.4 1.0 C A:GLN168 4.9 8.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca997 b:4.3 occ:1.00 O A:GLY155 2.4 7.4 1.0 O A:ILE159 2.4 5.7 1.0 O A:ASN157 2.4 7.7 1.0 OD2 A:ASP177 2.5 7.7 1.0 OD1 A:ASP154 2.5 5.7 1.0 OE2 A:GLU180 2.8 21.3 1.0 CG A:ASP177 3.3 6.4 1.0 C A:ILE159 3.5 4.9 1.0 CD A:GLU180 3.5 13.9 1.0 C A:ASN157 3.5 6.8 1.0 C A:GLY155 3.6 8.7 1.0 CG A:ASP154 3.6 6.5 1.0 N A:ILE159 3.9 4.7 1.0 CB A:ASP177 3.9 4.5 1.0 N A:ASN157 3.9 9.2 1.0 N A:GLY155 4.0 4.7 1.0 C A:PRO156 4.1 9.1 1.0 OE1 A:GLU180 4.2 11.1 1.0 CA A:ILE159 4.2 4.8 1.0 OD2 A:ASP154 4.2 4.2 1.0 CG A:GLU180 4.2 11.3 1.0 C A:ASP154 4.2 5.7 1.0 OD1 A:ASP177 4.2 4.6 1.0 CA A:ASN157 4.2 7.3 1.0 C A:GLY158 4.3 5.0 1.0 N A:ASP154 4.3 6.8 1.0 CA A:GLY155 4.4 7.7 1.0 O A:PRO156 4.4 9.3 1.0 N A:PRO156 4.5 9.4 1.0 N A:LEU160 4.5 5.2 1.0 CA A:PRO156 4.5 9.2 1.0 N A:GLY158 4.5 6.7 1.0 CB A:ILE159 4.6 5.9 1.0 CA A:ASP154 4.6 5.8 1.0 CA A:LEU160 4.6 4.3 1.0 CA A:GLY158 4.6 5.3 1.0 O A:ASP154 4.7 6.4 1.0 CB A:ASP154 4.7 5.3 1.0 O A:GLY158 4.9 6.1 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