Zinc in PDB 3tvc: Human MMP13 in Complex with L-Glutamate Motif Inhibitor

The structure of Human MMP13 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tvc was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, E.Cassar-Lajeunesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.92 / 2.43
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.303, 85.160, 40.916, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 23.4

The structure of Human MMP13 in Complex with L-Glutamate Motif Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Human MMP13 in Complex with L-Glutamate Motif Inhibitor (pdb code 3tvc). 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 MMP13 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tvc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human MMP13 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human MMP13 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.1 occ:1.00 NE2 A:HIS232 2.1 21.8 1.0 NE2 A:HIS222 2.1 10.9 1.0 O7 A:E3P1 2.2 28.6 1.0 NE2 A:HIS226 2.2 20.6 1.0 O6 A:E3P1 2.6 26.1 1.0 C1 A:E3P1 2.7 25.7 1.0 CE1 A:HIS222 3.0 14.2 1.0 CD2 A:HIS232 3.0 21.9 1.0 CE1 A:HIS232 3.0 18.6 1.0 CD2 A:HIS226 3.1 15.6 1.0 CD2 A:HIS222 3.1 12.2 1.0 CE1 A:HIS226 3.2 19.7 1.0 ND1 A:HIS232 4.1 24.9 1.0 ND1 A:HIS222 4.2 15.7 1.0 O A:HOH58 4.2 21.1 1.0 CG A:HIS232 4.2 26.8 1.0 C2 A:E3P1 4.2 19.6 1.0 CG A:HIS222 4.2 17.4 1.0 CG A:HIS226 4.3 13.4 1.0 ND1 A:HIS226 4.3 21.4 1.0 OE2 A:GLU223 4.5 21.4 1.0 C14 A:E3P1 4.6 14.6 1.0 C8 A:E3P1 4.6 10.5 1.0 C9 A:E3P1 4.8 14.5 1.0 C3 A:E3P1 4.9 14.7 1.0 CE A:MET240 4.9 14.3 1.0 N1 A:E3P1 4.9 17.7 1.0

Zinc binding site 2 out of 2 in the Human MMP13 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human MMP13 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:23.2 occ:1.00 NE2 A:HIS172 2.1 20.9 1.0 ND1 A:HIS200 2.1 20.9 1.0 NE2 A:HIS187 2.2 24.4 1.0 OD2 A:ASP174 2.2 28.1 1.0 CE1 A:HIS187 2.9 28.7 1.0 CG A:ASP174 2.9 29.1 1.0 CE1 A:HIS172 3.0 17.2 1.0 CD2 A:HIS172 3.1 23.1 1.0 CE1 A:HIS200 3.1 33.3 1.0 CG A:HIS200 3.1 18.7 1.0 OD1 A:ASP174 3.2 26.6 1.0 CD2 A:HIS187 3.3 22.4 1.0 CB A:HIS200 3.4 12.3 1.0 O A:TYR176 4.0 28.0 1.0 ND1 A:HIS187 4.1 22.1 1.0 ND1 A:HIS172 4.1 27.3 1.0 CG A:HIS172 4.2 40.0 1.0 NE2 A:HIS200 4.2 23.9 1.0 CD2 A:HIS200 4.3 23.4 1.0 CB A:ASP174 4.3 34.7 1.0 CG A:HIS187 4.3 19.9 1.0 O A:HOH16 4.6 25.3 1.0 CZ A:PHE178 4.7 23.3 1.0 CE2 A:PHE178 4.8 23.2 1.0 CB A:TYR176 4.8 28.8 1.0 CA A:HIS200 5.0 16.6 1.0 C A:TYR176 5.0 24.7 1.0

L.Devel, F.Beau, M.Amoura, L.Vera, E.Cassar-Lajeunesse, S.Garcia, B.Czarny, E.A.Stura, V.Dive. Simple Pseudo-Dipeptides with A P2' Glutamate: A Novel Inhibitor Family of Matrix Metalloproteases and Other Metzincins. J.Biol.Chem. V. 287 26647 2012.
ISSN: ISSN 0021-9258
PubMed: 22689580
DOI: 10.1074/JBC.M112.380782