Zinc in PDB 4i03: Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor

All present enzymatic activity of Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor:
3.4.24.65;

The structure of Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor, PDB code: 4i03 was solved by E.A.Stura, L.Vera, L.Devel, E.Cassar-Lajeunesse, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.790, 60.100, 54.920, 90.00, 116.67, 90.00
R / Rfree (%)	14.4 / 19.4

The structure of Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Human MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor (pdb code 4i03). 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 MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor, PDB code: 4i03:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human MMP12 in Complex with A Peg-Linked Bifunctional 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 MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.7 occ:1.00 CE1 A:HIS218 2.0 12.6 1.0 NE2 A:HIS222 2.1 14.0 1.0 NE2 A:HIS228 2.1 19.8 1.0 O4 A:L88306 2.4 38.8 0.5 O4E A:L88306 2.4 37.8 0.5 C10 A:L88306 2.7 39.5 0.5 NE2 A:HIS218 3.0 17.1 1.0 CD2 A:HIS228 3.0 16.2 1.0 ND1 A:HIS218 3.0 18.7 1.0 CE1 A:HIS222 3.0 17.5 1.0 CD2 A:HIS222 3.1 16.3 1.0 CE1 A:HIS228 3.2 18.5 1.0 O A:HOH513 4.1 36.4 1.0 CD2 A:HIS218 4.1 13.7 1.0 ND1 A:HIS222 4.2 17.2 1.0 CG A:HIS218 4.2 10.9 1.0 CG A:HIS228 4.2 17.4 1.0 CG A:HIS222 4.2 16.0 1.0 ND1 A:HIS228 4.2 15.6 1.0 C9 A:L88306 4.2 41.0 0.5 O A:HOH521 4.3 46.7 1.0 C1 A:EDO316 4.4 61.0 1.0 C13 A:L88306 4.5 31.4 0.5 O A:HOH401 4.7 26.2 1.0 C14 A:L88306 4.7 27.1 0.5 CE A:MET236 4.7 15.5 1.0 C2 A:EDO316 4.9 61.0 1.0 C27 A:L88306 4.9 29.2 0.5

Zinc binding site 2 out of 2 in the Human MMP12 in Complex with A Peg-Linked Bifunctional 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 MMP12 in Complex with A Peg-Linked Bifunctional L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.3 occ:1.00 OD2 A:ASP170 1.9 17.8 1.0 ND1 A:HIS196 2.0 15.3 1.0 CE1 A:HIS183 2.0 19.6 1.0 NE2 A:HIS168 2.1 14.2 1.0 NE2 A:HIS183 2.8 24.5 1.0 CG A:ASP170 2.9 22.6 1.0 CE1 A:HIS196 2.9 18.2 1.0 CD2 A:HIS168 3.0 14.7 1.0 CG A:HIS196 3.1 14.8 1.0 CE1 A:HIS168 3.1 19.1 1.0 OD1 A:ASP170 3.1 17.9 1.0 ND1 A:HIS183 3.2 22.9 1.0 CB A:HIS196 3.5 14.4 1.0 NE2 A:HIS196 4.1 16.2 1.0 CD2 A:HIS183 4.1 20.0 1.0 CG A:HIS168 4.2 17.1 1.0 CD2 A:HIS196 4.2 14.4 1.0 ND1 A:HIS168 4.2 17.2 1.0 O A:HIS172 4.2 19.0 1.0 CG A:HIS183 4.2 17.6 1.0 CB A:ASP170 4.2 20.0 1.0 CE2 A:PHE185 4.3 24.2 1.0 CZ A:PHE174 4.6 16.1 1.0 CZ A:PHE185 4.8 23.8 1.0 CE2 A:PHE174 4.8 17.3 1.0 O A:HOH403 4.9 19.1 1.0 CA A:HIS196 5.0 14.4 1.0

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015