Zinc in PDB 6hv2: Mmp-13 in Complex with the Peptide Imisf

The structure of Mmp-13 in Complex with the Peptide Imisf, PDB code: 6hv2 was solved by P.Mittl, R.Riedl, D.Hohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.46 / 1.71
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.928, 68.928, 133.563, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 26.3

The structure of Mmp-13 in Complex with the Peptide Imisf also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Mmp-13 in Complex with the Peptide Imisf (pdb code 6hv2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mmp-13 in Complex with the Peptide Imisf, PDB code: 6hv2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mmp-13 in Complex with the Peptide Imisf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mmp-13 in Complex with the Peptide Imisf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.8 occ:1.00 NE2 A:HIS232 2.0 34.8 1.0 NE2 A:HIS222 2.0 34.4 1.0 N B:ILE163 2.1 32.7 1.0 NE2 A:HIS226 2.2 31.9 1.0 O B:ILE163 2.3 44.5 1.0 CE1 A:HIS222 2.8 36.6 1.0 CA B:ILE163 2.8 36.9 1.0 C B:ILE163 2.8 39.2 1.0 CD2 A:HIS232 2.8 38.1 1.0 CD2 A:HIS226 3.0 27.7 1.0 CE1 A:HIS232 3.1 39.5 1.0 CD2 A:HIS222 3.2 40.2 1.0 CE1 A:HIS226 3.3 25.8 1.0 CB B:ILE163 3.4 35.3 1.0 ND1 A:HIS222 4.0 31.9 1.0 CG A:HIS232 4.0 35.5 1.0 N B:MET164 4.1 32.4 1.0 ND1 A:HIS232 4.1 41.0 1.0 CG A:HIS226 4.2 29.0 1.0 OE2 A:GLU223 4.2 41.2 1.0 CG A:HIS222 4.2 33.4 1.0 ND1 A:HIS226 4.3 27.7 1.0 CG1 B:ILE163 4.3 37.3 1.0 OE1 A:GLU223 4.4 40.9 1.0 O1 A:GOL306 4.4 44.0 1.0 CG2 B:ILE163 4.5 32.9 1.0 CD A:GLU223 4.6 35.7 1.0 CA A:PRO242 4.7 42.5 1.0 C1 A:GOL306 4.8 33.5 1.0 CB A:PRO242 4.8 35.0 1.0 CE A:MET240 4.8 28.8 1.0 CA B:MET164 4.9 39.3 1.0 CG B:MET164 5.0 46.2 1.0

Zinc binding site 2 out of 2 in the Mmp-13 in Complex with the Peptide Imisf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mmp-13 in Complex with the Peptide Imisf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:36.6 occ:1.00 NE2 A:HIS172 2.0 29.3 1.0 OD2 A:ASP174 2.0 38.0 1.0 ND1 A:HIS200 2.1 37.6 1.0 NE2 A:HIS187 2.2 35.6 1.0 CD2 A:HIS172 2.9 33.0 1.0 CG A:ASP174 3.0 40.2 1.0 CE1 A:HIS200 3.0 37.2 1.0 CE1 A:HIS172 3.1 34.4 1.0 CG A:HIS200 3.1 35.1 1.0 CE1 A:HIS187 3.1 42.4 1.0 CD2 A:HIS187 3.2 40.6 1.0 OD1 A:ASP174 3.2 31.0 1.0 CB A:HIS200 3.5 39.7 1.0 CG A:HIS172 4.1 39.2 1.0 ND1 A:HIS172 4.1 36.2 1.0 O A:TYR176 4.1 40.8 1.0 NE2 A:HIS200 4.2 40.4 1.0 CD2 A:HIS200 4.2 33.2 1.0 ND1 A:HIS187 4.2 37.3 1.0 CG A:HIS187 4.3 40.6 1.0 CB A:ASP174 4.3 33.2 1.0 CE1 A:PHE189 4.4 40.6 1.0 CZ A:PHE189 4.6 42.4 1.0 CZ A:PHE178 4.6 36.0 1.0 O A:HOH427 4.6 32.7 1.0 CE2 A:PHE178 4.9 37.4 1.0 CB A:TYR176 4.9 34.0 1.0 CA A:HIS200 5.0 33.5 1.0

F.M.Gall, D.Hohl, D.Frasson, T.Wermelinger, P.R.E.Mittl, M.Sievers, R.Riedl. Drug Design Inspired By Nature: Crystallographic Detection of An Auto-Tailored Protease Inhibitor Template. Angew.Chem.Int.Ed.Engl. V. 58 4051 2019.
ISSN: ESSN 1521-3773
PubMed: 30615822
DOI: 10.1002/ANIE.201812348