Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Mmp-13 in Complex with the Peptide Imisf, PDB code: 6hv2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Mmp-13 in Complex with the Peptide Imisf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303 b:50.1 occ:1.00 O A:GLY180 2.3 51.6 1.0 OD2 A:ASP202 2.3 51.2 1.0 O A:LEU184 2.3 39.0 1.0 OE2 A:GLU205 2.3 48.1 1.0 O A:SER182 2.3 55.8 1.0 OD1 A:ASP179 2.5 52.7 1.0 CG A:ASP202 3.4 46.4 1.0 C A:GLY180 3.5 55.0 1.0 C A:LEU184 3.5 42.2 1.0 C A:SER182 3.5 53.5 1.0 CD A:GLU205 3.6 55.4 1.0 CG A:ASP179 3.7 56.3 1.0 N A:SER182 3.9 63.5 1.0 N A:GLY180 3.9 45.3 1.0 N A:LEU184 3.9 49.4 1.0 C A:PRO181 4.1 60.4 1.0 CB A:ASP202 4.1 35.1 1.0 N A:ASP179 4.2 52.6 1.0 CA A:LEU184 4.2 44.9 1.0 C A:ASP179 4.2 50.2 1.0 CA A:SER182 4.2 60.1 1.0 CA A:GLY180 4.3 42.2 1.0 C A:GLY183 4.3 52.6 1.0 OD1 A:ASP202 4.4 51.6 1.0 OD2 A:ASP179 4.4 53.3 1.0 CG A:GLU205 4.4 56.2 1.0 N A:PRO181 4.4 64.2 1.0 OE1 A:GLU205 4.4 56.9 1.0 CB A:LEU184 4.5 49.1 1.0 CA A:PRO181 4.5 62.4 1.0 O A:PRO181 4.5 62.7 1.0 N A:GLY183 4.5 45.2 1.0 N A:LEU185 4.5 42.0 1.0 CA A:ASP179 4.6 52.7 1.0 O A:ASP179 4.6 49.9 1.0 CA A:GLY183 4.7 44.0 1.0 CA A:LEU185 4.7 43.6 1.0 CB A:ASP179 4.7 55.0 1.0 O A:GLY183 4.9 48.0 1.0 CB A:PHE178 5.0 40.5 1.0

Calcium binding site 2 out of 3 in the Mmp-13 in Complex with the Peptide Imisf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca304 b:39.2 occ:1.00 O A:HOH431 2.3 39.7 1.0 O A:GLY196 2.3 33.1 1.0 O A:ASN194 2.3 42.7 1.0 O A:HOH421 2.4 45.2 1.0 O A:ASP162 2.5 38.2 1.0 OD1 A:ASP198 2.5 39.8 1.0 C A:GLY196 3.5 30.9 1.0 CG A:ASP198 3.5 42.3 1.0 C A:ASN194 3.5 44.7 1.0 C A:ASP162 3.6 38.4 1.0 C A:TYR195 3.9 39.6 1.0 OD2 A:ASP198 4.0 36.7 1.0 N A:GLY196 4.0 34.8 1.0 O A:TYR195 4.0 36.0 1.0 N A:ASP198 4.1 34.0 1.0 O A:ALA161 4.1 45.1 1.0 O A:GLY192 4.3 36.1 1.0 CA A:GLY196 4.3 36.0 1.0 N A:ASN194 4.3 41.3 1.0 CA A:ASP162 4.4 39.3 1.0 CA A:ASN194 4.4 50.3 1.0 N A:GLY197 4.4 31.4 1.0 N A:TYR195 4.4 38.2 1.0 CA A:TYR195 4.4 36.7 1.0 N A:ILE163 4.5 42.5 1.0 CA A:GLY197 4.5 34.7 1.0 C A:GLY197 4.5 38.2 1.0 CB A:ASP198 4.6 37.2 1.0 N A:MET164 4.7 41.9 1.0 CA A:ILE163 4.7 31.4 1.0 C A:PRO193 4.7 40.6 1.0 CA A:ASP198 4.7 31.4 1.0 O A:HOH449 4.7 66.0 1.0 O A:HOH437 4.8 43.1 1.0 O A:PRO193 4.9 36.8 1.0

Calcium binding site 3 out of 3 in the Mmp-13 in Complex with the Peptide Imisf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-13 in Complex with the Peptide Imisf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:89.9 occ:1.00 OD2 A:ASP128 2.5 79.3 1.0 O A:GLU205 2.5 52.6 1.0 O A:ASP203 2.6 58.6 1.0 OD1 A:ASP128 2.9 88.4 1.0 CG A:ASP128 3.0 83.0 1.0 OD1 A:ASP203 3.1 69.4 1.0 C A:GLU205 3.6 54.7 1.0 C A:ASP203 3.6 54.1 1.0 OG1 A:THR126 4.0 63.2 1.0 CG A:ASP203 4.0 70.1 1.0 CA A:THR206 4.3 58.1 1.0 CA A:ASP203 4.3 55.0 1.0 N A:THR206 4.3 56.9 1.0 N A:GLU205 4.3 49.6 1.0 C A:ASP204 4.4 53.8 1.0 CB A:ASP128 4.5 75.8 1.0 N A:ASP204 4.6 47.6 1.0 CA A:GLU205 4.6 54.3 1.0 CB A:ASP203 4.6 57.6 1.0 CA A:ASP204 4.7 49.0 1.0 CD1 A:TRP207 4.7 54.3 1.0 O A:ASP204 4.8 59.9 1.0 N A:TRP207 4.8 50.7 1.0 OD2 A:ASP203 4.9 75.3 1.0 CD A:PRO127 5.0 61.2 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