Zinc in PDB 2ow9: Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor

The structure of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor, PDB code: 2ow9 was solved by A.G.Pavlovsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.71 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.764, 36.343, 71.684, 90.00, 93.53, 90.00
R / Rfree (%)	16.7 / 19.1

The structure of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Zinc atom in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor (pdb code 2ow9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor, PDB code: 2ow9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:11.4 occ:1.00 O A:HAE502 2.0 22.7 1.0 NE2 A:HIS201 2.1 11.3 1.0 NE2 A:HIS211 2.1 13.4 1.0 NE2 A:HIS205 2.1 12.0 1.0 O2 A:HAE502 2.5 25.5 1.0 O A:HOH836 2.7 20.3 1.0 N A:HAE502 2.9 24.4 1.0 CD2 A:HIS211 3.0 12.2 1.0 CD2 A:HIS201 3.0 10.4 1.0 CD2 A:HIS205 3.1 11.4 1.0 CE1 A:HIS201 3.1 11.1 1.0 C2 A:HAE502 3.1 25.8 1.0 CE1 A:HIS205 3.1 11.4 1.0 CE1 A:HIS211 3.1 14.4 1.0 OE2 A:GLU202 4.1 14.4 1.0 CG A:HIS211 4.2 13.3 1.0 ND1 A:HIS201 4.2 10.1 1.0 CG A:HIS201 4.2 10.7 1.0 O A:HOH813 4.2 32.0 1.0 ND1 A:HIS211 4.2 13.5 1.0 ND1 A:HIS205 4.2 10.5 1.0 CG A:HIS205 4.2 11.3 1.0 O A:HOH708 4.3 10.6 1.0 C1 A:HAE502 4.6 26.3 1.0 OE1 A:GLU202 4.6 14.1 1.0 CD A:GLU202 4.7 12.9 1.0 CE A:MET219 4.9 8.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:10.4 occ:1.00 NE2 A:HIS166 2.0 13.1 1.0 OD2 A:ASP153 2.0 12.4 1.0 NE2 A:HIS151 2.0 9.4 1.0 ND1 A:HIS179 2.1 10.4 1.0 CE1 A:HIS166 2.8 13.8 1.0 CD2 A:HIS151 2.9 9.5 1.0 CG A:ASP153 2.9 11.8 1.0 CE1 A:HIS179 3.1 10.1 1.0 CD2 A:HIS166 3.1 12.0 1.0 CG A:HIS179 3.1 9.2 1.0 OD1 A:ASP153 3.1 9.8 1.0 CE1 A:HIS151 3.1 9.5 1.0 CB A:HIS179 3.4 9.1 1.0 ND1 A:HIS166 4.0 14.0 1.0 CG A:HIS151 4.1 9.9 1.0 CG A:HIS166 4.1 11.3 1.0 ND1 A:HIS151 4.1 9.1 1.0 NE2 A:HIS179 4.2 10.1 1.0 O A:TYR155 4.2 13.3 1.0 CD2 A:HIS179 4.2 9.9 1.0 CB A:ASP153 4.3 11.8 1.0 CB A:TYR155 4.7 15.7 1.0 CE1 A:PHE168 4.8 13.1 1.0 CZ A:PHE157 4.8 9.8 1.0 O A:HOH859 4.8 26.6 1.0 CZ A:PHE168 4.9 13.3 1.0 CE2 A:PHE157 4.9 9.8 1.0 CA A:HIS179 4.9 8.6 1.0 C A:TYR155 4.9 13.6 1.0 O A:HOH710 5.0 9.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn606 b:19.0 occ:1.00 NE2 B:HIS205 2.1 15.9 1.0 NE2 B:HIS201 2.1 15.3 1.0 NE2 B:HIS211 2.1 19.3 1.0 O B:HAE502 2.4 49.3 1.0 N B:HAE502 2.7 49.2 1.0 CD2 B:HIS201 3.0 15.0 1.0 C2 B:HAE502 3.0 49.1 1.0 CD2 B:HIS205 3.1 14.9 1.0 CE1 B:HIS205 3.1 15.6 1.0 CD2 B:HIS211 3.1 19.4 1.0 CE1 B:HIS211 3.1 20.3 1.0 O2 B:HAE502 3.1 48.9 1.0 CE1 B:HIS201 3.1 15.2 1.0 C1 B:HAE502 4.2 48.7 1.0 ND1 B:HIS211 4.2 19.8 1.0 ND1 B:HIS205 4.2 15.8 1.0 CG B:HIS201 4.2 13.9 1.0 CG B:HIS211 4.2 19.6 1.0 CG B:HIS205 4.2 14.2 1.0 ND1 B:HIS201 4.2 15.3 1.0 OE2 B:GLU202 4.3 17.9 1.0 O B:HOH640 4.3 18.4 1.0 OE1 B:GLU202 4.7 18.0 1.0 CD B:GLU202 4.8 16.4 1.0 CE B:MET219 4.9 16.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of the MMP13 Catalytic Domain in Complex with Specific Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn607 b:13.7 occ:1.00 OD2 B:ASP153 1.9 15.1 1.0 NE2 B:HIS166 2.0 15.6 1.0 NE2 B:HIS151 2.0 12.3 1.0 ND1 B:HIS179 2.1 12.2 1.0 CG B:ASP153 2.9 13.8 1.0 CE1 B:HIS166 2.9 16.1 1.0 CD2 B:HIS151 2.9 12.4 1.0 CE1 B:HIS151 3.0 12.4 1.0 CD2 B:HIS166 3.1 15.1 1.0 CE1 B:HIS179 3.1 11.5 1.0 CG B:HIS179 3.1 12.0 1.0 OD1 B:ASP153 3.2 14.2 1.0 CB B:HIS179 3.4 11.9 1.0 ND1 B:HIS166 4.1 15.8 1.0 CG B:HIS151 4.1 11.5 1.0 ND1 B:HIS151 4.1 11.8 1.0 CG B:HIS166 4.2 15.0 1.0 NE2 B:HIS179 4.2 12.0 1.0 CD2 B:HIS179 4.2 11.3 1.0 CB B:ASP153 4.2 13.4 1.0 O B:TYR155 4.3 14.6 1.0 CZ B:PHE157 4.5 13.6 1.0 O B:HOH628 4.7 10.6 1.0 CE1 B:PHE168 4.7 17.9 1.0 O B:HOH655 4.7 22.2 1.0 CE2 B:PHE157 4.8 13.1 1.0 CZ B:PHE168 4.8 17.9 1.0 CA B:HIS179 4.9 11.5 1.0

A.R.Johnson, A.G.Pavlovsky, D.F.Ortwine, F.Prior, C.F.Man, D.A.Bornemeier, C.A.Banotai, W.T.Mueller, P.Mcconnell, C.Yan, V.Baragi, C.Lesch, W.H.Roark, M.Wilson, K.Datta, R.Guzman, H.K.Han, R.D.Dyer. Discovery and Characterization of A Novel Inhibitor of Matrix Metalloprotease-13 That Reduces Cartilage Damage in Vivo Without Joint Fibroplasia Side Effects. J.Biol.Chem. V. 282 27781 2007.
ISSN: ISSN 0021-9258
PubMed: 17623656
DOI: 10.1074/JBC.M703286200