Zinc in PDB 3lka: Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide

All present enzymatic activity of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide:
3.4.24.65;

The structure of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide, PDB code: 3lka was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.91 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.566, 60.194, 54.215, 90.00, 115.09, 90.00
R / Rfree (%)	16.9 / 21

The structure of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide (pdb code 3lka). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide, PDB code: 3lka:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn264 b:9.0 occ:1.00 NE2 A:HIS228 2.1 8.0 1.0 NE2 A:HIS222 2.1 3.9 1.0 NE2 A:HIS218 2.1 3.7 1.0 O A:HAE269 2.2 19.5 1.0 O2 A:HAE269 2.3 21.2 1.0 O A:HOH305 2.8 16.3 0.4 CD2 A:HIS218 3.0 2.8 1.0 CE1 A:HIS228 3.0 9.5 1.0 CD2 A:HIS222 3.0 3.2 1.0 C2 A:HAE269 3.1 22.1 1.0 N A:HAE269 3.1 18.8 1.0 CD2 A:HIS228 3.1 8.7 1.0 CE1 A:HIS222 3.2 3.5 1.0 CE1 A:HIS218 3.2 5.1 1.0 O A:HOH10 4.1 4.0 1.0 ND1 A:HIS228 4.1 7.9 1.0 N1 A:M4S1 4.1 19.9 1.0 OE1 A:GLU219 4.2 2.8 1.0 CG A:HIS218 4.2 5.1 1.0 CG A:HIS228 4.2 9.2 1.0 CG A:HIS222 4.2 5.0 1.0 ND1 A:HIS222 4.3 4.0 1.0 ND1 A:HIS218 4.3 7.1 1.0 O A:HOH97 4.4 18.5 1.0 C1 A:HAE269 4.6 21.5 1.0 OE2 A:GLU219 4.7 4.5 1.0 CD A:GLU219 4.9 3.8 1.0 CE A:MET236 4.9 7.8 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Mmp-12 Complexed with Hydroxamic Acid and Paramethoxy-Sulfonyl Amide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn265 b:11.7 occ:1.00 OD1 A:ASP170 1.9 8.2 0.7 CE1 A:HIS183 2.0 10.8 1.0 NE2 A:HIS168 2.1 7.6 1.0 ND1 A:HIS196 2.2 6.0 1.0 NE2 A:HIS183 2.7 15.6 1.0 CG A:ASP170 2.9 11.7 0.7 CD2 A:HIS168 3.0 8.3 1.0 CE1 A:HIS168 3.1 8.4 1.0 ND1 A:HIS183 3.1 14.0 1.0 OD2 A:ASP170 3.2 9.6 0.7 CG A:HIS196 3.2 6.9 1.0 CE1 A:HIS196 3.2 7.5 1.0 CB A:HIS196 3.4 5.8 1.0 CD2 A:HIS183 4.0 13.0 1.0 CG A:HIS168 4.1 9.8 1.0 ND1 A:HIS168 4.1 9.3 1.0 CG A:HIS183 4.2 8.8 1.0 O A:HIS172 4.2 16.9 1.0 CB A:ASP170 4.2 14.5 0.7 NE2 A:HIS196 4.3 8.7 1.0 CD2 A:HIS196 4.3 6.2 1.0 CE2 A:PHE185 4.5 14.2 1.0 CB A:HIS172 4.5 18.3 1.0 CZ A:PHE185 4.6 14.5 1.0 CZ A:PHE174 4.7 6.8 1.0 CE1 A:PHE174 4.8 7.3 1.0 C A:HIS172 4.9 16.5 1.0 CA A:HIS196 5.0 6.0 1.0

V.Borsi, V.Calderone, M.Fragai, C.Luchinat, N.Sarti. Entropic Contribution to the Linking Coefficient in Fragment Based Drug Design: A Case Study. J.Med.Chem. V. 53 4285 2010.
ISSN: ISSN 0022-2623
PubMed: 20415416
DOI: 10.1021/JM901723Z