Zinc in PDB 2d1o: Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor

All present enzymatic activity of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor:
3.4.24.17;

The structure of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1o was solved by T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.360, 50.950, 80.790, 90.00, 105.00, 90.00
R / Rfree (%)	18.3 / 20.6

The structure of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor (pdb code 2d1o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn257 b:14.9 occ:1.00 O33 A:FA41001 2.1 18.3 1.0 NE2 A:HIS211 2.1 10.5 1.0 NE2 A:HIS205 2.2 10.4 1.0 NE2 A:HIS201 2.2 12.3 1.0 O32 A:FA41001 2.3 14.3 1.0 C21 A:FA41001 2.8 19.5 1.0 N22 A:FA41001 2.9 17.4 1.0 CD2 A:HIS201 3.0 11.9 1.0 CD2 A:HIS211 3.1 10.8 1.0 CE1 A:HIS205 3.1 10.0 1.0 CD2 A:HIS205 3.1 9.9 1.0 CE1 A:HIS211 3.1 11.7 1.0 CE1 A:HIS201 3.3 10.8 1.0 O A:HOH1005 4.0 17.6 1.0 OE2 A:GLU202 4.2 12.7 1.0 CG A:HIS201 4.2 11.3 1.0 ND1 A:HIS211 4.2 11.3 1.0 CG A:HIS211 4.2 12.0 1.0 ND1 A:HIS205 4.2 10.7 1.0 CG A:HIS205 4.3 9.8 1.0 C18 A:FA41001 4.3 21.1 1.0 ND1 A:HIS201 4.3 11.5 1.0 CB A:PRO221 4.9 15.7 1.0 C20 A:FA41001 4.9 23.3 1.0 N17 A:FA41001 4.9 21.2 1.0

Zinc binding site 2 out of 4 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn258 b:16.4 occ:1.00 OD2 A:ASP153 2.0 18.0 1.0 NE2 A:HIS166 2.0 16.3 1.0 NE2 A:HIS151 2.0 18.0 1.0 ND1 A:HIS179 2.1 14.4 1.0 CE1 A:HIS166 2.7 18.0 1.0 CG A:ASP153 2.9 19.5 1.0 CD2 A:HIS151 3.0 17.1 1.0 CE1 A:HIS151 3.0 17.2 1.0 CE1 A:HIS179 3.1 14.8 1.0 OD1 A:ASP153 3.2 18.1 1.0 CG A:HIS179 3.2 14.8 1.0 CD2 A:HIS166 3.2 16.6 1.0 CB A:HIS179 3.5 14.1 1.0 ND1 A:HIS166 4.0 17.2 1.0 OH A:TYR168 4.0 22.1 1.0 ND1 A:HIS151 4.1 17.6 1.0 CG A:HIS151 4.1 18.5 1.0 CG A:HIS166 4.2 16.3 1.0 NE2 A:HIS179 4.2 14.7 1.0 O A:TYR155 4.2 24.4 1.0 CD2 A:HIS179 4.3 14.6 1.0 CB A:ASP153 4.3 22.2 1.0 CZ A:PHE157 4.5 21.0 1.0 CE2 A:PHE157 4.6 21.1 1.0 CE2 A:TYR168 4.7 20.0 1.0 CZ A:TYR168 4.8 20.3 1.0 CA A:HIS179 5.0 13.4 1.0

Zinc binding site 3 out of 4 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn262 b:16.3 occ:1.00 O33 B:FA41002 2.0 15.8 1.0 NE2 B:HIS211 2.1 15.5 1.0 NE2 B:HIS201 2.2 12.8 1.0 NE2 B:HIS205 2.2 15.2 1.0 O32 B:FA41002 2.2 12.5 1.0 C21 B:FA41002 2.7 17.0 1.0 N22 B:FA41002 2.8 14.2 1.0 CD2 B:HIS201 3.0 12.4 1.0 CD2 B:HIS205 3.0 13.7 1.0 CD2 B:HIS211 3.1 15.7 1.0 CE1 B:HIS211 3.2 15.9 1.0 CE1 B:HIS201 3.2 12.2 1.0 CE1 B:HIS205 3.3 15.0 1.0 O B:HOH1006 4.0 17.9 1.0 C18 B:FA41002 4.2 19.7 1.0 CG B:HIS201 4.2 12.5 1.0 CG B:HIS205 4.2 15.2 1.0 CG B:HIS211 4.2 16.3 1.0 OE2 B:GLU202 4.3 15.7 1.0 ND1 B:HIS211 4.3 16.3 1.0 ND1 B:HIS201 4.3 12.9 1.0 ND1 B:HIS205 4.3 14.1 1.0 C20 B:FA41002 4.7 23.6 1.0 N17 B:FA41002 4.8 19.5 1.0 CB B:PRO221 4.9 16.0 1.0

Zinc binding site 4 out of 4 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn263 b:17.6 occ:1.00 OD2 B:ASP153 2.0 20.7 1.0 NE2 B:HIS151 2.1 17.1 1.0 NE2 B:HIS166 2.1 16.9 1.0 ND1 B:HIS179 2.1 14.8 1.0 CD2 B:HIS151 3.0 16.2 1.0 CE1 B:HIS166 3.0 16.2 1.0 CG B:ASP153 3.0 21.5 1.0 CE1 B:HIS179 3.1 15.7 1.0 CG B:HIS179 3.2 15.2 1.0 CD2 B:HIS166 3.2 16.1 1.0 CE1 B:HIS151 3.2 17.6 1.0 OD1 B:ASP153 3.4 19.7 1.0 CB B:HIS179 3.5 14.1 1.0 OH B:TYR168 3.9 26.1 1.0 O B:TYR155 4.1 23.4 1.0 ND1 B:HIS166 4.1 16.1 1.0 CG B:HIS151 4.2 17.6 1.0 NE2 B:HIS179 4.2 16.5 1.0 ND1 B:HIS151 4.2 17.2 1.0 CG B:HIS166 4.2 15.3 1.0 CD2 B:HIS179 4.3 15.0 1.0 CB B:ASP153 4.4 23.2 1.0 CZ B:PHE157 4.6 18.5 1.0 CE2 B:TYR168 4.7 23.1 1.0 CE2 B:PHE157 4.7 18.2 1.0 CZ B:TYR168 4.7 24.3 1.0 CA B:HIS179 5.0 14.0 1.0

T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka. Crystal Structures of the Catalytic Domain of Human Stromelysin-1 (Mmp-3) and Collagenase-3 (Mmp-13) with A Hydroxamic Acid Inhibitor Sm-25453 Biochem.Biophys.Res.Commun. V. 344 315 2006.
ISSN: ISSN 0006-291X
PubMed: 16603129
DOI: 10.1016/J.BBRC.2006.03.098