Zinc in PDB 4g9l: Structure of MMP3 Complexed with Nngh Inhibitor.

All present enzymatic activity of Structure of MMP3 Complexed with Nngh Inhibitor.:
3.4.24.17;

The structure of Structure of MMP3 Complexed with Nngh Inhibitor., PDB code: 4g9l was solved by B.D.Belviso, F.Arnesano, V.Calderone, R.Caliandro, G.Natile, D.Siliqi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.81 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.990, 78.840, 106.730, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 27

The structure of Structure of MMP3 Complexed with Nngh Inhibitor. also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Structure of MMP3 Complexed with Nngh Inhibitor. (pdb code 4g9l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of MMP3 Complexed with Nngh Inhibitor., PDB code: 4g9l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of MMP3 Complexed with Nngh Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of MMP3 Complexed with Nngh Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.6 occ:1.00 OD2 A:ASP153 2.0 17.6 1.0 NE2 A:HIS166 2.0 7.8 1.0 ND1 A:HIS179 2.0 5.7 1.0 NE2 A:HIS151 2.1 5.6 1.0 CG A:ASP153 2.9 17.5 1.0 CE1 A:HIS166 2.9 4.7 1.0 CE1 A:HIS179 2.9 7.5 1.0 CD2 A:HIS151 3.0 11.4 1.0 CD2 A:HIS166 3.1 11.8 1.0 OD1 A:ASP153 3.1 16.5 1.0 CE1 A:HIS151 3.1 6.8 1.0 CG A:HIS179 3.1 7.7 1.0 CB A:HIS179 3.6 9.4 1.0 ND1 A:HIS166 4.1 8.2 1.0 NE2 A:HIS179 4.1 8.2 1.0 CG A:HIS151 4.1 12.4 1.0 CG A:HIS166 4.2 7.4 1.0 ND1 A:HIS151 4.2 13.0 1.0 CD2 A:HIS179 4.2 10.5 1.0 O A:TYR155 4.2 12.1 1.0 OH A:TYR168 4.3 14.7 1.0 CB A:ASP153 4.3 16.1 1.0 CE1 A:TYR168 4.5 14.3 1.0 CZ A:PHE157 4.6 6.8 1.0 CE2 A:PHE157 4.8 4.0 1.0 CZ A:TYR168 4.9 14.1 1.0

Zinc binding site 2 out of 4 in the Structure of MMP3 Complexed with Nngh Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of MMP3 Complexed with Nngh Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.3 occ:1.00 OXT B:THR255 1.7 25.1 1.0 NE2 A:HIS201 2.0 10.2 1.0 NE2 A:HIS205 2.1 18.4 1.0 NE2 A:HIS211 2.1 15.1 1.0 C B:THR255 2.6 24.2 1.0 O B:THR255 2.7 25.3 1.0 CE1 A:HIS201 2.9 9.0 1.0 CD2 A:HIS211 2.9 14.1 1.0 CE1 A:HIS205 3.0 14.9 1.0 CD2 A:HIS201 3.0 4.2 1.0 CE1 A:HIS211 3.1 18.9 1.0 CD2 A:HIS205 3.1 8.4 1.0 OE1 B:GLU254 3.8 39.8 1.0 CA B:THR255 4.0 23.4 1.0 ND1 A:HIS201 4.0 6.2 1.0 CG A:HIS201 4.1 6.8 1.0 ND1 A:HIS205 4.1 10.3 1.0 CG A:HIS211 4.1 13.5 1.0 ND1 A:HIS211 4.2 16.9 1.0 CG A:HIS205 4.2 10.2 1.0 N B:THR255 4.3 20.5 1.0 O A:HOH431 4.6 28.1 1.0 C B:GLU254 4.7 20.4 1.0 CE A:MET219 4.7 6.1 1.0 O B:GLU254 4.7 15.7 1.0 OE2 A:GLU202 4.9 10.5 1.0 CD B:GLU254 4.9 34.9 1.0 CB B:GLU254 5.0 21.1 1.0 CB B:THR255 5.0 22.8 1.0

Zinc binding site 3 out of 4 in the Structure of MMP3 Complexed with Nngh Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of MMP3 Complexed with Nngh Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:23.6 occ:1.00 NE2 B:HIS211 2.0 24.1 1.0 NE2 B:HIS201 2.1 23.7 1.0 NE2 B:HIS205 2.2 25.8 1.0 O5 B:NGH307 2.3 41.0 1.0 O4 B:NGH307 2.3 42.3 1.0 C11 B:NGH307 3.0 43.5 1.0 CD2 B:HIS211 3.0 26.9 1.0 N1 B:NGH307 3.0 42.0 1.0 CE1 B:HIS211 3.0 26.9 1.0 CE1 B:HIS201 3.0 19.6 1.0 CD2 B:HIS201 3.1 20.0 1.0 CD2 B:HIS205 3.1 22.9 1.0 CE1 B:HIS205 3.2 22.9 1.0 ND1 B:HIS211 4.1 28.7 1.0 CG B:HIS211 4.1 28.2 1.0 OE2 B:GLU202 4.1 17.9 1.0 ND1 B:HIS201 4.2 18.0 1.0 CG B:HIS201 4.2 20.7 1.0 O B:HOH423 4.3 21.0 1.0 ND1 B:HIS205 4.3 22.8 1.0 CG B:HIS205 4.3 20.3 1.0 C10 B:NGH307 4.4 44.5 1.0 CD B:GLU202 4.9 20.0 1.0 OE1 B:GLU202 5.0 19.5 1.0 C5 B:NGH307 5.0 37.4 1.0

Zinc binding site 4 out of 4 in the Structure of MMP3 Complexed with Nngh Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of MMP3 Complexed with Nngh Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:15.7 occ:1.00 OD2 B:ASP153 2.0 11.9 1.0 NE2 B:HIS166 2.1 14.4 1.0 ND1 B:HIS179 2.1 13.6 1.0 NE2 B:HIS151 2.1 13.1 1.0 CG B:ASP153 2.9 14.2 1.0 CG B:HIS179 3.0 15.6 1.0 CD2 B:HIS151 3.0 19.4 1.0 CE1 B:HIS166 3.0 13.8 1.0 CD2 B:HIS166 3.1 14.5 1.0 CE1 B:HIS179 3.1 13.9 1.0 OD1 B:ASP153 3.1 11.4 1.0 CE1 B:HIS151 3.1 13.3 1.0 CB B:HIS179 3.3 12.1 1.0 OH B:TYR168 3.9 21.8 1.0 ND1 B:HIS166 4.2 15.3 1.0 O B:TYR155 4.2 18.8 1.0 CD2 B:HIS179 4.2 11.5 1.0 NE2 B:HIS179 4.2 13.4 1.0 CG B:HIS151 4.2 17.4 1.0 ND1 B:HIS151 4.2 13.9 1.0 CB B:ASP153 4.2 15.8 1.0 CG B:HIS166 4.2 15.0 1.0 CE1 B:TYR168 4.5 19.5 1.0 CZ B:PHE157 4.6 12.3 1.0 CE2 B:PHE157 4.7 9.7 1.0 CZ B:TYR168 4.7 19.8 1.0 CA B:HIS179 4.9 13.3 1.0

B.D.Belviso, R.Caliandro, D.Siliqi, V.Calderone, F.Arnesano, G.Natile. Structure of Matrix Metalloproteinase-3 with A Platinum-Based Inhibitor. Chem.Commun.(Camb.) V. 49 5492 2013.
ISSN: ISSN 1359-7345
PubMed: 23660647
DOI: 10.1039/C3CC41278D