Zinc in PDB 4ja1: Structure of MMP3 Complexed with A Platinum-Based Inhibitor

All present enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor:
3.4.24.17;

The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor, PDB code: 4ja1 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)	34.22 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.119, 77.615, 106.048, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.4

The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor also contains other interesting chemical elements:

Platinum	(Pt)	3 atoms
Chlorine	(Cl)	4 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor (pdb code 4ja1). 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 A Platinum-Based Inhibitor, PDB code: 4ja1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based 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 A Platinum-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.7 occ:1.00 NE2 A:HIS201 1.9 17.2 1.0 NE2 A:HIS205 2.1 11.4 1.0 NE2 A:HIS211 2.1 28.7 1.0 CE1 A:HIS201 2.8 19.3 1.0 CE1 A:HIS205 2.9 14.8 1.0 CD2 A:HIS211 3.0 26.1 1.0 CD2 A:HIS201 3.0 18.7 1.0 CE1 A:HIS211 3.1 29.7 1.0 CD2 A:HIS205 3.2 12.1 1.0 ND1 A:HIS201 3.9 18.7 1.0 CG A:HIS201 4.1 15.8 1.0 ND1 A:HIS205 4.1 14.5 1.0 CG A:HIS211 4.1 26.3 1.0 ND1 A:HIS211 4.1 24.8 1.0 CG A:HIS205 4.2 13.6 1.0 CE A:MET219 4.7 16.0 1.0 OE2 A:GLU202 4.7 17.0 1.0 CA A:PRO221 4.8 39.5 1.0 OE1 A:GLU202 4.9 20.4 1.0 O A:PRO221 5.0 44.6 1.0

Zinc binding site 2 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based 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 A Platinum-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.8 occ:1.00 NE2 A:HIS166 2.0 14.4 1.0 NE2 A:HIS151 2.0 14.5 1.0 ND1 A:HIS179 2.0 14.0 1.0 OD2 A:ASP153 2.3 25.6 1.0 CE1 A:HIS166 2.9 13.3 1.0 CE1 A:HIS179 3.0 14.9 1.0 CE1 A:HIS151 3.0 18.5 1.0 CD2 A:HIS151 3.0 17.1 1.0 CD2 A:HIS166 3.0 12.9 1.0 CG A:HIS179 3.1 10.8 1.0 CG A:ASP153 3.2 22.4 1.0 OD1 A:ASP153 3.4 20.4 1.0 CB A:HIS179 3.5 11.6 1.0 ND1 A:HIS166 4.0 13.0 1.0 ND1 A:HIS151 4.1 17.9 1.0 NE2 A:HIS179 4.1 14.1 1.0 CG A:HIS166 4.1 13.2 1.0 CG A:HIS151 4.2 18.6 1.0 CD2 A:HIS179 4.2 12.0 1.0 O A:TYR155 4.3 20.0 1.0 OH A:TYR168 4.3 19.1 1.0 CB A:ASP153 4.5 22.3 1.0 CE1 A:TYR168 4.5 16.3 1.0 CZ A:PHE157 4.7 12.4 1.0 CE2 A:PHE157 4.7 9.7 1.0 CZ A:TYR168 4.9 17.9 1.0 CA A:HIS179 5.0 11.3 1.0

Zinc binding site 3 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based 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 A Platinum-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:27.0 occ:1.00 NE2 B:HIS205 2.1 20.9 1.0 NE2 B:HIS201 2.1 20.7 1.0 O5 B:NGH306 2.2 38.1 1.0 NE2 B:HIS211 2.3 29.0 1.0 O4 B:NGH306 2.3 34.1 1.0 C11 B:NGH306 2.9 38.7 1.0 N1 B:NGH306 3.0 37.8 1.0 CD2 B:HIS201 3.0 20.4 1.0 CD2 B:HIS205 3.0 20.7 1.0 CD2 B:HIS211 3.1 28.3 1.0 CE1 B:HIS205 3.1 20.0 1.0 CE1 B:HIS201 3.2 21.5 1.0 CE1 B:HIS211 3.4 31.6 1.0 O B:HOH437 4.0 27.4 1.0 ND1 B:HIS205 4.2 21.9 1.0 CG B:HIS205 4.2 20.2 1.0 CG B:HIS201 4.2 20.4 1.0 ND1 B:HIS201 4.3 19.6 1.0 CG B:HIS211 4.3 29.6 1.0 OE2 B:GLU202 4.3 23.8 1.0 C10 B:NGH306 4.4 40.2 1.0 ND1 B:HIS211 4.4 32.2 1.0 C5 B:NGH306 4.7 34.6 1.0 C4 B:NGH306 4.8 32.5 1.0 CB B:PRO221 4.9 34.2 1.0 N B:NGH306 4.9 40.6 1.0 CD B:GLU202 5.0 21.9 1.0 OE1 B:GLU202 5.0 24.2 1.0

Zinc binding site 4 out of 4 in the Structure of MMP3 Complexed with A Platinum-Based 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 A Platinum-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.8 occ:0.99 NE2 B:HIS166 1.9 19.5 1.0 OD2 B:ASP153 2.0 24.8 1.0 NE2 B:HIS151 2.1 19.3 1.0 ND1 B:HIS179 2.1 19.0 1.0 CE1 B:HIS166 2.8 20.4 1.0 CG B:ASP153 2.9 23.1 1.0 CD2 B:HIS166 3.0 21.6 1.0 CE1 B:HIS151 3.1 18.9 1.0 CE1 B:HIS179 3.1 18.7 1.0 CG B:HIS179 3.1 18.6 1.0 CD2 B:HIS151 3.2 19.8 1.0 OD1 B:ASP153 3.2 19.8 1.0 CB B:HIS179 3.5 16.4 1.0 ND1 B:HIS166 4.0 19.1 1.0 OH B:TYR168 4.0 25.6 1.0 CG B:HIS166 4.1 19.2 1.0 CB B:ASP153 4.2 23.1 1.0 ND1 B:HIS151 4.2 19.3 1.0 NE2 B:HIS179 4.2 16.3 1.0 O B:TYR155 4.2 26.2 1.0 CG B:HIS151 4.3 22.3 1.0 CD2 B:HIS179 4.3 17.8 1.0 CE1 B:TYR168 4.5 25.2 1.0 CE2 B:PHE157 4.6 20.0 1.0 CZ B:PHE157 4.7 21.8 1.0 CZ B:TYR168 4.7 27.3 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