Zinc in PDB 1g49: A Carboxylic Acid Based Inhibitor in Complex with MMP3

All present enzymatic activity of A Carboxylic Acid Based Inhibitor in Complex with MMP3:
3.4.24.17;

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1g49 was solved by M.G.Natchus, R.G.Bookland, B.De, N.G.Almstead, S.Pikul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.668, 77.112, 106.145, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 25.3

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the A Carboxylic Acid Based Inhibitor in Complex with MMP3 (pdb code 1g49). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1g49:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.1 occ:1.00 NE2 A:HIS205 2.1 12.5 1.0 NE2 A:HIS201 2.1 15.2 1.0 NE2 A:HIS211 2.4 26.3 1.0 CD2 A:HIS201 3.0 12.0 1.0 CE1 A:HIS205 3.1 12.2 1.0 CD2 A:HIS205 3.1 12.6 1.0 CD2 A:HIS211 3.1 26.2 1.0 CE1 A:HIS201 3.2 14.5 1.0 CE1 A:HIS211 3.4 23.7 1.0 CG A:HIS201 4.2 14.4 1.0 ND1 A:HIS205 4.2 11.5 1.0 CG A:HIS205 4.2 14.2 1.0 ND1 A:HIS201 4.3 14.6 1.0 CG A:HIS211 4.3 24.1 1.0 ND1 A:HIS211 4.3 24.0 1.0 CE A:MET219 4.7 12.0 1.0 O A:HOH364 4.7 20.8 1.0 OE2 A:GLU202 4.7 14.2 1.0 OE1 A:GLU202 4.9 18.1 1.0

Zinc binding site 2 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.9 occ:1.00 ND1 A:HIS179 2.0 16.1 1.0 OD2 A:ASP153 2.0 14.6 1.0 NE2 A:HIS166 2.0 13.4 1.0 NE2 A:HIS151 2.1 15.4 1.0 CE1 A:HIS179 2.9 13.5 1.0 CD2 A:HIS151 3.0 15.4 1.0 CG A:ASP153 3.0 18.2 1.0 CG A:HIS179 3.0 14.7 1.0 CD2 A:HIS166 3.0 12.9 1.0 CE1 A:HIS166 3.0 11.7 1.0 CE1 A:HIS151 3.1 15.9 1.0 OD1 A:ASP153 3.3 16.8 1.0 CB A:HIS179 3.4 14.3 1.0 NE2 A:HIS179 4.0 14.3 1.0 CD2 A:HIS179 4.1 14.7 1.0 ND1 A:HIS166 4.1 12.2 1.0 CG A:HIS151 4.1 16.0 1.0 CG A:HIS166 4.2 13.7 1.0 ND1 A:HIS151 4.2 16.0 1.0 CB A:ASP153 4.3 18.6 1.0 OH A:TYR168 4.4 15.5 1.0 O A:TYR155 4.4 16.0 1.0 CE1 A:TYR168 4.6 13.0 1.0 CZ A:PHE157 4.7 16.3 1.0 CE1 A:PHE157 4.8 16.0 1.0 CA A:HIS179 4.9 14.4 1.0 O A:HOH319 4.9 14.3 1.0 CZ A:TYR168 4.9 15.7 1.0

Zinc binding site 3 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:24.6 occ:1.00 OA B:111901 1.9 38.1 1.0 NE2 B:HIS711 2.1 26.7 1.0 NE2 B:HIS701 2.2 23.6 1.0 OB B:111901 2.3 37.0 1.0 NE2 B:HIS705 2.3 19.0 1.0 NA B:111901 2.8 38.4 1.0 C20 B:111901 2.9 38.7 1.0 CD2 B:HIS711 2.9 24.0 1.0 CD2 B:HIS701 3.0 21.5 1.0 CD2 B:HIS705 3.1 19.6 1.0 CE1 B:HIS711 3.3 23.7 1.0 CE1 B:HIS701 3.4 21.3 1.0 CE1 B:HIS705 3.4 21.2 1.0 O B:HOH88 4.1 20.4 1.0 CG B:HIS711 4.1 24.5 1.0 CG B:HIS701 4.3 21.3 1.0 ND1 B:HIS711 4.3 24.3 1.0 OE2 B:GLU702 4.3 19.5 1.0 CG B:HIS705 4.3 19.2 1.0 ND1 B:HIS701 4.4 20.5 1.0 C8 B:111901 4.4 38.0 1.0 ND1 B:HIS705 4.4 19.7 1.0 C9 B:111901 4.8 38.7 1.0 CE B:MET719 4.9 19.0 1.0 C1 B:111901 5.0 36.1 1.0 C17 B:111901 5.0 40.4 1.0 C6 B:111901 5.0 35.7 1.0 OE1 B:GLU702 5.0 20.1 1.0

Zinc binding site 4 out of 4 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:17.4 occ:1.00 NE2 B:HIS651 2.0 15.3 1.0 NE2 B:HIS666 2.0 16.9 1.0 ND1 B:HIS679 2.1 15.5 1.0 OD2 B:ASP653 2.2 19.2 1.0 CE1 B:HIS666 2.9 17.1 1.0 CG B:ASP653 2.9 17.9 1.0 CD2 B:HIS651 3.0 16.2 1.0 CE1 B:HIS651 3.1 15.6 1.0 CE1 B:HIS679 3.1 11.9 1.0 CG B:HIS679 3.1 14.1 1.0 CD2 B:HIS666 3.2 17.3 1.0 OD1 B:ASP653 3.2 15.1 1.0 CB B:HIS679 3.4 14.1 1.0 OH B:TYR668 4.0 16.4 1.0 ND1 B:HIS666 4.1 17.5 1.0 CG B:HIS651 4.1 16.0 1.0 ND1 B:HIS651 4.1 16.1 1.0 O B:TYR655 4.2 16.4 1.0 NE2 B:HIS679 4.2 10.5 1.0 CG B:HIS666 4.2 16.4 1.0 CD2 B:HIS679 4.2 13.8 1.0 CB B:ASP653 4.3 17.4 1.0 CE1 B:TYR668 4.6 16.1 1.0 CZ B:PHE657 4.6 15.8 1.0 CE1 B:PHE657 4.7 14.0 1.0 CZ B:TYR668 4.8 18.4 1.0 CA B:HIS679 5.0 14.7 1.0

M.G.Natchus, R.G.Bookland, B.De, N.G.Almstead, S.Pikul. Development of New Hydroxamate Matrix Metalloproteinase Inhibitors Derived From Functionalized 4-Aminoprolines. J.Med.Chem. V. 43 4948 2000.
ISSN: ISSN 0022-2623
PubMed: 11150165
DOI: 10.1021/JM000246E