Zinc in PDB 1d8m: Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor

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

The structure of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor, PDB code: 1d8m was solved by S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.960, 78.590, 105.930, 90.00, 90.00, 90.00
R / Rfree (%)	27.7 / 31.5

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

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor (pdb code 1d8m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor, PDB code: 1d8m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.8 occ:1.00 NE2 A:HIS201 2.0 2.0 1.0 NE2 A:HIS205 2.3 2.0 1.0 NE2 A:HIS211 2.4 4.1 1.0 CD2 A:HIS201 2.8 2.0 1.0 CE1 A:HIS201 3.2 2.5 1.0 CD2 A:HIS205 3.2 2.0 1.0 CE1 A:HIS211 3.4 2.0 1.0 CD2 A:HIS211 3.4 4.4 1.0 CE1 A:HIS205 3.4 2.7 1.0 CG A:HIS201 4.1 2.0 1.0 ND1 A:HIS201 4.2 2.0 1.0 CG A:HIS205 4.4 2.0 1.0 ND1 A:HIS205 4.4 2.0 1.0 ND1 A:HIS211 4.5 2.0 1.0 OE2 A:GLU202 4.5 2.0 1.0 CG A:HIS211 4.5 2.9 1.0 OE1 A:GLU202 5.0 7.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.8 occ:1.00 NE2 A:HIS151 2.1 2.0 1.0 NE2 A:HIS166 2.1 2.0 1.0 ND1 A:HIS179 2.1 7.4 1.0 OD2 A:ASP153 2.2 15.8 1.0 CE1 A:HIS166 2.8 2.0 1.0 CG A:ASP153 3.0 9.3 1.0 CE1 A:HIS179 3.0 7.6 1.0 CD2 A:HIS151 3.0 2.0 1.0 OD1 A:ASP153 3.0 13.7 1.0 CE1 A:HIS151 3.1 2.0 1.0 CG A:HIS179 3.2 4.7 1.0 CD2 A:HIS166 3.3 2.0 1.0 CB A:HIS179 3.6 3.7 1.0 OH A:TYR168 3.9 6.1 1.0 O A:TYR155 4.0 2.7 1.0 ND1 A:HIS166 4.0 2.0 1.0 NE2 A:HIS179 4.1 2.0 1.0 CG A:HIS151 4.1 2.8 1.0 ND1 A:HIS151 4.1 2.0 1.0 CD2 A:HIS179 4.2 2.0 1.0 CG A:HIS166 4.3 2.0 1.0 CB A:ASP153 4.4 6.0 1.0 CE1 A:TYR168 4.5 2.0 1.0 CZ A:TYR168 4.7 2.0 1.0 O A:HOH12 4.7 2.0 1.0 CZ A:PHE157 4.7 2.0 1.0 C A:TYR155 4.9 5.8 1.0 CB A:TYR155 5.0 10.9 1.0 CE1 A:PHE157 5.0 2.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:6.5 occ:1.00 OA B:BBH901 1.8 20.0 1.0 OB B:BBH901 2.0 17.1 1.0 NE2 B:HIS705 2.2 2.0 1.0 NE2 B:HIS701 2.2 2.5 1.0 NE2 B:HIS711 2.6 8.2 1.0 NA B:BBH901 2.6 15.5 1.0 C B:BBH901 2.7 16.8 1.0 CD2 B:HIS701 2.9 7.4 1.0 CD2 B:HIS705 3.0 2.0 1.0 CE1 B:HIS705 3.2 5.1 1.0 CE1 B:HIS701 3.4 2.0 1.0 CE1 B:HIS711 3.5 5.2 1.0 CD2 B:HIS711 3.6 6.3 1.0 OE2 B:GLU702 3.8 2.0 1.0 C13 B:BBH901 4.2 17.6 1.0 CG B:HIS701 4.2 2.0 1.0 CG B:HIS705 4.2 2.0 1.0 ND1 B:HIS705 4.3 3.0 1.0 ND1 B:HIS701 4.4 2.0 1.0 C6 B:BBH901 4.6 8.2 1.0 ND1 B:HIS711 4.6 6.2 1.0 CD B:GLU702 4.7 2.0 1.0 CG B:HIS711 4.7 4.4 1.0 C5 B:BBH901 4.8 10.5 1.0 C14 B:BBH901 4.8 17.0 1.0 OE1 B:GLU702 4.8 2.0 1.0 N12 B:BBH901 4.8 15.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:9.7 occ:1.00 NE2 B:HIS651 2.0 2.0 1.0 NE2 B:HIS666 2.0 2.0 1.0 ND1 B:HIS679 2.1 3.7 1.0 OD2 B:ASP653 2.2 7.9 1.0 CD2 B:HIS651 2.8 3.6 1.0 CE1 B:HIS666 3.0 2.0 1.0 CG B:HIS679 3.0 2.7 1.0 CE1 B:HIS679 3.0 2.0 1.0 CD2 B:HIS666 3.1 3.6 1.0 CG B:ASP653 3.1 7.8 1.0 CE1 B:HIS651 3.1 2.0 1.0 CB B:HIS679 3.4 2.0 1.0 OD1 B:ASP653 3.5 6.8 1.0 CG B:HIS651 4.0 4.6 1.0 O B:TYR655 4.0 8.8 1.0 OH B:TYR668 4.0 2.8 1.0 NE2 B:HIS679 4.1 2.0 1.0 ND1 B:HIS666 4.1 2.3 1.0 CD2 B:HIS679 4.1 2.0 1.0 ND1 B:HIS651 4.1 2.0 1.0 CG B:HIS666 4.2 2.0 1.0 CE1 B:PHE657 4.4 2.0 1.0 CZ B:PHE657 4.4 2.0 1.0 CB B:ASP653 4.4 4.8 1.0 CE1 B:TYR668 4.8 2.0 1.0 CA B:HIS679 4.9 2.0 1.0 CZ B:TYR668 4.9 2.0 1.0

S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling. Heterocycle-Based Mmp Inhibitors with P2' Substituents. Bioorg.Med.Chem.Lett. V. 11 1009 2001.
ISSN: ISSN 0960-894X
PubMed: 11327577
DOI: 10.1016/S0960-894X(01)00137-8