Zinc in PDB 1bqo: Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors

All present enzymatic activity of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors:
3.4.24.17;

The structure of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors, PDB code: 1bqo was solved by S.Pikul, K.L.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, T.J.Rydel, C.M.Dunaway, F.Gu, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.900, 79.000, 106.100, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 29.4

The structure of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors (pdb code 1bqo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors, PDB code: 1bqo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.7 occ:1.00 NE2 A:HIS211 2.1 7.1 1.0 NE2 A:HIS201 2.3 4.5 1.0 NE2 A:HIS205 2.3 11.0 1.0 CD2 A:HIS201 3.0 2.9 1.0 CE1 A:HIS211 3.0 6.8 1.0 CD2 A:HIS211 3.1 11.8 1.0 CE1 A:HIS205 3.2 9.4 1.0 CD2 A:HIS205 3.3 5.9 1.0 CE1 A:HIS201 3.4 2.0 1.0 ND1 A:HIS211 4.2 9.1 1.0 CG A:HIS201 4.2 2.0 1.0 CG A:HIS211 4.3 11.7 1.0 ND1 A:HIS205 4.3 7.9 1.0 OE2 A:GLU202 4.3 6.1 1.0 ND1 A:HIS201 4.4 2.0 1.0 CG A:HIS205 4.4 6.6 1.0 OE1 A:GLU202 4.8 10.5 1.0 CE2 A:TYR223 4.9 11.8 1.0 CD A:GLU202 4.9 2.6 1.0

Zinc binding site 2 out of 4 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.6 occ:1.00 OD2 A:ASP153 2.0 9.0 1.0 NE2 A:HIS151 2.1 3.6 1.0 NE2 A:HIS166 2.1 11.8 1.0 ND1 A:HIS179 2.1 3.2 1.0 CE1 A:HIS179 3.0 3.6 1.0 CG A:ASP153 3.0 7.9 1.0 CD2 A:HIS151 3.0 8.5 1.0 CE1 A:HIS166 3.0 8.6 1.0 CE1 A:HIS151 3.1 5.8 1.0 CD2 A:HIS166 3.2 10.4 1.0 CG A:HIS179 3.2 6.4 1.0 OD1 A:ASP153 3.3 8.8 1.0 CB A:HIS179 3.6 10.4 1.0 O A:TYR155 4.1 5.2 1.0 NE2 A:HIS179 4.1 3.8 1.0 CG A:HIS151 4.2 11.1 1.0 ND1 A:HIS166 4.2 8.0 1.0 ND1 A:HIS151 4.2 7.8 1.0 CG A:HIS166 4.3 7.1 1.0 CD2 A:HIS179 4.3 3.1 1.0 CB A:ASP153 4.3 8.5 1.0 OH A:TYR168 4.5 8.1 1.0 CZ A:PHE157 4.5 2.0 1.0 CE1 A:TYR168 4.7 5.4 1.0 CE2 A:PHE157 4.9 2.0 1.0 CE1 A:PHE157 4.9 3.8 1.0

Zinc binding site 3 out of 4 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.2 occ:1.00 O26 B:N25401 1.9 30.0 1.0 O24 B:N25401 2.0 29.1 1.0 NE2 B:HIS201 2.3 2.0 1.0 NE2 B:HIS205 2.3 23.8 1.0 NE2 B:HIS211 2.3 15.5 1.0 C23 B:N25401 2.7 25.8 1.0 N25 B:N25401 2.8 24.0 1.0 CD2 B:HIS201 2.9 2.0 1.0 CD2 B:HIS205 3.2 21.5 1.0 CD2 B:HIS211 3.2 21.4 1.0 CE1 B:HIS205 3.3 20.9 1.0 CE1 B:HIS211 3.4 16.7 1.0 CE1 B:HIS201 3.4 2.0 1.0 OE2 B:GLU202 4.0 5.9 1.0 C28 B:N25401 4.1 35.7 1.0 C29 B:N25401 4.1 38.5 1.0 CG B:HIS201 4.2 2.0 1.0 C13 B:N25401 4.2 22.2 1.0 CG B:HIS205 4.3 18.9 1.0 ND1 B:HIS205 4.4 17.7 1.0 CG B:HIS211 4.4 20.4 1.0 ND1 B:HIS201 4.4 2.0 1.0 ND1 B:HIS211 4.4 21.0 1.0 C27 B:N25401 4.5 31.9 1.0 C30 B:N25401 4.5 39.0 1.0 OE1 B:GLU202 4.7 2.0 1.0 CD B:GLU202 4.8 4.3 1.0 C32 B:N25401 4.9 31.9 1.0 C6 B:N25401 4.9 10.5 1.0 C31 B:N25401 4.9 35.1 1.0 C1 B:N25401 4.9 12.1 1.0

Zinc binding site 4 out of 4 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:16.8 occ:1.00 OD2 B:ASP153 1.9 19.7 1.0 NE2 B:HIS166 2.0 3.7 1.0 ND1 B:HIS179 2.1 10.4 1.0 NE2 B:HIS151 2.2 3.8 1.0 CG B:ASP153 2.9 14.8 1.0 CE1 B:HIS179 2.9 8.9 1.0 CE1 B:HIS166 3.0 4.5 1.0 CE1 B:HIS151 3.0 7.2 1.0 CG B:HIS179 3.1 11.8 1.0 CD2 B:HIS166 3.1 3.5 1.0 CD2 B:HIS151 3.3 3.0 1.0 OD1 B:ASP153 3.4 19.1 1.0 CB B:HIS179 3.5 11.3 1.0 OH B:TYR168 4.1 13.6 1.0 NE2 B:HIS179 4.1 7.5 1.0 ND1 B:HIS166 4.1 4.4 1.0 CD2 B:HIS179 4.2 10.6 1.0 CG B:HIS166 4.2 5.2 1.0 CB B:ASP153 4.2 13.6 1.0 O B:TYR155 4.2 13.0 1.0 ND1 B:HIS151 4.2 6.1 1.0 CG B:HIS151 4.4 8.6 1.0 CE2 B:PHE157 4.5 4.2 1.0 CZ B:PHE157 4.5 2.4 1.0 CE2 B:TYR168 4.6 6.2 1.0 CZ B:TYR168 4.8 8.4 1.0

S.Pikul, K.L.Mcdow Dunham, N.G.Almstead, B.De, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, T.Rydel, C.M.Dunaway, F.Gu, G.E.Mieling. Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 41 3568 1998.
ISSN: ISSN 0022-2623
PubMed: 9733482
DOI: 10.1021/JM980253R