Zinc in PDB 5boy: X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate, PDB code: 5boy was solved by N.A.Farrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.42 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.079, 36.051, 95.908, 90.00, 131.26, 90.00
R / Rfree (%)	16 / 19

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate (pdb code 5boy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate, PDB code: 5boy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.8 occ:1.00 NE2 A:HIS232 2.0 13.3 1.0 NE2 A:HIS226 2.1 11.7 1.0 NE2 A:HIS222 2.2 14.3 1.0 O A:HOH401 2.2 15.5 1.0 CD2 A:HIS232 2.9 10.7 1.0 CE1 A:HIS226 3.0 15.0 1.0 CD2 A:HIS226 3.0 10.7 1.0 CD2 A:HIS222 3.1 10.9 1.0 CE1 A:HIS232 3.1 14.1 1.0 CE1 A:HIS222 3.2 13.2 1.0 CG A:HIS232 4.1 13.2 1.0 OE2 A:GLU223 4.1 11.8 1.0 ND1 A:HIS226 4.1 10.8 1.0 ND1 A:HIS232 4.2 12.7 1.0 CG A:HIS226 4.2 13.9 1.0 CG A:HIS222 4.2 12.3 1.0 ND1 A:HIS222 4.3 13.4 1.0 OE1 A:GLU223 4.6 13.8 1.0 O A:HOH516 4.7 19.3 1.0 CD A:GLU223 4.7 11.8 1.0 CE A:MET240 4.8 11.6 1.0 O12 A:4UE306 4.8 24.5 1.0 C14 A:4UE306 4.8 34.6 1.0

Zinc binding site 2 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.5 occ:1.00 OD2 A:ASP174 2.0 12.3 1.0 NE2 A:HIS172 2.1 11.0 1.0 NE2 A:HIS187 2.1 9.8 1.0 ND1 A:HIS200 2.1 10.6 1.0 CD2 A:HIS172 2.9 10.8 1.0 CG A:ASP174 3.0 12.0 1.0 CE1 A:HIS187 3.0 12.1 1.0 CE1 A:HIS200 3.1 14.3 1.0 CD2 A:HIS187 3.1 8.3 1.0 CG A:HIS200 3.1 10.9 1.0 CE1 A:HIS172 3.2 10.0 1.0 OD1 A:ASP174 3.3 10.5 1.0 CB A:HIS200 3.5 8.9 1.0 CG A:HIS172 4.1 11.5 1.0 O A:TYR176 4.1 14.2 1.0 ND1 A:HIS187 4.2 9.5 1.0 ND1 A:HIS172 4.2 11.7 1.0 NE2 A:HIS200 4.2 13.2 1.0 CD2 A:HIS200 4.2 12.0 1.0 CG A:HIS187 4.2 9.7 1.0 CB A:ASP174 4.3 11.9 1.0 CE1 A:PHE189 4.4 13.6 1.0 CZ A:PHE178 4.7 10.1 1.0 CE2 A:PHE178 4.7 9.9 1.0 CB A:TYR176 4.8 14.5 1.0 CZ A:PHE189 4.8 18.9 1.0 C A:TYR176 4.9 12.1 1.0 CA A:HIS200 5.0 10.9 1.0

Zinc binding site 3 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.3 occ:1.00 NE2 B:HIS232 2.1 15.3 1.0 NE2 B:HIS222 2.1 11.9 1.0 NE2 B:HIS226 2.1 14.9 1.0 O B:HOH482 2.2 19.0 1.0 CD2 B:HIS232 2.9 16.9 1.0 CD2 B:HIS222 3.0 12.6 1.0 CD2 B:HIS226 3.0 13.8 1.0 CE1 B:HIS232 3.1 22.2 1.0 CE1 B:HIS226 3.2 18.5 1.0 CE1 B:HIS222 3.2 14.0 1.0 OE2 B:GLU223 4.1 17.4 1.0 CG B:HIS232 4.1 16.0 1.0 ND1 B:HIS232 4.2 19.1 1.0 CG B:HIS222 4.2 12.7 1.0 CG B:HIS226 4.2 17.2 1.0 C13 B:4UE306 4.2 24.7 1.0 ND1 B:HIS222 4.2 12.3 1.0 ND1 B:HIS226 4.2 14.3 1.0 O12 B:4UE306 4.6 23.1 1.0 O B:HOH514 4.7 17.9 1.0 CD B:GLU223 4.8 15.7 1.0 CE B:MET240 4.8 14.3 1.0 OE1 B:GLU223 4.8 14.7 1.0 O B:HOH548 4.9 34.4 1.0

Zinc binding site 4 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Co-Structure of Mmp-13 with Ethyl 5-(1-Methyl-1H-Imidazol-5-Yl)- 1H-Indole-2-Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.7 occ:1.00 OD2 B:ASP174 2.0 11.8 1.0 NE2 B:HIS172 2.0 9.7 1.0 NE2 B:HIS187 2.1 9.1 1.0 ND1 B:HIS200 2.1 11.7 1.0 CG B:ASP174 2.9 12.2 1.0 CD2 B:HIS172 2.9 10.7 1.0 CE1 B:HIS187 2.9 11.1 1.0 CE1 B:HIS200 3.0 16.4 1.0 CE1 B:HIS172 3.1 11.2 1.0 CG B:HIS200 3.2 13.1 1.0 CD2 B:HIS187 3.2 12.9 1.0 OD1 B:ASP174 3.2 13.5 1.0 CB B:HIS200 3.5 9.2 1.0 CG B:HIS172 4.1 12.9 1.0 ND1 B:HIS187 4.1 11.7 1.0 ND1 B:HIS172 4.1 11.9 1.0 NE2 B:HIS200 4.2 16.0 1.0 O B:TYR176 4.2 12.2 1.0 CD2 B:HIS200 4.2 12.0 1.0 CG B:HIS187 4.3 12.9 1.0 CB B:ASP174 4.3 12.0 1.0 CE1 B:PHE189 4.7 16.2 1.0 CE2 B:PHE178 4.7 9.1 1.0 CZ B:PHE178 4.7 11.7 1.0 O B:HOH437 4.7 16.2 1.0 CB B:TYR176 4.8 15.2 1.0 CZ B:PHE189 4.9 19.1 1.0

S.J.Taylor, A.Abeywardane, S.Liang, I.Muegge, A.K.Padyana, Z.Xiong, M.Hill-Drzewi, B.Farmer, X.Li, B.Collins, J.X.Li, A.Heim-Riether, J.Proudfoot, Q.Zhang, D.Goldberg, L.Zuvela-Jelaska, H.Zaher, J.Li, N.A.Farrow. Fragment-Based Discovery of Indole Inhibitors of Matrix Metalloproteinase-13. J. Med. Chem. V. 54 8174 2011.
ISSN: ISSN 1520-4804
PubMed: 22017539
DOI: 10.1021/JM201129M