Zinc in PDB 5bot: X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-1H-Indole-2- Carboxylate

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

Resolution Low / High (Å)	50.98 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.641, 35.953, 95.824, 90.00, 130.78, 90.00
R / Rfree (%)	n/a / 22.9

The structure of X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate (pdb code 5bot). 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-Carbamoyl-1H-Indole-2- Carboxylate, PDB code: 5bot:
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-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.4 occ:1.00 NE2 A:HIS232 2.1 16.4 1.0 NE2 A:HIS226 2.1 15.5 1.0 NE2 A:HIS222 2.2 18.4 1.0 CD2 A:HIS232 3.0 17.6 1.0 CD2 A:HIS226 3.0 14.9 1.0 CD2 A:HIS222 3.1 16.8 1.0 CE1 A:HIS226 3.1 19.9 1.0 CE1 A:HIS232 3.2 20.9 1.0 CE1 A:HIS222 3.2 16.6 1.0 OE2 A:GLU223 4.1 16.5 1.0 CG A:HIS232 4.1 18.1 1.0 CG A:HIS226 4.2 16.6 1.0 ND1 A:HIS232 4.2 21.2 1.0 ND1 A:HIS226 4.2 16.2 1.0 CG A:HIS222 4.3 16.3 1.0 ND1 A:HIS222 4.3 18.1 1.0 OE1 A:GLU223 4.4 18.1 1.0 O A:HOH618 4.6 40.4 1.0 CD A:GLU223 4.6 15.1 1.0 O A:HOH537 4.7 24.7 1.0 O13 A:4UM301 4.7 30.6 1.0 O A:HOH596 4.9 43.1 1.0 CE A:MET240 4.9 15.7 1.0 CA A:PRO242 4.9 24.3 1.0 O A:HOH478 5.0 35.5 1.0

Zinc binding site 2 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:18.1 occ:1.00 OD2 A:ASP174 2.0 19.9 1.0 NE2 A:HIS172 2.1 14.7 1.0 NE2 A:HIS187 2.1 18.7 1.0 ND1 A:HIS200 2.1 16.4 1.0 CD2 A:HIS172 2.9 16.3 1.0 CG A:ASP174 2.9 17.4 1.0 CE1 A:HIS187 3.0 18.6 1.0 CE1 A:HIS200 3.1 17.5 1.0 CG A:HIS200 3.1 15.5 1.0 CD2 A:HIS187 3.2 16.2 1.0 OD1 A:ASP174 3.2 16.9 1.0 CE1 A:HIS172 3.2 15.6 1.0 CB A:HIS200 3.4 11.6 1.0 O A:TYR176 4.1 20.2 1.0 CG A:HIS172 4.1 16.4 1.0 ND1 A:HIS187 4.2 21.2 1.0 ND1 A:HIS172 4.2 14.8 1.0 NE2 A:HIS200 4.2 16.1 1.0 CD2 A:HIS200 4.3 15.4 1.0 CG A:HIS187 4.3 17.4 1.0 CB A:ASP174 4.3 16.2 1.0 CE1 A:PHE189 4.5 19.9 1.0 CB A:TYR176 4.7 22.3 1.0 CZ A:PHE189 4.7 20.1 1.0 CE2 A:PHE178 4.8 14.7 1.0 CZ A:PHE178 4.8 17.5 1.0 C A:TYR176 4.9 17.6 1.0 CA A:HIS200 4.9 15.4 1.0

Zinc binding site 3 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:21.4 occ:1.00 NE2 B:HIS222 2.1 19.2 1.0 NE2 B:HIS226 2.1 20.6 1.0 NE2 B:HIS232 2.1 22.8 1.0 O B:HOH532 2.2 25.2 1.0 CD2 B:HIS232 2.9 22.4 1.0 CD2 B:HIS222 3.0 17.1 1.0 CD2 B:HIS226 3.1 18.8 1.0 CE1 B:HIS226 3.2 20.8 1.0 CE1 B:HIS222 3.2 18.8 1.0 CE1 B:HIS232 3.2 27.4 1.0 CG B:HIS232 4.1 21.7 1.0 C16 B:4UM301 4.1 27.4 1.0 CG B:HIS222 4.2 17.7 1.0 OE2 B:GLU223 4.2 21.2 1.0 CG B:HIS226 4.2 20.8 1.0 ND1 B:HIS222 4.2 16.8 1.0 ND1 B:HIS232 4.2 23.5 1.0 ND1 B:HIS226 4.2 20.9 1.0 O B:HOH590 4.5 37.8 1.0 O B:HOH548 4.6 18.8 1.0 O12 B:4UM301 4.6 21.0 1.0 OE1 B:GLU223 4.7 22.4 1.0 CD B:GLU223 4.8 19.2 1.0 CE B:MET240 4.9 18.6 1.0

Zinc binding site 4 out of 4 in the X-Ray Co-Structure of Mmp-13 with Ethyl 5-Carbamoyl-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-Carbamoyl-1H-Indole-2- Carboxylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:18.4 occ:1.00 OD2 B:ASP174 2.0 17.3 1.0 NE2 B:HIS172 2.1 17.4 1.0 ND1 B:HIS200 2.1 16.3 1.0 NE2 B:HIS187 2.1 16.2 1.0 CD2 B:HIS172 2.9 13.8 1.0 CG B:ASP174 2.9 19.2 1.0 CE1 B:HIS187 3.0 20.0 1.0 CE1 B:HIS200 3.0 16.2 1.0 CG B:HIS200 3.2 15.6 1.0 CE1 B:HIS172 3.2 17.2 1.0 OD1 B:ASP174 3.2 16.1 1.0 CD2 B:HIS187 3.2 18.1 1.0 CB B:HIS200 3.5 15.8 1.0 CG B:HIS172 4.1 14.8 1.0 ND1 B:HIS187 4.2 16.1 1.0 NE2 B:HIS200 4.2 16.6 1.0 O B:TYR176 4.2 16.4 1.0 ND1 B:HIS172 4.2 15.0 1.0 CD2 B:HIS200 4.3 15.8 1.0 CB B:ASP174 4.3 17.5 1.0 CG B:HIS187 4.3 17.1 1.0 CE1 B:PHE189 4.6 19.9 1.0 CZ B:PHE178 4.6 15.5 1.0 O B:HOH417 4.7 19.2 1.0 CE2 B:PHE178 4.7 14.9 1.0 CB B:TYR176 4.8 19.1 1.0 CZ B:PHE189 4.9 22.2 1.0 CA B:HIS200 5.0 14.1 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