Chlorine in PDB 6n47: The Structure of Sb-2-204-Tubulin Complex

The structure of The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47 was solved by K.Arnst, S.Banerjee, Y.Wang, W.Li, D.Miller, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.295, 157.835, 182.068, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.6

The structure of The Structure of Sb-2-204-Tubulin Complex also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Chlorine atom in the The Structure of Sb-2-204-Tubulin Complex (pdb code 6n47). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Structure of Sb-2-204-Tubulin Complex, PDB code: 6n47:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:74.4 occ:1.00 N A:LYS163 3.3 60.4 1.0 N A:GLY162 3.4 44.5 1.0 C A:TYR161 3.5 45.3 1.0 CE A:LYS164 3.6 69.5 1.0 CA A:TYR161 3.6 45.4 1.0 CB A:LYS163 3.7 70.8 1.0 CG A:LYS163 4.1 74.4 1.0 CA A:LYS163 4.1 65.4 1.0 O A:TYR161 4.2 50.2 1.0 C A:GLY162 4.2 52.0 1.0 CA A:GLY162 4.2 48.0 1.0 CD A:LYS164 4.4 65.3 1.0 CG A:LYS164 4.4 59.9 1.0 CB A:TYR161 4.5 42.3 1.0 NZ A:LYS164 4.5 73.9 1.0 O A:ASP160 4.6 49.5 1.0 N A:TYR161 4.7 49.8 1.0 N A:LYS164 4.7 60.8 1.0 C A:LYS163 4.9 64.0 1.0

Chlorine binding site 2 out of 3 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:35.2 occ:1.00 CL11 B:KB4506 0.0 35.2 1.0 C09 B:KB4506 1.8 31.6 1.0 N08 B:KB4506 2.6 31.8 1.0 N10 B:KB4506 2.7 30.2 1.0 O B:HOH626 3.5 32.3 1.0 CD2 B:LEU240 3.5 31.3 1.0 CB B:ALA248 3.5 35.4 1.0 CG B:LEU240 3.8 32.8 1.0 C07 B:KB4506 3.9 30.3 1.0 C04 B:KB4506 3.9 30.7 1.0 CD2 B:LEU253 4.0 26.6 1.0 CB B:LEU253 4.1 25.2 1.0 CB B:CYS239 4.3 35.5 1.0 O B:ASP249 4.3 28.4 1.0 CD1 B:LEU253 4.3 25.3 1.0 CG B:LEU253 4.4 25.3 1.0 C05 B:KB4506 4.5 30.1 1.0 O B:VAL236 4.5 38.6 1.0 CD1 B:LEU240 4.6 33.0 1.0 C B:CYS239 4.7 37.2 1.0 N B:LEU240 4.7 37.6 1.0 CA B:ALA248 4.7 38.9 1.0 O B:HOH608 4.8 28.4 1.0 C B:ALA248 4.8 34.0 1.0 O B:CYS239 4.8 42.6 1.0 N B:ASP249 4.9 30.4 1.0 C B:ASP249 4.9 28.5 1.0 N12 B:KB4506 5.0 27.5 1.0 CA B:CYS239 5.0 34.8 1.0

Chlorine binding site 3 out of 3 in the The Structure of Sb-2-204-Tubulin Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Sb-2-204-Tubulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl503 b:50.7 occ:1.00 CL11 D:KB4503 0.0 50.7 1.0 C09 D:KB4503 1.8 50.7 1.0 N08 D:KB4503 2.6 48.6 1.0 N10 D:KB4503 2.7 50.2 1.0 CD2 D:LEU240 3.6 40.6 1.0 CB D:ALA248 3.7 40.8 1.0 C07 D:KB4503 3.9 43.3 1.0 CB D:LEU253 3.9 31.6 1.0 C04 D:KB4503 3.9 49.1 1.0 CD1 D:LEU253 3.9 30.9 1.0 O D:HOH611 3.9 43.4 1.0 CG D:LEU240 3.9 39.6 1.0 CD2 D:LEU253 4.1 31.6 1.0 CG D:LEU253 4.2 31.8 1.0 CB D:CYS239 4.2 43.3 1.0 O D:ASP249 4.3 27.4 1.0 C05 D:KB4503 4.4 48.0 1.0 N D:LEU240 4.5 40.0 1.0 C D:CYS239 4.6 42.7 1.0 N D:ASP249 4.6 30.9 1.0 O D:VAL236 4.7 50.2 1.0 CD1 D:LEU240 4.8 38.1 1.0 C D:ASP249 4.8 31.1 1.0 C D:ALA248 4.8 36.2 1.0 CA D:ALA248 4.9 39.9 1.0 CA D:LEU253 4.9 29.1 1.0 CA D:CYS239 4.9 43.3 1.0 N12 D:KB4503 4.9 38.2 1.0 O D:CYS239 5.0 41.7 1.0

K.E.Arnst, S.Banerjee, Y.Wang, H.Chen, Y.Li, L.Yang, W.Li, D.D.Miller, W.Li. X-Ray Crystal Structure Guided Discovery and Antitumor Efficacy of Dihydroquinoxalinone As Potent Tubulin Polymerization Inhibitors. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31714738
DOI: 10.1021/ACSCHEMBIO.9B00696