Chlorine in PDB 6cn8: High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I

The structure of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I, PDB code: 6cn8 was solved by C.Abad-Zapatero, N.W.Wolf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.40 / 1.40
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	109.758, 109.758, 109.758, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.5

The structure of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I (pdb code 6cn8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I, PDB code: 6cn8:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:16.7 occ:0.51 NA A:NA203 2.7 22.4 1.0 OG1 A:THR30 2.9 14.6 1.0 N A:ALA121 2.9 13.7 1.0 N A:GLY118 3.0 14.7 1.0 CA A:GLY118 3.1 14.6 1.0 C A:GLY118 3.1 15.0 1.0 N A:ALA120 3.4 13.9 1.0 O A:GLY118 3.5 15.4 1.0 CB A:ALA121 3.5 16.3 1.0 CB A:THR30 3.5 13.7 1.0 CB A:ALA120 3.6 14.8 1.0 N A:VAL119 3.6 15.6 1.0 CA A:ALA120 3.7 14.6 1.0 C A:ALA120 3.8 14.5 1.0 CA A:ALA121 3.8 14.8 1.0 CG2 A:THR30 3.9 14.9 1.0 C A:VAL119 4.1 15.0 1.0 OE1 A:GLU115 4.2 16.5 1.0 O3 A:PO4201 4.2 16.0 1.0 C A:GLU117 4.3 17.1 1.0 N A:GLU117 4.4 15.7 1.0 CD A:ARG83 4.4 14.7 1.0 CA A:VAL119 4.5 15.1 1.0 CD2 A:LEU112 4.5 17.8 1.0 CG A:LEU112 4.7 17.0 1.0 O A:LEU112 4.9 15.7 1.0 CA A:GLU117 4.9 16.2 1.0 CA A:THR30 5.0 14.2 1.0 O A:ALA120 5.0 14.8 1.0

Chlorine binding site 2 out of 4 in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:17.7 occ:1.00 OG1 A:THR6 3.1 18.0 1.0 O A:HOH453 3.1 29.8 1.0 O A:HOH344 3.2 21.2 1.0 O A:HOH320 3.3 17.2 1.0 N A:THR105 3.4 15.0 1.0 CA A:GLY104 3.5 16.2 1.0 CB A:ARG8 3.8 29.9 1.0 CB A:THR6 3.9 17.7 1.0 CG2 A:THR105 3.9 17.1 1.0 CD A:ARG8 3.9 34.9 1.0 CG2 A:THR6 3.9 18.9 1.0 C A:GLY104 4.0 15.0 1.0 OE1 A:GLU106 4.0 17.2 1.0 NE A:ARG8 4.3 37.0 1.0 O A:HOH408 4.3 22.9 1.0 CG A:ARG8 4.3 32.3 1.0 N A:ALA9 4.5 23.6 1.0 CA A:THR105 4.5 15.1 1.0 OG1 A:THR105 4.5 16.1 1.0 CB A:THR105 4.5 15.9 1.0 CD A:GLU106 4.8 17.4 1.0 CA A:ARG8 4.8 28.8 1.0 O A:HOH423 4.9 19.6 1.0 N A:GLY104 4.9 15.6 1.0 OE2 A:GLU106 4.9 18.2 1.0 CB A:ALA9 4.9 19.5 1.0 C A:ARG8 4.9 36.9 1.0

Chlorine binding site 3 out of 4 in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:34.2 occ:1.00 N A:GLU57 3.2 21.8 1.0 CG A:GLU57 3.6 36.2 1.0 CB A:GLU57 3.7 30.4 1.0 N A:LEU56 3.7 19.1 1.0 CB A:SER55 3.8 21.1 1.0 O A:HOH385 3.8 23.8 1.0 CB A:LEU56 4.0 21.2 1.0 CA A:GLU57 4.1 24.0 1.0 OG A:SER55 4.1 22.6 1.0 CA A:LEU56 4.1 19.0 1.0 C A:LEU56 4.2 20.5 1.0 C A:SER55 4.4 19.5 1.0 CA A:SER55 4.6 19.4 1.0 CD A:GLU57 4.9 41.1 1.0 O A:HOH476 4.9 39.1 1.0

Chlorine binding site 4 out of 4 in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl207 b:31.1 occ:1.00 N A:PHE2 3.1 23.7 1.0 CE A:MET1 3.3 74.8 1.0 N A:GLU3 3.4 26.6 1.0 O B:HOH107 3.6 30.1 1.0 CB B:F7P1 3.7 18.2 1.0 CA A:PHE2 3.8 21.5 1.0 CB A:PHE2 3.8 20.8 1.0 CB A:MET1 3.8 28.4 1.0 C A:MET1 3.8 24.8 1.0 CA A:MET1 4.1 27.5 1.0 C A:PHE2 4.1 22.6 1.0 CG A:GLU3 4.3 45.8 1.0 CG B:F7P1 4.3 18.4 1.0 CB A:GLU3 4.3 38.2 1.0 SD A:MET1 4.4 60.7 1.0 CA A:GLU3 4.5 30.3 1.0 CG A:PHE2 4.6 19.5 1.0 CG A:MET1 4.6 34.4 1.0 CD A:GLU3 4.7 51.7 1.0 O A:HOH457 4.7 49.1 1.0 CD2 A:PHE2 4.7 19.7 1.0 O A:MET1 4.8 23.0 1.0 CD2 B:F7P1 4.8 17.2 1.0

N.M.Wolf, H.Lee, M.P.Choules, G.F.Pauli, R.Phansalkar, J.R.Anderson, W.Gao, J.Ren, B.D.Santarsiero, H.Lee, J.Cheng, Y.Y.Jin, N.A.Ho, N.M.Duc, J.W.Suh, C.Abad-Zapatero, S.Cho. High-Resolution Structure of CLPC1-Rufomycin and Ligand Binding Studies Provide A Framework to Design and Optimize Anti-Tuberculosis Leads. Acs Infect Dis. V. 5 829 2019.
ISSN: ESSN 2373-8227
PubMed: 30990022
DOI: 10.1021/ACSINFECDIS.8B00276