Sodium 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:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the High-Resolution Structure of CLPC1-Ntd Binding to Rufomycin-I, PDB code: 6cn8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium 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 Sodium with other atoms in the Na 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:Na203 b:22.4 occ:1.00 CL A:CL202 2.7 16.7 0.5 OE1 A:GLU115 2.8 16.5 1.0 O A:LEU112 2.9 15.7 1.0 N A:GLY116 3.5 16.4 1.0 CB A:GLU115 3.6 16.2 1.0 CG2 A:VAL87 3.6 16.9 1.0 C A:LEU112 3.7 15.3 1.0 CD A:GLU115 3.8 16.6 1.0 CG2 A:THR30 3.8 14.9 1.0 CG A:LEU112 3.9 17.0 1.0 CA A:LEU112 3.9 15.6 1.0 CD2 A:LEU112 4.1 17.8 1.0 CG A:GLU115 4.1 17.1 1.0 N A:GLU117 4.1 15.7 1.0 C A:GLU115 4.2 16.5 1.0 CB A:THR30 4.2 13.7 1.0 N A:GLY118 4.2 14.7 1.0 CA A:GLY116 4.3 17.5 1.0 CA A:GLU115 4.4 16.5 1.0 OG1 A:THR30 4.4 14.6 1.0 CD A:ARG83 4.4 14.7 1.0 CB A:LEU112 4.5 16.5 1.0 C A:GLY116 4.6 17.0 1.0 N A:GLU115 4.8 16.3 1.0 CG A:ARG83 4.8 14.5 1.0 CB A:ALA121 4.8 16.3 1.0 CA A:GLY118 4.8 14.6 1.0 OE2 A:GLU115 4.9 16.4 1.0 N A:ILE113 5.0 15.4 1.0 O A:GLY111 5.0 16.0 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na205 b:20.3 occ:1.00 O A:HOH493 4.4 31.8 1.0 O A:HOH328 4.8 34.5 1.0 O A:HOH333 4.8 34.7 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na208 b:19.9 occ:0.33 O A:HOH350 2.3 19.4 1.0 O A:HOH427 2.5 18.5 1.0 NA A:NA209 3.3 19.3 0.3 O A:GLY128 4.0 20.0 1.0 O A:HOH362 4.3 21.4 1.0 CA A:GLY128 4.3 18.4 1.0 O A:HOH441 4.5 44.9 1.0 C A:GLY128 4.6 18.5 1.0 O A:HOH374 4.9 20.1 1.0 O A:HOH387 4.9 23.2 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na209 b:19.3 occ:0.33 O A:HOH357 2.4 18.8 1.0 O A:HOH427 2.4 18.5 1.0 NA A:NA208 3.3 19.9 0.3 O A:HOH374 3.9 20.1 1.0 O A:HOH362 4.2 21.4 1.0 CG A:GLU130 4.5 19.1 1.0 O A:HOH485 4.6 29.4 1.0 OE2 A:GLU130 4.6 21.4 1.0 O A:HOH350 4.9 19.4 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