Sodium in PDB 8sss: Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER

The structure of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER, PDB code: 8sss was solved by J.R.Horton, J.Yang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.013, 41.147, 135.661, 90, 105.18, 90
R / Rfree (%)	19.9 / 23.1

The structure of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER also contains other interesting chemical elements:

Zinc

(Zn)

14 atoms

The binding sites of Sodium atom in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER (pdb code 8sss). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER, PDB code: 8sss:

Sodium binding site 1 out of 1 in the Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Znfs 1-7 of Ccctc-Binding Factor (Ctcf) Complexed with 23MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:53.5 occ:1.00 O A:CYS353 2.3 42.1 1.0 O A:HOH616 2.4 63.2 1.0 O A:CYS356 2.4 47.4 1.0 O F:HOH104 2.4 36.0 1.0 O F:HOH107 2.5 42.5 1.0 O A:HOH614 2.5 42.6 1.0 C A:CYS353 3.6 41.3 1.0 C A:CYS356 3.6 48.0 1.0 O D:HOH629 3.6 49.4 1.0 OP1 F:DG9 3.9 47.4 1.0 CA A:ASP357 4.1 48.5 1.0 N A:ASP357 4.3 46.3 1.0 OD1 A:ASP357 4.4 75.7 1.0 N A:CYS353 4.4 43.3 1.0 CA A:SER354 4.4 44.1 1.0 N A:SER354 4.4 41.7 1.0 CA A:CYS353 4.5 40.0 1.0 N A:CYS356 4.6 43.0 1.0 CB A:LYS352 4.6 48.9 1.0 C A:ASP357 4.7 45.1 1.0 CA A:CYS356 4.7 43.4 1.0 C A:SER354 4.7 43.7 1.0 O A:TYR358 4.8 47.3 1.0 O D:SER372 4.9 49.2 1.0 C A:LYS352 4.9 43.0 1.0 CB A:CYS353 5.0 39.6 1.0

J.Yang, J.R.Horton, B.Liu, V.G.Corces, R.M.Blumenthal, X.Zhang, X.Cheng. Structures of Ctcf-Dna Complexes Including All 11 Zinc Fingers. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37439339
DOI: 10.1093/NAR/GKAD594