Sodium in PDB 8ssq: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4, PDB code: 8ssq 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)	41.86 / 3.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	352.07, 67.768, 61.194, 90, 92.59, 90
R / Rfree (%)	24 / 27.1

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 also contains other interesting chemical elements:

Zinc

(Zn)

17 atoms

The binding sites of Sodium atom in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 (pdb code 8ssq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4, PDB code: 8ssq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na710 b:122.7 occ:1.00 ND1 A:HIS509 3.8 151.8 1.0 OP2 C:DT7 3.8 133.8 1.0 N A:ARG505 4.0 161.5 1.0 CB A:CYS504 4.0 143.9 1.0 CA A:CYS504 4.2 140.3 1.0 CE1 A:HIS509 4.3 153.0 1.0 CD A:ARG505 4.6 137.4 1.0 C A:CYS504 4.7 146.0 1.0 O5' C:DT7 4.7 133.6 1.0 CG A:ARG505 4.7 134.4 1.0 P C:DT7 4.8 155.2 1.0 CB A:ARG505 4.8 132.5 1.0 CE A:LYS493 4.9 147.0 1.0 CG A:HIS509 5.0 139.4 1.0

Sodium binding site 2 out of 2 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35-4 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:139.9 occ:1.00 N3 E:DG26 3.2 160.2 1.0 C2 F:DA11 3.6 196.1 1.0 O2 E:DT25 3.8 190.6 1.0 O4' E:DG26 3.8 169.4 1.0 N2 E:DG26 3.9 177.3 1.0 C2 E:DG26 3.9 171.6 1.0 C1' E:DG26 4.0 180.4 1.0 C4 E:DG26 4.1 167.8 1.0 N3 F:DA11 4.2 200.3 1.0 O4' E:DG27 4.4 177.9 1.0 N9 E:DG26 4.4 175.7 1.0 N1 F:DA11 4.6 190.7 1.0 C4' E:DG26 4.6 182.9 1.0 C2 E:DT25 4.8 181.6 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