Sodium in PDB 8ssr: Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20, PDB code: 8ssr 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)	37.59 / 3.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	362.211, 68.09, 61.988, 90, 94.87, 90
R / Rfree (%)	24.9 / 28.4

The structure of Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20 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- 20 (pdb code 8ssr). 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- 20, PDB code: 8ssr:
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- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na710 b:182.6 occ:1.00 NE A:ARG508 2.5 142.2 1.0 NH2 A:ARG508 2.6 160.0 1.0 OE1 A:GLN506 2.6 174.6 1.0 CE1 A:HIS509 2.6 135.6 1.0 NE2 A:HIS509 2.6 144.6 1.0 CD A:GLN506 2.8 160.0 1.0 CZ A:ARG508 2.9 143.0 1.0 NE2 A:GLN506 3.3 153.1 1.0 ND1 A:HIS509 3.5 121.9 1.0 CG A:GLN506 3.5 136.9 1.0 CD2 A:HIS509 3.6 136.2 1.0 CB A:GLN506 3.6 151.2 1.0 CD A:ARG508 3.7 144.0 1.0 CG A:ARG508 4.0 142.9 1.0 CG A:HIS509 4.1 133.5 1.0 NH1 A:ARG508 4.2 143.6 1.0 N7 B:DG26 4.6 138.3 1.0 N6 C:DA8 4.6 174.1 1.0

Sodium binding site 2 out of 2 in the Znfs 3-11 of Ccctc-Binding Factor (Ctcf) Complexed with 35MER Dna 35- 20


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- 20 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:122.2 occ:1.00 N3 C:DG22 3.9 95.1 1.0 O2 B:DT15 4.0 115.8 1.0 C1' C:DG22 4.0 87.7 1.0 C2 C:DA21 4.4 104.6 1.0 O4' C:DG22 4.4 108.4 1.0 C4 C:DG22 4.6 88.0 1.0 N9 C:DG22 4.7 86.4 1.0 N3 C:DA21 4.7 96.8 1.0 C2 C:DG22 4.7 102.5 1.0 N3 B:DG16 4.8 118.0 1.0 N2 C:DG22 4.8 112.7 1.0 C4' C:DG22 4.9 100.9 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