Sodium in PDB 3i3c: Crystal Structural of CBX5 Chromo Shadow Domain

The structure of Crystal Structural of CBX5 Chromo Shadow Domain, PDB code: 3i3c was solved by M.F.Amaya, Z.Li, Y.Li, I.Kozieradzki, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, J.Min, H.Ouyang, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.660, 126.587, 31.399, 90.00, 90.00, 90.00
R / Rfree (%)	26.6 / 30.3

The binding sites of Sodium atom in the Crystal Structural of CBX5 Chromo Shadow Domain (pdb code 3i3c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structural of CBX5 Chromo Shadow Domain, PDB code: 3i3c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structural of CBX5 Chromo Shadow Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structural of CBX5 Chromo Shadow Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na76 b:53.6 occ:1.00 N A:GLN64 3.2 21.4 1.0 C A:CYS62 3.3 22.8 1.0 CA A:CYS62 3.3 23.6 1.0 CB A:GLN64 3.5 20.9 1.0 N A:PRO63 3.5 20.9 1.0 CB A:CYS62 3.7 24.4 1.0 N A:ILE65 3.7 23.6 1.0 CA A:GLN64 3.8 21.0 1.0 O A:CYS62 3.8 23.1 1.0 CD A:PRO63 3.8 20.5 1.0 C A:PRO63 4.1 21.7 1.0 CG A:GLN64 4.1 19.5 1.0 C A:GLN64 4.2 21.9 1.0 CA A:PRO63 4.4 20.7 1.0 CG1 A:ILE65 4.4 23.7 1.0 CD1 A:ILE65 4.4 23.1 1.0 CG A:PRO63 4.5 20.2 1.0 CB A:ILE65 4.5 24.3 1.0 N A:CYS62 4.6 25.2 1.0 CA A:ILE65 4.7 23.7 1.0 O A:LYS61 4.8 25.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structural of CBX5 Chromo Shadow Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structural of CBX5 Chromo Shadow Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na76 b:57.3 occ:1.00 N B:GLN64 3.2 21.4 1.0 CB B:GLN64 3.4 20.8 1.0 CA B:CYS62 3.5 23.6 1.0 C B:CYS62 3.5 22.7 1.0 N B:PRO63 3.6 20.9 1.0 N B:ILE65 3.6 23.2 1.0 CA B:GLN64 3.7 21.0 1.0 CB B:CYS62 3.7 24.6 1.0 CD B:PRO63 3.9 20.5 1.0 CG B:GLN64 4.0 19.3 1.0 O B:CYS62 4.1 23.1 1.0 C B:GLN64 4.1 21.7 1.0 C B:PRO63 4.2 21.4 1.0 CG1 B:ILE65 4.4 23.6 1.0 CA B:PRO63 4.4 20.6 1.0 CD1 B:ILE65 4.5 22.8 1.0 CG B:PRO63 4.6 20.0 1.0 CB B:ILE65 4.6 24.1 1.0 CA B:ILE65 4.7 23.7 1.0 N B:CYS62 4.8 25.0 1.0

Z.Li, Y.Li, M.F.Amaya, A.M.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.Bochkarev, J.Min, H.Ouyang. Crystal Structural of CBX5 Chromo Shadow Domain To Be Published.