Sodium in PDB 1gv2: Crystal Structure of C-Myb R2R3

The structure of Crystal Structure of C-Myb R2R3, PDB code: 1gv2 was solved by T.H.Tahirov, K.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.12 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.722, 28.250, 44.129, 90.00, 90.87, 90.00
R / Rfree (%)	19.3 / 21

The binding sites of Sodium atom in the Crystal Structure of C-Myb R2R3 (pdb code 1gv2). 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 Structure of C-Myb R2R3, PDB code: 1gv2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of C-Myb R2R3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of C-Myb R2R3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1191 b:10.5 occ:1.00 O A:LEU173 2.3 9.6 1.0 O A:ALA170 2.4 8.9 1.0 O A:HOH2052 2.4 8.9 1.0 O A:ARG176 2.4 11.1 1.0 OD1 A:ASN136 2.5 10.6 1.0 O A:HOH2051 2.8 13.4 1.0 C A:LEU173 3.4 9.3 1.0 C A:ALA170 3.5 7.4 1.0 CG A:ASN136 3.6 9.3 1.0 C A:ARG176 3.6 11.4 1.0 N A:ARG176 3.9 8.8 1.0 O A:PRO174 4.2 15.1 1.0 CA A:ALA170 4.2 9.7 1.0 C A:PRO174 4.3 12.5 1.0 CA A:ARG176 4.3 9.9 1.0 CA A:LEU173 4.3 8.8 1.0 N A:LEU173 4.3 7.0 1.0 N A:PRO174 4.3 12.0 1.0 O A:HIS135 4.4 10.6 1.0 CB A:ALA170 4.4 11.2 1.0 CA A:ASN136 4.4 5.8 1.0 CA A:PRO174 4.5 13.0 1.0 CB A:ASN136 4.5 5.9 1.0 N A:LYS171 4.5 8.0 1.0 ND2 A:ASN136 4.5 7.9 1.0 CB A:LEU173 4.6 9.4 1.0 CA A:LYS171 4.6 9.8 1.0 N A:THR177 4.7 8.4 1.0 N A:GLY175 4.8 11.5 1.0 C A:LYS171 4.8 12.5 1.0 CB A:ARG176 4.9 10.0 1.0 C A:HIS135 4.9 6.7 1.0 CA A:THR177 5.0 8.0 1.0 C A:GLY175 5.0 11.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of C-Myb R2R3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of C-Myb R2R3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1192 b:19.6 occ:1.00 O A:ALA119 2.3 11.6 1.0 O A:ARG125 2.4 14.8 1.0 O A:LEU122 2.4 20.9 1.0 O A:HOH2016 2.6 33.1 1.0 O A:HOH2017 2.6 21.7 1.0 C A:ALA119 3.4 12.8 1.0 C A:ARG125 3.5 12.6 1.0 N A:ARG125 3.6 14.3 1.0 C A:LEU122 3.6 18.6 1.0 CA A:ARG125 4.1 12.6 1.0 CA A:LYS120 4.1 14.9 1.0 N A:GLY124 4.1 15.3 1.0 N A:LYS120 4.1 13.5 1.0 N A:LEU122 4.2 14.1 1.0 CA A:ALA119 4.3 10.3 1.0 C A:LYS120 4.3 16.2 1.0 CB A:ALA119 4.4 10.2 1.0 CA A:LEU122 4.4 14.9 1.0 C A:GLY124 4.4 15.9 1.0 O A:LYS120 4.5 17.7 1.0 C A:LYS123 4.5 15.9 1.0 N A:LYS123 4.6 17.6 1.0 N A:ILE126 4.6 11.3 1.0 CB A:ARG125 4.6 11.7 1.0 CA A:GLY124 4.6 12.9 1.0 CB A:LEU122 4.7 17.1 1.0 CA A:LYS123 4.7 17.4 1.0 CA A:ILE126 4.9 12.3 1.0 N A:HIS121 4.9 14.3 1.0

T.H.Tahirov, H.Morii, H.Uedaira, M.Sasaki, A.Sarai, S.Adachi, S.Y.Park, N.Kamiya, K.Ogata. Crystal Structure of C-Myb Dna-Binding Domain: Specific Na+ Binding and Correlation with uc(Nmr) Structure To Be Published.