Sodium in PDB 7ocb: Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B

The structure of Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B, PDB code: 7ocb was solved by C.Johansson, T.Krojer, K.Park, Y.Xiong, J.Jin, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.66 / 1.42
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.477, 115.477, 43.721, 90, 90, 90
R / Rfree (%)	18 / 20.6

The structure of Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B (pdb code 7ocb). 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 SPINDLIN1 in Complex with the Inhibitor XY49-92B, PDB code: 7ocb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B


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 SPINDLIN1 in Complex with the Inhibitor XY49-92B within 5.0Å range: probe atom residue distance (Å) B Occ B:Na307 b:33.1 occ:1.00 HZ1 B:LYS148 2.4 41.6 1.0 O B:GLU187 2.8 22.3 1.0 NZ B:LYS148 3.2 34.6 1.0 HZ2 B:LYS148 3.3 41.6 1.0 HZ3 B:LYS148 3.4 41.6 1.0 HB3 B:GLU187 3.8 23.2 1.0 C B:GLU187 4.0 20.4 1.0 OD1 B:ASP189 4.1 20.7 1.0 CE B:LYS148 4.4 33.3 1.0 HA3 B:GLY188 4.4 25.1 1.0 OD2 B:ASP189 4.5 19.7 1.0 HE3 B:LYS148 4.5 40.0 1.0 O B:HOH526 4.5 36.7 1.0 HE2 B:LYS148 4.6 40.0 1.0 CG B:ASP189 4.6 19.5 1.0 CB B:GLU187 4.7 19.4 1.0 CA B:GLU187 4.8 19.7 1.0 HA B:GLU187 4.9 23.7 1.0 N B:GLY188 5.0 19.1 1.0 CA B:GLY188 5.0 20.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B


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 SPINDLIN1 in Complex with the Inhibitor XY49-92B within 5.0Å range: probe atom residue distance (Å) B Occ B:Na308 b:36.0 occ:1.00 HH11 B:ARG107 2.1 24.3 1.0 O B:HOH530 2.7 17.7 1.0 HA B:ASP250 2.7 17.8 1.0 O B:HOH501 2.8 45.7 1.0 NH1 B:ARG107 2.9 20.2 1.0 HH22 B:ARG107 3.0 18.3 1.0 O B:ASP249 3.4 19.0 1.0 HH12 B:ARG107 3.5 24.3 1.0 CA B:ASP250 3.6 14.8 1.0 NH2 B:ARG107 3.7 15.3 1.0 CZ B:ARG107 3.7 17.3 1.0 HD2 B:PHE251 3.8 24.6 1.0 H B:PHE251 3.8 15.0 1.0 CD2 B:PHE251 3.9 20.5 1.0 C B:ASP249 3.9 18.3 1.0 N B:ASP250 4.0 13.9 1.0 O B:HOH548 4.0 55.8 1.0 N B:PHE251 4.1 12.5 1.0 C B:ASP250 4.1 13.4 1.0 OD1 B:ASP250 4.1 19.2 1.0 CE2 B:PHE251 4.3 24.4 1.0 HE2 B:PHE251 4.4 29.3 1.0 HB3 B:PHE251 4.4 14.4 1.0 CG B:PHE251 4.4 14.7 1.0 HH21 B:ARG107 4.5 18.3 1.0 H B:ASP250 4.6 16.7 1.0 CB B:ASP250 4.7 16.2 1.0 HZ2 B:TRP62 4.7 18.1 1.0 CB B:PHE251 4.8 12.0 1.0 HB2 B:ASP250 4.9 19.4 1.0 CG B:ASP250 4.9 16.8 1.0 HA B:ASP249 4.9 22.8 1.0 CZ B:PHE251 5.0 21.1 1.0

C.Johansson, T.Krojer, K.Park, Y.Xiong, J.Jin, U.Oppermann. Crystal Structure of SPINDLIN1 in Complex with the Inhibitor XY49-92B To Be Published.