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

Protein crystallography data

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

Other elements in 7ocb:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

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 7ocb

Go back to Sodium Binding Sites List in 7ocb
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 7ocb

Go back to Sodium Binding Sites List in 7ocb
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

Reference:

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.
Page generated: Fri Apr 7 15:23:44 2023

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