Sodium in PDB 8b5d: Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq

The structure of Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq, PDB code: 8b5d was solved by J.Whittaker, A.Guskov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.22 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.61, 91.5, 57.91, 90, 107.81, 90
R / Rfree (%)	19.7 / 26.3

The binding sites of Sodium atom in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq (pdb code 8b5d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq, PDB code: 8b5d:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:47.3 occ:1.00 O A:HOH589 2.7 47.1 1.0 O A:HOH561 3.6 36.3 1.0 OE2 A:GLU100 3.7 33.3 1.0 N A:ASP99 3.7 39.7 1.0 CA A:THR98 4.1 38.4 1.0 CB A:THR98 4.2 35.1 1.0 OD2 A:ASP99 4.2 58.3 1.0 CG A:ASP99 4.4 45.6 1.0 C A:THR98 4.5 39.8 1.0 CG A:PRO208 4.5 32.1 1.0 CB A:ASP99 4.5 40.0 1.0 CD A:PRO208 4.6 39.6 1.0 CA A:ASP99 4.8 41.2 1.0 CD A:GLU100 4.8 48.5 1.0 CG2 A:THR98 4.8 34.8 1.0 OD1 A:ASP99 4.9 57.4 1.0 O A:ILE97 5.0 36.6 1.0

Sodium binding site 2 out of 4 in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:55.5 occ:1.00 OE1 A:GLU100 4.1 47.9 1.0 OE1 A:GLU151 4.1 38.8 1.0 CG2 A:THR147 4.3 35.2 1.0 CD2 A:LEU207 4.4 35.5 1.0 CB A:THR147 4.7 31.8 1.0 CD1 A:LEU207 4.8 30.1 1.0 O A:ALA144 4.9 28.2 1.0 CD A:GLU151 4.9 40.6 1.0 N A:TRP148 4.9 30.1 1.0 CG2 A:THR98 4.9 34.8 1.0

Sodium binding site 3 out of 4 in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:56.2 occ:1.00 OE1 B:GLU151 3.8 51.7 1.0 CD2 B:LEU207 3.9 36.4 1.0 O B:ALA144 4.2 34.2 1.0 CB B:TRP148 4.3 35.2 1.0 CD1 B:LEU207 4.3 44.4 1.0 N B:TRP148 4.3 37.0 1.0 CD B:GLU151 4.4 49.1 1.0 CG2 B:THR147 4.4 34.1 1.0 CA B:TRP148 4.4 38.5 1.0 OE2 B:GLU151 4.5 46.9 1.0 CD1 B:TRP148 4.5 44.4 1.0 CB B:THR147 4.7 37.2 1.0 CG B:LEU207 4.8 39.2 1.0 CB B:ALA144 4.8 29.7 1.0 CG B:TRP148 4.9 37.0 1.0 CD1 B:LEU116 5.0 40.3 1.0 C B:THR147 5.0 40.2 1.0 C B:ALA144 5.0 27.2 1.0

Sodium binding site 4 out of 4 in the Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:48.5 occ:1.00 O B:ILE97 2.7 37.9 1.0 N B:GLY209 2.9 31.6 1.0 C1 B:GOL403 3.3 43.4 1.0 CD B:PRO208 3.4 35.8 1.0 CA B:GLY209 3.5 30.7 1.0 N B:PRO208 3.5 27.1 1.0 CB B:LEU207 3.5 36.9 1.0 CG2 B:THR96 3.7 37.5 1.0 C B:LEU207 3.8 34.6 1.0 CG B:PRO208 3.8 35.8 1.0 C B:ILE97 3.9 36.0 1.0 O3 B:GOL403 3.9 73.4 1.0 C B:PRO208 4.0 33.2 1.0 O1 B:GOL403 4.0 53.3 1.0 CG2 B:THR98 4.0 33.6 1.0 CA B:LEU207 4.1 37.0 1.0 CA B:PRO208 4.2 36.7 1.0 C2 B:GOL403 4.3 51.7 1.0 CA B:THR98 4.3 40.2 1.0 O B:LEU207 4.4 36.1 1.0 C3 B:GOL403 4.5 61.6 1.0 O2 B:GOL403 4.5 53.5 1.0 C B:GLY209 4.5 33.7 1.0 OG B:SER114 4.6 36.0 1.0 N B:THR98 4.6 36.5 1.0 CG B:LEU207 4.6 39.2 1.0 N B:GLY210 4.6 37.1 1.0 CB B:THR98 4.6 40.2 1.0 CB B:PRO208 4.7 32.8 1.0 CD2 B:LEU207 4.9 36.4 1.0 CD1 B:LEU207 4.9 44.4 1.0

J.Whittaker, A.Guskov. Exploring the Ligand Binding and Conformational Dynamics of Receptor Domain 1 of the Abc Transporter Glnpq To Be Published.