Sodium in PDB 5ovz: High Resolution Structure of the Pbp Noct in Complex with Nopaline

The structure of High Resolution Structure of the Pbp Noct in Complex with Nopaline, PDB code: 5ovz was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.40 / 1.75
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	114.260, 114.260, 37.910, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19

The binding sites of Sodium atom in the High Resolution Structure of the Pbp Noct in Complex with Nopaline (pdb code 5ovz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the High Resolution Structure of the Pbp Noct in Complex with Nopaline, PDB code: 5ovz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:47.0 occ:1.00 O A:HOH552 2.7 35.8 1.0 O A:GLY167 2.9 24.4 1.0 NE A:ARG102 3.0 23.3 1.0 NH1 A:ARG102 3.3 23.4 1.0 CZ A:ARG102 3.6 25.0 1.0 CD1 A:ILE81 3.7 31.3 1.0 C A:GLY167 4.1 24.8 1.0 CZ2 A:TRP77 4.1 25.4 1.0 O2 A:EDO305 4.1 50.2 1.0 CD A:ARG102 4.1 23.8 1.0 O A:HOH572 4.1 47.4 1.0 C2 A:EDO305 4.1 48.1 1.0 CG A:ARG102 4.3 23.2 1.0 CE2 A:TRP77 4.4 26.7 1.0 NE1 A:TRP77 4.5 25.8 1.0 O A:HOH537 4.6 26.8 1.0 CA A:GLY167 4.6 23.4 1.0 CG1 A:ILE81 4.7 24.0 1.0 CH2 A:TRP77 4.8 26.4 1.0 CE A:MET96 4.9 24.9 1.0 NH2 A:ARG102 4.9 22.9 1.0

Sodium binding site 2 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:76.5 occ:1.00 O A:HOH568 3.0 69.8 1.0 NZ A:LYS269 3.1 84.2 1.0 CE A:LYS269 4.0 76.9 1.0 CD A:LYS269 4.5 67.9 1.0

Sodium binding site 3 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:72.4 occ:1.00 O A:HOH423 3.1 50.3 1.0 O B:HOH477 3.3 62.5 1.0 O A:GLN273 3.4 34.1 1.0 O A:TRP274 3.9 33.3 1.0 CD B:PRO218 4.1 42.0 1.0 CG B:PRO218 4.3 47.6 1.0 C A:TRP274 4.4 33.1 1.0 O A:HOH536 4.4 60.8 1.0 C A:GLN273 4.5 35.5 1.0 N A:GLY276 4.8 31.4 1.0 CA A:TRP274 4.8 28.4 1.0 O B:HOH403 4.8 54.1 1.0 O A:HOH426 4.9 42.9 1.0

Sodium binding site 4 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:70.5 occ:1.00 O A:HOH575 3.1 52.0 1.0 NH2 A:ARG229 3.8 57.9 1.0 NH1 A:ARG229 3.9 42.0 1.0 O A:HOH593 3.9 61.7 1.0 CD A:LYS212 4.1 38.9 1.0 CE A:MET225 4.3 31.8 1.0 CZ A:ARG229 4.4 67.5 1.0 CE A:LYS212 4.5 54.4 1.0 NZ A:LYS212 4.6 59.1 1.0 O A:HOH578 4.7 64.2 1.0 CG A:LYS212 4.9 31.8 1.0

Sodium binding site 5 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:74.6 occ:1.00 NE2 B:GLN146 3.1 46.4 1.0 CG B:PRO138 3.6 52.0 1.0 OE1 B:GLN146 3.8 47.2 1.0 CD B:GLN146 3.9 54.1 1.0 O B:ASN141 4.2 54.3 1.0 CB B:PRO138 4.5 46.3 1.0 CD B:PRO138 4.5 47.4 1.0 O B:PRO138 4.6 47.7 1.0 CG2 B:THR143 4.6 49.0 1.0 OD1 B:ASN141 4.7 88.5 1.0 CB B:ASN141 4.9 53.3 1.0

Sodium binding site 6 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:82.6 occ:1.00 O B:THR185 3.0 48.1 1.0 C B:THR185 3.9 47.1 1.0 CZ B:TYR186 4.1 53.0 1.0 CE2 B:TYR186 4.1 46.0 1.0 CE1 B:TYR186 4.1 45.6 1.0 CD2 B:TYR186 4.1 44.6 1.0 CG B:TYR186 4.2 43.1 1.0 CD1 B:TYR186 4.2 44.8 1.0 CB B:SER184 4.3 50.9 1.0 N B:THR185 4.3 43.8 1.0 O B:HOH448 4.6 50.7 1.0 CA B:TYR186 4.6 41.5 1.0 OH B:TYR186 4.6 54.7 1.0 N B:TYR186 4.7 42.1 1.0 C B:SER184 4.8 46.8 1.0 CA B:THR185 4.8 42.9 1.0 CA B:SER184 4.9 46.1 1.0

Sodium binding site 7 out of 7 in the High Resolution Structure of the Pbp Noct in Complex with Nopaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High Resolution Structure of the Pbp Noct in Complex with Nopaline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:62.8 occ:1.00 NH2 B:ARG229 3.5 57.3 1.0 NH1 B:ARG229 3.8 51.9 1.0 O B:HOH474 3.9 70.6 1.0 CZ B:ARG229 4.1 68.1 1.0 CE B:MET225 4.2 43.4 1.0 CD B:LYS212 4.5 48.5 1.0 NZ B:LYS212 4.7 55.1 1.0 CE B:LYS212 4.9 54.8 1.0

A.Vigouroux, A.El Sahili, J.Lang, M.Aumont-Nicaise, Y.Dessaux, D.Faure, S.Morera. How to Be A Highly Affine Octopine Binding Protein to Exploit the Constructued Octopine-Niche on Plant Host To Be Published.