Sodium in PDB 6qdt: Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide

The structure of Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide, PDB code: 6qdt was solved by S.A.Andrei, A.Kaplan, A.E.Fournier, C.Ottman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.87 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.657, 112.411, 62.749, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.2

The structure of Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide (pdb code 6qdt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide, PDB code: 6qdt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide


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 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:37.7 occ:1.00 O A:HOH676 2.4 45.9 1.0 O A:THR231 2.4 44.4 1.0 O A:THR228 2.4 22.3 1.0 O A:HOH711 2.5 51.3 1.0 O A:HOH661 3.0 49.9 1.0 HG21 A:THR228 3.3 27.2 1.0 C A:THR231 3.5 40.7 1.0 C A:THR228 3.6 19.9 1.0 HA A:THR228 3.8 23.4 1.0 HG23 A:THR228 3.9 27.2 1.0 OXT A:THR231 3.9 45.1 1.0 CG2 A:THR228 4.0 22.6 1.0 H A:THR231 4.1 33.0 1.0 CA A:THR228 4.2 19.5 1.0 HA A:LEU229 4.5 23.6 1.0 HG1 A:THR231 4.6 35.4 1.0 O A:HOH575 4.6 37.8 1.0 N A:THR231 4.6 27.5 1.0 CA A:THR231 4.6 33.0 1.0 N A:LEU229 4.7 17.8 1.0 OG1 A:THR231 4.8 29.5 1.0 HG22 A:THR228 4.8 27.2 1.0 CB A:THR228 4.8 20.7 1.0 O A:LEU229 4.9 22.0 1.0 CA A:LEU229 4.9 19.7 1.0 C A:LEU229 4.9 19.9 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide


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 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:17.8 occ:1.00 O A:GLU161 2.3 15.7 1.0 O A:HOH650 2.3 35.3 1.0 O A:HOH642 2.4 31.7 1.0 O A:HOH588 2.6 26.2 1.0 C A:GLU161 3.5 14.1 1.0 HA A:MET162 3.5 16.8 1.0 HB3 A:GLU161 4.0 16.3 1.0 HA A:GLU161 4.1 16.8 1.0 HD3 A:PRO163 4.2 18.7 1.0 CA A:GLU161 4.4 14.1 1.0 CA A:MET162 4.4 14.0 1.0 N A:MET162 4.4 12.1 1.0 OE2 A:GLU115 4.5 23.5 0.6 CB A:GLU161 4.7 13.7 1.0 OE1 A:GLU161 4.7 32.6 1.0 HG2 A:MET162 4.8 19.4 1.0 CD A:PRO163 5.0 15.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:4.9 occ:0.50 O A:HOH598 2.2 36.8 1.0 OE1 A:GLU2 2.4 11.6 1.0 O A:HOH451 2.5 11.1 1.0 CD A:GLU2 3.4 11.7 1.0 OE2 A:GLU2 3.8 12.6 1.0 HA A:GLU2 4.1 10.3 1.0 H A:ARG3 4.2 10.1 1.0 O A:HOH627 4.3 10.3 1.0 O A:HOH779 4.5 12.5 1.0 HB3 A:GLU2 4.7 10.4 1.0 CG A:GLU2 4.7 9.4 1.0 CA A:GLU2 4.9 8.6 1.0 HG2 A:GLU2 4.9 11.3 1.0 CB A:GLU2 5.0 8.6 1.0 N A:ARG3 5.0 8.4 1.0 O A:HOH459 5.0 18.8 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:55.3 occ:0.89 OE1 A:GLU110 2.2 34.8 0.6 O A:HOH551 2.6 30.1 1.0 O A:HOH767 2.7 28.1 1.0 O A:GLY33 2.8 11.0 1.0 HG3 A:GLU35 2.9 19.7 1.0 CD A:GLU110 2.9 16.6 0.6 HA A:GLU34 3.1 11.3 1.0 OE2 A:GLU110 3.3 16.1 0.6 HG3 A:GLU110 3.3 15.2 0.5 O A:HOH686 3.4 39.3 1.0 H A:GLU35 3.4 12.1 1.0 O A:HOH678 3.4 30.1 1.0 O A:HOH436 3.6 15.3 1.0 N A:GLU35 3.7 10.0 1.0 CG A:GLU35 3.8 16.4 1.0 O A:HOH404 3.8 15.4 1.0 O A:HOH422 3.8 24.7 1.0 HG2 A:GLU35 3.9 19.7 1.0 C A:GLY33 3.9 8.9 1.0 CA A:GLU34 3.9 9.4 1.0 HB3 A:GLU110 4.0 13.0 0.6 C A:GLU34 4.0 8.8 1.0 CG A:GLU110 4.2 12.6 0.5 HB3 A:GLU110 4.2 13.3 0.5 CG A:GLU110 4.2 13.3 0.6 OE2 A:GLU35 4.4 23.7 1.0 N A:GLU34 4.4 8.1 1.0 HG2 A:GLU110 4.5 16.1 0.6 CB A:GLU110 4.6 10.8 0.6 CB A:GLU110 4.6 11.1 0.5 HB2 A:GLU110 4.6 13.3 0.5 CA A:GLU35 4.6 9.4 1.0 CD A:GLU35 4.6 21.5 1.0 HA A:GLU35 4.6 11.3 1.0 HB2 A:GLU110 4.7 13.0 0.6 CB A:GLU35 4.7 12.2 1.0 CD A:GLU110 4.8 16.1 0.5 OE1 A:GLU34 4.8 46.6 1.0 HG2 A:GLU110 4.8 15.2 0.5 O A:GLU34 4.9 10.2 1.0 HB2 A:GLU35 4.9 14.6 1.0 HG3 A:GLU110 4.9 16.1 0.6

Sodium binding site 5 out of 5 in the Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of 14-3-3SIGMA in Complex with A RAPGEF2 PT740 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:26.0 occ:1.00 O A:LYS77 2.3 38.9 1.0 O A:HOH665 2.4 37.9 1.0 OE1 A:GLU80 2.5 13.0 1.0 OE2 A:GLU80 2.8 14.8 1.0 CD A:GLU80 2.9 13.1 1.0 O A:HOH454 2.9 18.5 1.0 HA3 A:GLY78 3.2 34.4 1.0 C A:LYS77 3.4 39.6 1.0 CA A:GLY78 4.0 28.7 1.0 HB3 A:LYS77 4.0 53.9 1.0 HD2 A:PRO79 4.1 21.5 1.0 N A:GLY78 4.1 35.6 1.0 HA A:LYS77 4.2 51.6 1.0 CG A:GLU80 4.2 11.9 1.0 HB2 A:GLU80 4.3 12.7 1.0 CA A:LYS77 4.3 43.0 1.0 HG2 A:GLU80 4.4 14.3 1.0 H A:GLU80 4.5 13.6 1.0 HA2 A:GLY78 4.7 34.4 1.0 CB A:LYS77 4.7 44.9 1.0 C A:GLY78 4.7 20.5 1.0 CB A:GLU80 4.8 10.7 1.0 HG3 A:GLU80 4.9 14.3 1.0 H A:GLY78 4.9 42.8 1.0 CD A:PRO79 4.9 18.0 1.0

A.Kaplan, S.A.Andrei, C.Ottmann, A.E.Fournier. A Single-Agent Polypharmacological Approach to Stimulate Axon Regeneration To Be Published.