Sodium in PDB 6g8q: 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide

The structure of 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide, PDB code: 6g8q was solved by S.A.Andrei, V.Thijssen, L.Brunsveld, C.Ottmann, L.G.Milroy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.95 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.108, 111.900, 62.620, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.5

The structure of 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide (pdb code 6g8q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide, PDB code: 6g8q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:34.3 occ:1.00 O A:HOH626 2.4 35.0 1.0 O A:LYS77 2.4 38.4 1.0 OE1 A:GLU80 2.5 14.7 1.0 O A:HOH457 2.7 29.3 1.0 OE2 A:GLU80 2.7 20.1 1.0 CD A:GLU80 2.8 21.3 1.0 HA3 A:GLY78 3.2 34.7 1.0 C A:LYS77 3.5 49.0 1.0 HD2 A:PRO79 4.0 24.1 1.0 CA A:GLY78 4.1 28.9 1.0 CG A:GLU80 4.2 13.4 1.0 N A:GLY78 4.2 31.8 1.0 HG2 A:GLU80 4.3 16.1 1.0 HB2 A:GLU80 4.3 16.3 1.0 HB3 A:LYS77 4.3 64.5 1.0 HA A:LYS77 4.4 64.8 1.0 H A:GLU80 4.5 16.8 1.0 CA A:LYS77 4.5 54.0 1.0 HA2 A:GLY78 4.7 34.7 1.0 C A:GLY78 4.8 24.0 1.0 CB A:GLU80 4.8 13.6 1.0 HG3 A:GLU80 4.8 16.1 1.0 CD A:PRO79 4.9 20.1 1.0 CB A:LYS77 5.0 53.8 1.0 H A:GLY78 5.0 38.1 1.0

Sodium binding site 2 out of 3 in the 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:20.3 occ:1.00 O A:GLU161 2.3 21.3 1.0 O A:HOH584 2.4 38.6 1.0 O A:HOH474 2.6 36.3 1.0 C A:GLU161 3.5 19.4 1.0 HA A:MET162 3.5 21.3 0.5 HA A:MET162 3.6 21.3 0.5 HB3 A:GLU161 4.1 21.2 1.0 HA A:GLU161 4.2 19.6 1.0 HD3 A:PRO163 4.2 24.4 1.0 CA A:MET162 4.3 17.7 0.5 N A:MET162 4.3 13.2 1.0 CA A:GLU161 4.4 16.3 1.0 O A:HOH588 4.4 41.6 1.0 OE2 A:GLU115 4.4 35.6 0.6 CA A:MET162 4.4 17.8 0.5 HG3 A:MET162 4.5 23.7 0.5 HG2 A:MET162 4.7 23.7 0.5 OE1 A:GLU161 4.7 36.8 1.0 CB A:GLU161 4.8 17.6 1.0 CD A:PRO163 4.9 20.4 1.0 O A:HOH674 4.9 42.6 1.0 HD2 A:PRO163 5.0 24.4 1.0

Sodium binding site 3 out of 3 in the 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 14-3-3SIGMA in Complex with A A130BETA3A and Q133BETA3Q Mutated Yap PS127 Phosphopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:11.8 occ:0.50 OE1 A:GLU2 2.4 23.2 1.0 O A:HOH441 2.5 16.2 1.0 O A:HOH640 2.5 45.1 1.0 O A:HOH633 2.6 37.3 1.0 O A:HOH713 2.6 44.7 1.0 CD A:GLU2 3.4 21.2 1.0 OE2 A:GLU2 3.8 20.2 1.0 HA A:GLU2 4.0 13.6 1.0 H A:ARG3 4.1 14.7 1.0 O A:HOH589 4.3 16.7 1.0 O A:HOH720 4.4 20.0 1.0 HB3 A:GLU2 4.5 17.3 1.0 CG A:GLU2 4.6 13.1 1.0 CA A:GLU2 4.8 11.3 1.0 HG2 A:GLU2 4.8 15.7 1.0 CB A:GLU2 4.9 14.4 1.0 O A:HOH467 4.9 31.6 1.0 N A:ARG3 4.9 12.2 1.0

S.A.Andrei, V.Thijssen, L.Brunsveld, C.Ottmann, L.G.Milroy. A Study on the Effect of Synthetic Alpha-to-BETA3-Amino Acid Mutations on the Binding of Phosphopeptides to 14-3-3 Proteins. Chem.Commun.(Camb.) 2019.
ISSN: ESSN 1364-548X
PubMed: 31763628
DOI: 10.1039/C9CC07982C