Sodium in PDB 6fi5: Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA, PDB code: 6fi5 was solved by S.A.Andrei, F.A.Meijer, C.Ottmann, L.G.Milroy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.38 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.928, 112.209, 62.360, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.7

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA (pdb code 6fi5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA, PDB code: 6fi5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA


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 C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:12.7 occ:0.50 OE1 A:GLU2 2.3 22.3 1.0 O A:HOH593 2.4 41.2 1.0 O A:HOH407 2.6 15.9 1.0 CD A:GLU2 3.3 20.8 1.0 OE2 A:GLU2 3.7 19.2 1.0 HA A:GLU2 4.0 20.1 1.0 H A:ARG3 4.1 15.2 1.0 O A:HOH594 4.3 16.5 1.0 O A:HOH715 4.5 17.2 1.0 CG A:GLU2 4.6 15.3 1.0 HB3 A:GLU2 4.6 15.1 1.0 HG2 A:GLU2 4.8 18.4 1.0 CA A:GLU2 4.8 16.7 1.0 CB A:GLU2 4.9 12.6 1.0 N A:ARG3 4.9 12.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA


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 C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:19.8 occ:1.00 O A:GLU161 2.3 20.6 1.0 O A:HOH584 2.4 33.5 1.0 O A:HOH499 2.4 62.9 1.0 O A:HOH603 2.5 42.0 1.0 C A:GLU161 3.5 20.2 1.0 HA A:MET162 3.5 17.8 0.5 HA A:MET162 3.6 18.8 0.5 HB3 A:GLU161 4.0 19.1 1.0 HD3 A:PRO163 4.0 31.1 1.0 HA A:GLU161 4.2 17.4 1.0 CA A:MET162 4.3 14.9 0.5 N A:MET162 4.3 16.6 0.5 N A:MET162 4.4 16.8 0.5 CA A:GLU161 4.4 14.5 1.0 CA A:MET162 4.4 15.7 0.5 HG2 A:MET162 4.6 23.9 0.5 CB A:GLU161 4.7 15.9 1.0 OE1 A:GLU161 4.7 43.2 1.0 HG3 A:MET162 4.7 25.4 0.5 HG3 A:MET162 4.8 23.9 0.5 CD A:PRO163 5.0 25.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA


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 C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:49.5 occ:1.00 O A:HOH704 2.4 34.1 1.0 OE1 A:GLU80 2.5 17.4 1.0 O A:HOH648 2.8 44.0 1.0 CD A:GLU80 2.8 19.6 1.0 OE2 A:GLU80 2.9 18.1 1.0 O A:HOH465 3.0 41.5 1.0 HA3 A:GLY78 3.3 30.5 1.0 H A:GLY78 4.0 39.6 1.0 HB2 A:GLU80 4.0 17.4 1.0 CG A:GLU80 4.1 15.5 1.0 CA A:GLY78 4.1 25.4 1.0 HG2 A:GLU80 4.1 18.6 1.0 HD2 A:PRO79 4.1 21.1 1.0 H A:GLU80 4.3 19.9 1.0 N A:GLY78 4.3 33.0 1.0 CB A:GLU80 4.6 14.5 1.0 C A:GLY78 4.7 16.4 1.0 O A:HOH513 4.8 22.6 1.0 HG3 A:GLU80 4.8 18.6 1.0 HA2 A:GLY78 4.8 30.5 1.0 CD A:PRO79 4.9 17.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA


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 C-Terminal Modified Tau Peptide-Hybrid 3.2D with 14-3-3SIGMA within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:37.6 occ:0.96 O A:HOH625 2.3 44.9 1.0 O A:HOH412 2.3 27.3 1.0 OE2 A:GLU89 2.4 22.4 1.0 O A:HOH629 2.4 53.4 1.0 CD A:GLU89 3.4 16.9 1.0 HG2 A:GLU89 3.8 18.6 1.0 HE22 A:GLN93 3.9 22.8 1.0 O A:HOH622 4.0 36.6 1.0 O A:HOH431 4.0 30.7 1.0 HH12 A:ARG85 4.0 24.4 1.0 HG2 A:GLU86 4.1 22.0 1.0 CG A:GLU89 4.1 15.5 1.0 HB3 A:GLU89 4.2 15.0 1.0 OE1 A:GLU89 4.3 16.8 1.0 HH11 A:ARG85 4.3 24.4 1.0 OE1 A:GLN93 4.4 17.4 1.0 NH1 A:ARG85 4.5 20.3 1.0 NE2 A:GLN93 4.5 19.0 1.0 HA A:GLU86 4.5 14.5 1.0 HG1 A:THR90 4.6 27.3 1.0 CB A:GLU89 4.8 12.5 1.0 HB3 A:GLU86 4.8 15.9 1.0 CD A:GLN93 4.9 12.8 1.0 OG1 A:THR90 5.0 22.8 1.0 HG3 A:GLU89 5.0 18.6 1.0 CG A:GLU86 5.0 18.3 1.0

S.A.Andrei, F.A.Meijer, J.F.Neves, L.Brunsveld, I.Landrieu, C.Ottmann, L.G.Milroy. Inhibition of 14-3-3/Tau By Hybrid Small-Molecule Peptides Operating Via Two Different Binding Modes. Acs Chem Neurosci V. 9 2639 2018.
ISSN: ESSN 1948-7193
PubMed: 29722962
DOI: 10.1021/ACSCHEMNEURO.8B00118