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Sodium in PDB 6fav: Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA

Protein crystallography data

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA, PDB code: 6fav 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) 47.33 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.789, 70.140, 128.259, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 6fav:

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA (pdb code 6fav). 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 C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA, PDB code: 6fav:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6fav

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Sodium binding site 1 out of 5 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I 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 4.2F-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:35.7
occ:1.00
 O A:HOH586 2.3 48.3 1.0
OXT A:THR231 2.3 32.3 1.0
O A:THR228 2.3 26.4 1.0
O A:HOH731 2.4 54.6 1.0
O A:HOH661 2.4 43.9 1.0
HG23 A:THR228 3.1 30.1 0.3
HG22 A:THR228 3.4 30.1 0.3
C A:THR228 3.5 23.4 1.0
C A:THR231 3.5 30.3 1.0
HB A:THR228 3.6 28.3 0.7
HA A:THR228 3.6 27.5 0.3
HA A:THR228 3.7 27.3 0.7
CG2 A:THR228 3.7 25.1 0.3
O A:HOH562 3.8 50.2 1.0
O A:THR231 4.0 31.9 1.0
CA A:THR228 4.0 22.7 0.7
CA A:THR228 4.0 22.9 0.3
H A:THR231 4.2 27.9 1.0
CB A:THR228 4.3 23.6 0.7
HG21 A:THR228 4.5 30.1 0.3
CB A:THR228 4.5 24.1 0.3
HA A:LEU229 4.6 25.9 1.0
O A:HOH683 4.6 41.5 1.0
N A:LEU229 4.6 21.2 1.0
CA A:THR231 4.7 26.6 1.0
N A:THR231 4.7 23.3 1.0
HG1 A:THR231 4.9 32.6 1.0
CA A:LEU229 4.9 21.6 1.0
O A:LEU229 4.9 22.8 1.0
C A:LEU229 5.0 20.6 1.0
HG23 A:THR228 5.0 29.3 0.7

Sodium binding site 2 out of 5 in 6fav

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Sodium binding site 2 out of 5 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I 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 4.2F-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:40.5
occ:1.00
 O A:GLU161 2.4 21.6 1.0
O A:HOH645 2.4 37.1 1.0
O A:HOH571 2.4 48.2 1.0
O A:HOH653 2.7 44.1 1.0
HA A:MET162 3.5 21.8 0.3
HA A:MET162 3.5 20.1 0.7
C A:GLU161 3.6 19.6 1.0
HD3 A:PRO163 4.0 23.5 1.0
HG3 A:MET162 4.2 22.9 0.3
O A:HOH521 4.2 48.3 1.0
HB3 A:GLU161 4.3 26.2 1.0
CA A:MET162 4.3 18.1 0.3
HA A:GLU161 4.3 24.7 1.0
CA A:MET162 4.3 16.8 0.7
N A:MET162 4.4 18.5 0.3
N A:MET162 4.4 17.4 0.7
CA A:GLU161 4.5 20.6 1.0
HD2 A:PRO163 4.7 23.5 1.0
CD A:PRO163 4.7 19.6 1.0
HG2 A:MET162 4.8 19.1 0.7
HG2 A:MET162 4.9 22.9 0.3
CG A:MET162 4.9 19.1 0.3
CB A:GLU161 4.9 21.8 1.0

Sodium binding site 3 out of 5 in 6fav

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Sodium binding site 3 out of 5 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I 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 4.2F-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:19.0
occ:0.75
 O A:HOH610 2.2 37.6 1.0
O A:GLY-1 2.4 15.8 1.0
O A:HOH660 2.4 41.6 1.0
C A:GLY-1 3.4 14.7 1.0
HA A:SER0 3.8 15.8 1.0
HZ1 A:LYS32 3.8 21.4 1.0
O A:HOH666 3.9 42.5 1.0
HZ2 A:LYS32 4.0 21.4 1.0
HA2 A:GLY-1 4.0 19.5 1.0
HA3 A:GLY-1 4.0 19.5 1.0
CA A:GLY-1 4.1 16.2 1.0
NZ A:LYS32 4.3 17.8 1.0
N A:SER0 4.3 13.4 1.0
CA A:SER0 4.5 13.2 1.0
HZ3 A:LYS32 4.5 21.4 1.0
O A:HOH668 4.7 32.1 1.0

Sodium binding site 4 out of 5 in 6fav

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Sodium binding site 4 out of 5 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I 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 4.2F-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:19.8
occ:0.94
 O C:HOH451 2.3 44.5 1.0
O C:HOH637 2.3 43.1 1.0
OE2 C:GLU2 2.4 18.7 0.6
O C:HOH413 2.7 19.5 1.0
HG2 C:GLU2 3.2 18.2 0.4
CD C:GLU2 3.3 18.0 0.6
OE1 C:GLU2 3.6 18.1 0.6
HA C:GLU2 4.0 16.4 0.6
HA C:GLU2 4.0 15.9 0.4
CG C:GLU2 4.1 15.2 0.4
H C:ARG3 4.3 16.9 1.0
OE2 C:GLU2 4.3 14.6 0.4
HB3 C:GLU2 4.4 17.1 0.4
O C:HOH695 4.5 23.6 1.0
O C:HOH580 4.5 18.1 1.0
CD C:GLU2 4.5 15.5 0.4
O C:HOH577 4.6 20.6 1.0
CG C:GLU2 4.6 17.0 0.6
O C:HOH672 4.6 48.3 1.0
CB C:GLU2 4.7 14.2 0.4
HB3 C:GLU2 4.7 18.3 0.6
CA C:GLU2 4.8 13.3 0.4
HG3 C:GLU2 4.8 18.2 0.4
CA C:GLU2 4.8 13.7 0.6
O C:HOH404 4.9 47.9 1.0
HG2 C:GLU2 4.9 20.4 0.6
CB C:GLU2 5.0 15.2 0.6

Sodium binding site 5 out of 5 in 6fav

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Sodium binding site 5 out of 5 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA


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 C-Terminal Modified Tau Peptide-Hybrid 4.2F-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:35.1
occ:0.91
 O C:HOH444 2.3 43.4 1.0
O C:HOH609 2.4 39.7 1.0
OE1 C:GLU80 2.6 17.9 1.0
O C:HOH429 2.9 28.0 1.0
CD C:GLU80 3.0 17.7 1.0
OE2 C:GLU80 3.0 20.2 1.0
HA3 C:GLY78 3.1 30.8 1.0
CA C:GLY78 4.0 25.6 1.0
HD2 C:PRO79 4.1 24.7 1.0
CG C:GLU80 4.2 15.6 1.0
HB2 C:GLU80 4.3 17.1 1.0
N C:GLY78 4.3 29.9 1.0
HG2 C:GLU80 4.3 18.8 1.0
H C:GLU80 4.5 18.4 1.0
HA2 C:GLY78 4.6 30.8 1.0
C C:GLY78 4.8 22.6 1.0
CB C:GLU80 4.8 14.3 1.0
HG3 C:GLU80 5.0 18.8 1.0
CD C:PRO79 5.0 20.6 1.0

Reference:

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
Page generated: Tue Oct 8 08:43:14 2024

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