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

Protein crystallography data

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-I with 14-3-3SIGMA, PDB code: 6fau 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) 47.35 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.800, 70.260, 128.180, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.4

Other elements in 6fau:

The structure of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA (pdb code 6fau). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-I with 14-3-3SIGMA, PDB code: 6fau:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6fau

Go back to Sodium Binding Sites List in 6fau
Sodium binding site 1 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:55.0
occ:1.00
 O A:HOH712 2.3 38.4 1.0
HZ1 A:LYS32 2.5 19.2 1.0
O A:HOH412 2.5 16.2 1.0
O A:HOH732 2.5 43.7 1.0
O A:HOH679 2.5 38.8 1.0
HZ3 A:LYS32 2.6 19.2 1.0
NZ A:LYS32 2.9 16.0 1.0
HD3 A:LYS32 3.1 15.2 1.0
O A:GLY-1 3.2 15.4 1.0
HD2 A:LYS32 3.4 15.2 1.0
CD A:LYS32 3.6 12.7 1.0
HZ2 A:LYS32 3.6 19.2 1.0
HA2 A:GLY-1 3.6 17.9 1.0
CE A:LYS32 3.8 14.0 1.0
C A:GLY-1 4.1 14.2 1.0
O A:HOH541 4.2 16.9 1.0
CA A:GLY-1 4.3 14.9 1.0
HA A:LYS32 4.3 14.0 1.0
HE2 A:LYS32 4.4 16.8 1.0
HE3 A:LYS32 4.5 16.8 1.0
HA3 A:GLY-1 4.5 17.9 1.0
O A:HOH491 5.0 33.5 1.0

Sodium binding site 2 out of 7 in 6fau

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Sodium binding site 2 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:28.9
occ:1.00
 O A:HOH555 2.2 44.0 1.0
O A:HOH762 2.3 48.5 1.0
O A:HOH523 2.3 42.3 1.0
O A:THR228 2.3 26.5 1.0
OXT A:THR231 2.4 30.7 1.0
O A:HOH657 2.4 49.6 1.0
C A:THR228 3.5 23.3 1.0
C A:THR231 3.5 29.1 1.0
HB A:THR228 3.6 31.6 1.0
HA A:THR228 3.7 27.5 1.0
O A:THR231 4.0 31.8 1.0
CA A:THR228 4.0 22.9 1.0
O A:HOH483 4.1 51.2 1.0
H A:THR231 4.2 25.8 1.0
CB A:THR228 4.3 26.3 1.0
O A:HOH702 4.5 35.5 1.0
HA A:LEU229 4.5 25.6 1.0
N A:LEU229 4.6 20.8 1.0
N A:THR231 4.7 21.5 1.0
CA A:THR231 4.7 24.9 1.0
CA A:LEU229 4.9 21.4 1.0
O A:LEU229 4.9 21.5 1.0
C A:LEU229 4.9 20.1 1.0
HG1 A:THR231 5.0 30.9 1.0
HG21 A:THR228 5.0 32.5 1.0

Sodium binding site 3 out of 7 in 6fau

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Sodium binding site 3 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:28.0
occ:1.00
 O A:GLU161 2.3 17.1 0.5
O A:HOH558 2.4 41.5 1.0
O A:HOH656 2.4 32.6 1.0
O A:GLU161 2.5 17.3 0.5
O A:HOH490 2.5 37.8 1.0
HA A:MET162 3.5 20.5 0.5
HA A:MET162 3.5 16.1 0.5
C A:GLU161 3.5 15.7 0.5
C A:GLU161 3.5 17.1 0.5
HD3 A:PRO163 4.0 21.7 1.0
HB3 A:GLU161 4.1 23.9 0.5
O A:HOH672 4.1 43.8 1.0
HB3 A:GLU161 4.3 21.5 0.5
HA A:GLU161 4.3 20.9 0.5
HA A:GLU161 4.3 21.3 0.5
CA A:MET162 4.3 17.1 0.5
N A:MET162 4.3 16.7 0.5
CA A:MET162 4.3 13.4 0.5
O A:HOH430 4.4 37.7 1.0
N A:MET162 4.4 14.0 0.5
CA A:GLU161 4.5 17.8 0.5
CA A:GLU161 4.5 17.4 0.5
O A:HOH670 4.6 42.6 1.0
HG2 A:MET162 4.6 26.2 0.5
O A:HOH758 4.6 37.4 1.0
CB A:GLU161 4.8 19.9 0.5
CD A:PRO163 4.8 18.1 1.0
HD2 A:PRO163 4.8 21.7 1.0
HG2 A:MET162 4.9 13.1 0.5
CB A:GLU161 4.9 17.9 0.5
OE1 A:GLU161 5.0 27.7 0.5

Sodium binding site 4 out of 7 in 6fau

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Sodium binding site 4 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:42.3
occ:0.78
 HZ3 A:LYS195 2.2 25.3 0.4
O A:HOH567 2.7 23.1 1.0
HG A:SER192 2.8 16.6 0.5
HD2 A:LYS195 2.8 21.1 0.4
HG21 A:ILE191 2.9 17.9 1.0
NZ A:LYS195 3.0 21.1 0.4
HZ1 A:LYS195 3.2 25.3 0.4
OG A:SER192 3.4 13.9 0.5
HA A:SER192 3.5 14.6 0.5
HA A:SER192 3.5 15.6 0.5
HZ2 A:LYS195 3.6 25.3 0.4
CD A:LYS195 3.6 17.5 0.4
CE A:LYS195 3.7 19.3 0.4
HB2 A:SER192 3.7 17.4 0.5
HG23 A:ILE191 3.7 17.9 1.0
CG2 A:ILE191 3.7 14.9 1.0
HE3 A:LYS195 3.9 23.2 0.4
HD3 A:LYS195 3.9 21.1 0.4
CA A:SER192 4.1 12.2 0.5
CA A:SER192 4.1 13.0 0.5
N A:SER192 4.2 12.0 1.0
O A:HOH667 4.2 29.2 1.0
HD3 A:LYS195 4.3 22.5 0.6
H A:SER192 4.3 14.4 0.5
H A:SER192 4.3 14.4 0.5
CB A:SER192 4.3 12.0 0.5
HB A:ILE191 4.4 16.4 1.0
HG22 A:ILE191 4.4 17.9 1.0
CB A:SER192 4.4 14.5 0.5
O A:HOH613 4.5 40.0 1.0
C A:ILE191 4.6 12.2 1.0
HE2 A:LYS195 4.6 23.2 0.4
CB A:ILE191 4.7 13.7 1.0
HB3 A:SER192 4.7 14.4 0.5
O A:ILE191 4.8 12.7 1.0
HB2 A:LYS195 4.8 18.4 0.4
CG A:LYS195 4.8 16.2 0.4
HD2 A:LYS195 4.9 22.5 0.6
HG3 A:LYS195 4.9 19.4 0.4
HG A:SER192 4.9 20.9 0.5
HB3 A:LYS195 4.9 18.1 0.6
O A:GLU188 4.9 13.9 0.5
O A:GLU188 5.0 11.6 0.5

Sodium binding site 5 out of 7 in 6fau

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Sodium binding site 5 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:34.5
occ:0.76
 O A:HOH599 2.4 47.0 1.0
O A:HOH706 2.5 35.5 1.0
O A:HOH702 2.7 35.5 1.0
O A:HOH518 2.7 35.4 1.0
OG1 A:THR228 2.8 28.1 1.0
O A:ASP225 2.9 15.5 1.0
HG1 A:THR228 3.0 33.8 1.0
HA A:ASP225 3.2 17.9 1.0
H A:LEU229 3.4 24.9 1.0
HB2 A:LEU229 3.4 26.1 1.0
N A:LEU229 3.6 20.8 1.0
C A:ASP225 3.7 14.5 1.0
HB3 A:ASP225 3.8 19.1 1.0
CA A:ASP225 3.8 14.9 1.0
HA A:LEU229 3.9 25.6 1.0
CB A:THR228 3.9 26.3 1.0
C A:THR228 4.0 23.3 1.0
HB A:THR228 4.1 31.6 1.0
CA A:LEU229 4.1 21.4 1.0
CB A:LEU229 4.2 21.8 1.0
CB A:ASP225 4.3 15.9 1.0
O A:HOH557 4.4 19.3 1.0
OD1 A:ASP225 4.5 18.8 1.0
CA A:THR228 4.5 22.9 1.0
H A:THR228 4.6 23.0 1.0
HB3 A:LEU229 4.6 26.1 1.0
O A:THR228 4.7 26.5 1.0
HD11 A:LEU229 4.7 32.8 1.0
CG A:ASP225 4.8 17.6 1.0
O A:HOH657 4.8 49.6 1.0
N A:THR228 4.9 19.2 1.0
O A:ARG224 4.9 15.8 1.0
N A:ASN226 5.0 13.5 1.0

Sodium binding site 6 out of 7 in 6fau

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Sodium binding site 6 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 6 of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:46.6
occ:1.00
 HA C:GLU200 2.9 18.6 1.0
HB3 C:ASP199 3.1 19.7 1.0
O C:ASP199 3.2 16.1 1.0
HG2 C:GLU200 3.3 22.9 1.0
HB1 C:ALA203 3.3 16.5 1.0
C C:ASP199 3.5 15.8 1.0
CA C:GLU200 3.7 15.5 1.0
N C:GLU200 3.8 15.9 1.0
O C:HOH553 3.9 41.3 1.0
HG3 C:GLU200 3.9 22.9 1.0
CG C:GLU200 4.0 19.1 1.0
CB C:ASP199 4.0 16.4 1.0
CB C:ALA203 4.1 13.8 1.0
HB3 C:ALA203 4.1 16.5 1.0
HB2 C:ASP199 4.2 19.7 1.0
H C:GLU200 4.3 19.1 1.0
CA C:ASP199 4.4 15.7 1.0
O C:HOH477 4.4 24.3 1.0
CB C:GLU200 4.4 17.2 1.0
H C:ALA203 4.5 16.8 1.0
HB2 C:ALA203 4.6 16.5 1.0
O C:HOH426 4.7 42.5 1.0
C C:GLU200 4.7 15.2 1.0
HA C:ASP199 4.8 18.8 1.0
HB3 C:GLU200 4.8 20.6 1.0
O C:GLU200 4.9 16.0 1.0

Sodium binding site 7 out of 7 in 6fau

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Sodium binding site 7 out of 7 in the Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-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 7 of Crystal Structure of C-Terminal Modified Tau Peptide-Hybrid 4.2E-I with 14-3-3SIGMA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:46.4
occ:0.88
 OD1 C:ASP204 2.5 21.1 1.0
O C:HOH714 2.6 43.1 1.0
HD2 C:PRO164 3.0 24.6 1.0
O C:HOH454 3.1 27.1 1.0
CG C:ASP204 3.4 18.6 1.0
HG3 C:PRO164 3.6 25.9 1.0
CD C:PRO164 3.6 20.5 1.0
HD3 C:PRO164 3.6 24.6 1.0
OD2 C:ASP204 3.7 18.9 1.0
HG2 C:PRO164 3.7 25.9 1.0
CG C:PRO164 3.9 21.6 1.0
O C:HOH444 4.3 26.8 1.0
HA C:PRO163 4.7 27.6 1.0
HB3 C:PRO163 4.7 31.2 1.0
CB C:ASP204 4.7 17.9 1.0
HB3 C:ASP204 4.8 21.5 1.0
O C:HOH477 4.9 24.3 1.0
HB2 C:PRO163 5.0 31.2 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 08:43:04 2024

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