Sodium in PDB 6y7t: Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding

The structure of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding, PDB code: 6y7t was solved by X.Guillory, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.90 / 2.50
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.151, 63.119, 167.021, 90, 101.29, 90
R / Rfree (%)	21.9 / 26.8

The binding sites of Sodium atom in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding (pdb code 6y7t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding, PDB code: 6y7t:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:33.5 occ:1.00 O A:HOH439 2.7 36.1 1.0 O A:HOH403 3.8 49.6 1.0 O A:GLU83 3.9 42.0 1.0 CB A:LYS87 4.1 44.9 1.0 CA A:TYR84 4.1 39.8 1.0 C A:GLU83 4.1 42.6 1.0 N A:TYR84 4.2 41.9 1.0 CB A:GLU83 4.3 44.3 1.0 CD A:LYS87 4.3 52.2 1.0 CG A:LYS87 4.4 48.1 1.0 CD1 A:TYR84 4.4 38.6 1.0 NZ A:LYS87 4.5 54.6 1.0 CB A:TYR84 4.5 39.0 1.0 CA A:GLU83 4.9 43.7 1.0

Sodium binding site 2 out of 5 in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:31.9 occ:1.00 O P:HOH454 2.7 38.5 1.0 NZ F:LYS9 3.3 38.0 1.0 O P:GLU83 3.9 35.0 1.0 CE F:LYS9 3.9 37.9 1.0 CD P:LYS87 3.9 50.9 1.0 CD F:LYS9 3.9 36.1 1.0 CA P:TYR84 3.9 36.3 1.0 C P:GLU83 4.0 37.1 1.0 CB P:LYS87 4.1 46.6 1.0 N P:TYR84 4.1 37.8 1.0 CD1 P:TYR84 4.2 33.5 1.0 CB P:GLU83 4.3 37.9 1.0 CZ F:PHE25 4.3 32.9 1.0 CG P:LYS87 4.4 48.1 1.0 CB P:TYR84 4.4 36.6 1.0 CE F:MET1 4.5 37.5 1.0 CE1 F:PHE25 4.5 32.8 1.0 CA P:GLU83 4.8 39.5 1.0 CG P:TYR84 4.8 35.7 1.0

Sodium binding site 3 out of 5 in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding within 5.0Å range: probe atom residue distance (Å) B Occ K:Na301 b:31.8 occ:1.00 O K:GLU83 3.8 32.7 1.0 CD K:LYS87 3.9 50.4 1.0 CA K:TYR84 3.9 36.1 1.0 C K:GLU83 3.9 35.7 1.0 N K:TYR84 4.0 36.5 1.0 CB K:LYS87 4.2 42.5 1.0 CD1 K:TYR84 4.2 33.7 1.0 CB K:GLU83 4.2 35.4 1.0 CB K:TYR84 4.3 36.6 1.0 CG K:LYS87 4.5 45.8 1.0 CA K:GLU83 4.7 37.3 1.0 CG K:TYR84 4.8 35.7 1.0

Sodium binding site 4 out of 5 in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding within 5.0Å range: probe atom residue distance (Å) B Occ P:Na301 b:28.1 occ:1.00 O F:HOH448 2.8 36.7 1.0 NZ P:LYS9 3.1 35.0 1.0 CD P:LYS9 3.8 34.6 1.0 O F:HOH401 3.8 47.4 1.0 CE P:LYS9 3.8 35.5 1.0 CA F:TYR84 4.0 35.0 1.0 O F:GLU83 4.0 31.6 1.0 C F:GLU83 4.1 34.5 1.0 CB F:LYS87 4.2 41.1 1.0 N F:TYR84 4.2 35.0 1.0 CZ P:PHE25 4.2 38.7 1.0 CD1 F:TYR84 4.2 35.4 1.0 CB F:GLU83 4.3 36.6 1.0 CB F:TYR84 4.3 34.4 1.0 CE1 P:PHE25 4.4 38.7 1.0 CE P:MET1 4.4 39.3 1.0 CD F:LYS87 4.4 50.6 1.0 CG F:LYS87 4.5 44.3 1.0 CG F:TYR84 4.8 34.1 1.0 CA F:GLU83 4.9 37.4 1.0 NZ F:LYS87 4.9 56.7 1.0 O P:HOH434 4.9 47.0 1.0 CG P:LYS9 5.0 35.9 1.0

Sodium binding site 5 out of 5 in the Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Conjugation of Lysine-Specific Molecular Tweezers with Exos Derived Peptidic Inhibitor Enhance Affinity Towards Target Protein 14-3-3 Through Ditopic Binding within 5.0Å range: probe atom residue distance (Å) B Occ P:Na302 b:42.6 occ:1.00 O P:ALA29 2.5 36.3 1.0 O P:GLU34 2.7 48.1 1.0 N P:GLU34 3.2 46.7 1.0 NE P:ARG3 3.2 38.6 1.0 C P:ALA29 3.4 38.9 1.0 NH2 P:ARG3 3.5 38.5 1.0 C P:GLU34 3.5 48.0 1.0 CA P:GLU34 3.6 49.6 1.0 O P:VAL30 3.6 39.8 1.0 CA P:VAL30 3.7 38.8 1.0 CB P:GLU34 3.7 53.9 1.0 N P:GLY33 3.8 40.8 1.0 CZ P:ARG3 3.8 37.5 1.0 N P:VAL30 3.9 38.3 1.0 C P:VAL30 3.9 39.1 1.0 CB P:LYS32 4.1 40.3 1.0 CD2 P:LEU36 4.1 42.2 1.0 C P:GLY33 4.2 44.1 1.0 C P:LYS32 4.3 41.3 1.0 CD P:ARG3 4.3 38.1 1.0 N P:LYS32 4.3 39.1 1.0 CG P:GLU34 4.4 57.9 1.0 CA P:LYS32 4.4 40.8 1.0 CA P:GLY33 4.5 41.3 1.0 CA P:ALA29 4.6 38.6 1.0 CG P:ARG3 4.7 36.4 1.0 N P:GLU35 4.8 47.8 1.0 N P:GLU31 4.9 37.4 1.0 CG P:LYS32 4.9 39.0 1.0 O P:GLU35 4.9 42.4 1.0

X.Guillory, I.Hadrovic, P.J.De Vink, T.Schrader, C.Ottmann. Supramolecular Enhancement of Natural 14-3-3 Protein Ligands To Be Published.