Sodium in PDB 4yy2: Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121

The structure of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121, PDB code: 4yy2 was solved by J.P.Hallinan, P.Bradley, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.139, 68.603, 152.357, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 28.3

The binding sites of Sodium atom in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 (pdb code 4yy2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121, PDB code: 4yy2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:74.4 occ:1.00 O A:HOH332 2.0 66.4 1.0 O A:HOH315 3.5 51.4 1.0 OG1 A:THR6 4.3 33.5 1.0 CD1 A:LEU42 4.5 33.9 1.0 OG1 A:THR39 4.7 34.0 1.0 CD1 A:LEU75 4.7 36.1 1.0 CD1 A:LEU9 4.7 35.5 1.0 O B:HOH311 4.8 55.7 1.0 OG1 A:THR72 4.9 36.4 1.0

Sodium binding site 2 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:53.3 occ:1.00 O A:HOH312 1.6 49.5 1.0 O A:HOH335 1.9 58.0 1.0 OE1 A:GLU23 3.4 35.9 1.0 CG2 A:THR20 3.9 38.3 1.0 O A:GLY18 4.0 34.1 1.0 CA A:THR19 4.1 33.8 1.0 OE2 A:GLU23 4.2 39.4 1.0 N A:THR20 4.2 33.9 1.0 CD A:GLU23 4.2 40.6 1.0 C A:THR19 4.5 33.4 1.0 C A:GLY18 4.9 38.0 1.0 N A:THR19 4.9 31.2 1.0 CB A:THR19 5.0 38.3 1.0

Sodium binding site 3 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:72.6 occ:1.00 O A:HOH336 1.7 49.4 1.0 O B:HOH308 1.7 55.5 1.0 OG1 B:THR72 3.6 35.4 1.0 CD1 B:LEU9 4.3 33.9 1.0 OG A:SER66 4.4 40.7 1.0 CB B:PRO5 4.4 34.5 1.0 OG1 B:THR6 4.7 35.5 1.0 CB B:THR72 4.9 35.8 1.0

Sodium binding site 4 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:49.0 occ:1.00 O A:HOH337 1.5 68.8 1.0 O B:HOH335 1.7 63.8 1.0 CA B:SER70 3.5 44.2 1.0 CB B:SER70 3.6 54.4 1.0 O B:GLY68 3.8 35.1 1.0 N B:SER70 3.8 35.7 1.0 O B:LYS69 4.0 38.3 1.0 C B:LYS69 4.0 36.2 1.0 O B:HOH306 4.2 41.7 1.0 CD B:PRO71 4.6 38.4 1.0 CG A:GLU59 4.6 48.8 1.0 C B:GLY68 4.7 37.7 1.0 C B:SER70 4.9 40.6 1.0 CB A:GLU55 4.9 44.1 1.0 CA B:LYS69 5.0 34.8 1.0 OG B:SER70 5.0 55.5 1.0

Sodium binding site 5 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:59.3 occ:1.00 O B:HOH335 4.5 63.8 1.0

Sodium binding site 6 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:69.5 occ:1.00 O B:HOH340 2.3 56.9 1.0 CA B:GLY68 3.8 37.4 1.0 O B:LEU65 3.8 36.3 1.0 NA B:NA206 4.0 53.0 1.0 O B:HOH306 4.0 41.7 1.0 N B:GLY68 4.1 35.9 1.0 O B:SER66 4.3 38.5 1.0 C B:SER66 4.8 38.9 1.0 O B:HOH333 4.8 57.9 1.0 C B:PHE67 4.9 37.3 1.0 C B:GLY68 5.0 37.7 1.0

Sodium binding site 7 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:60.9 occ:1.00 O B:HOH346 2.9 52.6 1.0 O B:HOH322 3.0 43.5 1.0 CD1 B:LEU62 4.5 39.1 1.0 CB B:LYS58 4.7 31.5 1.0 OE2 B:GLU59 4.8 44.2 1.0 CD B:LYS58 4.9 32.7 1.0

Sodium binding site 8 out of 8 in the Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Computationally Designed Left-Handed Alpha/Alpha Toroid with 3 Repeats in Space Group P212121 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:53.0 occ:1.00 O B:HOH333 1.7 57.9 1.0 O B:HOH340 2.0 56.9 1.0 NA B:NA204 4.0 69.5 1.0 O B:HOH315 4.3 50.8 1.0 O B:PHE67 4.7 39.5 1.0 O B:SER66 4.7 38.5 1.0

L.Doyle, J.Hallinan, J.Bolduc, F.Parmeggiani, D.Baker, B.L.Stoddard, P.Bradley. Rational Design of Alpha-Helical Tandem Repeat Proteins with Closed Architectures. Nature V. 528 585 2015.
ISSN: ESSN 1476-4687
PubMed: 26675735
DOI: 10.1038/NATURE16191