Sodium in PDB 8bfd: Racemic Structure of Pk-7 (310HD-U2U5)

The structure of Racemic Structure of Pk-7 (310HD-U2U5), PDB code: 8bfd was solved by P.Kumar, N.G.Paterson, D.N.Woolfson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.10 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	21.23, 21.905, 26.521, 105.85, 112.44, 95.26
R / Rfree (%)	20.3 / 25.6

The binding sites of Sodium atom in the Racemic Structure of Pk-7 (310HD-U2U5) (pdb code 8bfd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Racemic Structure of Pk-7 (310HD-U2U5), PDB code: 8bfd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Racemic Structure of Pk-7 (310HD-U2U5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Racemic Structure of Pk-7 (310HD-U2U5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:28.4 occ:1.00 O A:GLU20 2.8 9.5 1.0 CG A:GLU20 2.9 14.8 0.7 C A:GLU20 3.5 8.7 1.0 CB2 A:AIB24 3.6 11.4 1.0 CA A:GLU20 3.6 9.5 1.0 N A:AIB24 3.6 9.0 1.0 CB A:GLU20 3.8 11.4 1.0 CB2 A:AIB23 3.9 10.5 1.0 CB1 A:AIB24 3.9 13.4 1.0 CA A:AIB24 3.9 10.6 1.0 CD A:GLU20 4.1 18.5 0.8 OE2 A:GLU20 4.4 22.7 1.0 C A:AIB23 4.5 9.4 1.0 CA A:AIB23 4.7 9.2 1.0 N A:AIB21 4.8 7.6 1.0

Sodium binding site 2 out of 4 in the Racemic Structure of Pk-7 (310HD-U2U5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Racemic Structure of Pk-7 (310HD-U2U5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:26.5 occ:1.00 O A:HOH201 2.7 21.7 1.0 O A:HOH208 3.0 18.4 1.0 NZ B:DLY25 4.1 21.1 0.9 OE2 A:GLU8 4.2 16.8 1.0 O A:HOH217 4.6 22.3 1.0

Sodium binding site 3 out of 4 in the Racemic Structure of Pk-7 (310HD-U2U5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Racemic Structure of Pk-7 (310HD-U2U5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:35.1 occ:1.00 O B:HOH211 2.4 40.1 1.0 CB2 B:AIB24 4.2 13.0 1.0 CB1 B:AIB24 4.5 14.1 1.0 O B:HOH215 4.9 24.9 1.0 CA B:AIB24 5.0 11.7 1.0 O B:DGL20 5.0 10.6 1.0

Sodium binding site 4 out of 4 in the Racemic Structure of Pk-7 (310HD-U2U5)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Racemic Structure of Pk-7 (310HD-U2U5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:36.5 occ:1.00 O B:DLY7 3.0 8.0 1.0 CG B:DLY7 3.1 14.5 1.0 C B:DLY7 3.8 8.3 1.0 CB2 B:AIB11 3.8 8.2 1.0 N B:AIB11 3.8 6.7 1.0 CB1 B:AIB11 3.9 9.0 1.0 CA B:DLY7 3.9 10.3 1.0 CB2 B:AIB10 4.0 10.6 1.0 CB B:DLY7 4.0 12.8 1.0 CA B:AIB11 4.0 7.0 1.0 NZ B:DLY7 4.1 23.7 0.7 CD B:DLY7 4.1 18.8 1.0 CB1 A:AIB23 4.2 11.0 1.0 C B:AIB10 4.5 7.2 1.0 CE B:DLY7 4.7 22.0 0.7 CA B:AIB10 4.8 8.3 1.0 N B:DGL8 4.9 7.5 1.0

P.Kumar, N.G.Paterson, J.Clayden, D.N.Woolfson. De Novo Design of Discrete, Stable 3 10 -Helix Peptide Assemblies. Nature V. 607 387 2022.
ISSN: ESSN 1476-4687
PubMed: 35732733
DOI: 10.1038/S41586-022-04868-X