Sodium in PDB 6ug6: C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2

The structure of C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2, PDB code: 6ug6 was solved by V.K.Mulligan, C.S.Kang, I.Antselovich, M.R.Sawaya, T.O.Yeates, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 1.10
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	28.530, 29.960, 30.100, 109.50, 108.86, 107.91
R / Rfree (%)	18 / 21.4

The binding sites of Sodium atom in the C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2 (pdb code 6ug6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2, PDB code: 6ug6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:5.7 occ:0.50 O A:HOH207 2.1 16.9 1.0 O A:ASP8 2.3 5.6 1.0 O A:HOH206 2.6 7.9 1.0 O A:HOH212 2.6 10.7 0.8 HA A:PRO9 2.9 6.8 1.0 C A:ASP8 3.2 4.4 1.0 H A:ASP8 3.6 4.1 1.0 CA A:PRO9 3.7 6.3 1.0 O A:HOH203 3.8 5.8 1.0 N A:PRO9 3.9 5.5 1.0 N A:ASP8 4.2 4.2 1.0 HB3 A:ASP8 4.2 5.3 1.0 CA A:ASP8 4.3 4.3 1.0 C A:PRO9 4.3 6.2 1.0 O A:ARG10 4.4 4.6 1.0 HA A:PRO1 4.5 8.3 1.0 O A:ARG6 4.6 5.7 1.0 H A:ARG10 4.6 5.0 1.0 N A:ARG10 4.7 4.9 1.0 HB3 A:PRO1 4.7 11.7 1.0 CB A:ASP8 4.8 5.3 1.0 HB3 A:PRO9 4.9 9.3 1.0 CB A:PRO9 4.9 10.6 1.0 O A:PRO9 5.0 8.2 1.0

Sodium binding site 2 out of 2 in the C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C3 Symmetric Peptide Design Number 1, Sporty, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:10.1 occ:0.75 O C:HOH209 1.9 31.8 1.0 O C:HOH208 2.1 19.3 1.0 O C:ASP4 2.3 6.0 1.0 O C:HOH207 2.6 7.9 1.0 O C:HOH210 2.7 12.5 0.8 O C:HOH206 2.7 9.0 1.0 HA C:PRO5 2.9 7.0 1.0 C C:ASP4 3.3 4.5 1.0 H C:ASP4 3.6 3.9 1.0 CA C:PRO5 3.7 6.6 1.0 O C:HOH202 3.9 5.6 1.0 N C:PRO5 3.9 5.7 1.0 N C:ASP4 4.2 3.9 1.0 HB3 C:ASP4 4.2 5.1 1.0 CA C:ASP4 4.3 4.3 1.0 C C:PRO5 4.4 6.3 1.0 O C:ARG6 4.4 4.5 1.0 HA C:PRO9 4.5 8.3 1.0 O C:ARG2 4.6 5.7 1.0 H C:ARG6 4.6 5.1 1.0 N C:ARG6 4.7 4.9 1.0 CB C:ASP4 4.8 5.1 1.0 HB3 C:PRO5 4.9 9.4 1.0 HB3 C:PRO9 4.9 12.3 1.0 CB C:PRO5 4.9 10.5 1.0 O C:PRO5 5.0 7.6 1.0

V.K.Mulligan, C.S.Kang, M.R.Sawaya, S.Rettie, X.Li, I.Antselovich, T.W.Craven, A.M.Watkins, J.W.Labonte, F.Dimaio, T.O.Yeates, D.Baker. Computational Design of Mixed Chirality Peptide Macrocycles with Internal Symmetry. Protein Sci. V. 29 2433 2020.
ISSN: ESSN 1469-896X
PubMed: 33058266
DOI: 10.1002/PRO.3974