Sodium in PDB 6ugc: C3 Symmetric Peptide Design Number 3

The structure of C3 Symmetric Peptide Design Number 3, PDB code: 6ugc 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)	25.51 / 0.90
Space group	P 3 1 c
Cell size a, b, c (Å), α, β, γ (°)	51.030, 51.030, 36.020, 90.00, 90.00, 120.00
R / Rfree (%)	11.8 / 14.3

The structure of C3 Symmetric Peptide Design Number 3 also contains other interesting chemical elements:

Cadmium

(Cd)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Sodium atom in the C3 Symmetric Peptide Design Number 3 (pdb code 6ugc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 26 binding sites of Sodium where determined in the C3 Symmetric Peptide Design Number 3, PDB code: 6ugc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 26 in the C3 Symmetric Peptide Design Number 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:3.6 occ:1.00 O A:ASP3 2.3 4.3 1.0 O A:ASP9 2.3 3.9 1.0 O A:ASP6 2.3 4.4 1.0 O K:HOH205 2.4 6.8 1.0 OD1 K:ASP2 2.4 5.7 1.0 O K:HOH206 2.4 5.5 1.0 HA K:ASP2 3.1 4.9 1.0 H A:ASP6 3.2 48.7 1.0 H A:ASP3 3.2 4.1 1.0 C A:ASP6 3.3 3.9 1.0 C A:ASP9 3.3 4.2 1.0 C A:ASP3 3.3 3.4 1.0 H A:ASP9 3.3 4.0 1.0 HA A:PRO1 3.4 4.6 1.0 CG K:ASP2 3.5 5.1 1.0 HA A:PRO4 3.5 5.2 1.0 HA A:PRO7 3.6 5.0 1.0 HB3 A:ASP6 3.9 4.2 1.0 CA K:ASP2 3.9 4.7 1.0 N A:ASP6 3.9 4.6 1.0 N A:ASP3 3.9 4.0 1.0 CA A:PRO1 4.0 4.8 1.0 HB3 A:ASP3 4.0 5.2 1.0 HB3 K:ASP2 4.0 4.8 1.0 N A:PRO1 4.0 4.0 1.0 CB K:ASP2 4.0 5.1 1.0 N A:ASP9 4.0 3.9 1.0 HB3 A:ASP9 4.1 7.7 1.0 N A:PRO7 4.1 4.7 1.0 CA A:PRO7 4.1 5.0 1.0 CA A:ASP6 4.1 3.8 1.0 N A:PRO4 4.2 4.3 1.0 CA A:PRO4 4.2 5.1 1.0 CA A:ASP3 4.2 4.3 1.0 C A:PRO1 4.2 4.5 1.0 CA A:ASP9 4.2 4.0 1.0 C A:PRO7 4.3 4.6 1.0 O A:PRO1 4.4 5.2 1.0 C A:PRO4 4.4 4.2 1.0 O A:PRO7 4.5 7.2 1.0 O K:PRO1 4.5 8.9 1.0 OD2 K:ASP2 4.5 8.5 1.0 CB A:ASP6 4.5 4.2 1.0 CB A:ASP3 4.6 5.3 1.0 O K:ASP2 4.6 6.1 1.0 CB A:ASP9 4.7 4.0 1.0 N A:ASP2 4.7 4.7 1.0 C K:ASP2 4.8 4.9 1.0 N A:ASP5 4.8 3.9 1.0 O A:PRO4 4.8 5.4 1.0 N K:ASP2 4.8 4.6 1.0 N A:ASP8 4.9 4.9 1.0 H A:ASP5 4.9 4.0 1.0 O K:HOH207 4.9 18.4 1.0 H A:ASP2 5.0 4.7 1.0 HB2 K:ASP2 5.0 5.1 1.0

Sodium binding site 2 out of 26 in the C3 Symmetric Peptide Design Number 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:11.3 occ:0.50 NA A:NA102 0.0 11.3 0.5 O A:HOH211 2.1 3.3 0.3 NA A:NA102 2.3 4.7 0.5 O A:HOH211 2.6 5.1 0.7 O A:HOH210 2.6 25.7 1.0 HD3 D:PRO7 4.1 8.3 1.0 O A:ASP2 4.3 7.0 1.0 HG3 D:PRO7 4.4 9.5 1.0 HD2 D:PRO7 4.6 8.2 1.0 CD D:PRO7 4.7 8.6 1.0 O A:HOH207 4.8 25.3 1.0 O D:ASP5 5.0 8.2 1.0

Sodium binding site 3 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:4.7 occ:0.50 NA A:NA102 0.0 4.7 0.5 O A:ASP2 2.3 7.0 1.0 NA A:NA102 2.3 11.3 0.5 O A:HOH210 2.4 25.7 1.0 O A:HOH211 2.4 3.3 0.3 O A:HOH211 2.8 5.1 0.7 O A:HOH207 2.9 25.3 1.0 C A:ASP2 3.4 4.7 1.0 HB2 A:ASP2 3.5 6.0 1.0 HA A:ASP3 3.7 4.5 1.0 HD2 D:PRO7 3.7 8.2 1.0 OD1 A:ASP2 3.9 9.2 1.0 HD3 A:PRO4 4.0 5.5 1.0 HD3 D:PRO7 4.0 8.3 1.0 CB A:ASP2 4.1 6.0 1.0 CA A:ASP2 4.2 4.7 1.0 HA A:ASP2 4.3 13.8 1.0 CD D:PRO7 4.3 8.6 1.0 CG A:ASP2 4.3 7.5 1.0 N A:ASP3 4.4 4.0 1.0 HD2 A:PRO4 4.4 5.8 1.0 HA D:ASP6 4.4 13.2 1.0 CA A:ASP3 4.5 4.3 1.0 O D:ASP5 4.6 8.2 1.0 CD A:PRO4 4.7 5.9 1.0 HG3 D:PRO7 4.7 9.5 1.0 HB2 A:ASP3 4.9 5.3 1.0 CG D:PRO7 5.0 9.3 1.0 HB3 A:ASP2 5.0 6.0 1.0

Sodium binding site 4 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:13.3 occ:1.00 O A:HOH201 1.9 17.8 1.0 OD2 A:ASP3 2.4 6.7 1.0 OD1 A:ASP3 2.7 6.8 1.0 CG A:ASP3 2.9 5.8 1.0 O D:HOH206 3.0 24.2 1.0 HB2 A:ASP5 3.1 6.0 1.0 NA B:NA103 3.2 20.0 1.0 NA D:NA102 3.2 13.5 1.0 O B:HOH207 3.8 30.3 1.0 CB A:ASP5 4.0 6.1 1.0 H A:ASP5 4.1 4.0 1.0 HB2 A:ASP6 4.2 4.0 1.0 OD2 B:ASP3 4.2 7.7 1.0 HB3 A:ASP5 4.3 5.9 1.0 O D:HOH201 4.3 4.5 1.0 CB A:ASP3 4.4 5.3 1.0 O A:HOH202 4.4 4.3 1.0 O D:HOH204 4.6 18.0 1.0 HB2 A:ASP3 4.7 5.3 1.0 OD2 D:ASP3 4.7 7.4 1.0 OD2 A:ASP5 4.7 9.2 1.0 HB3 A:ASP3 4.8 5.2 1.0 CG A:ASP5 4.8 6.7 1.0 CA A:ASP5 4.8 4.5 1.0 N A:ASP5 4.9 3.9 1.0

Sodium binding site 5 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:5.8 occ:1.00 O B:ASP9 2.4 5.1 1.0 O B:ASP6 2.4 6.5 1.0 O B:ASP3 2.4 4.9 1.0 O B:HOH212 2.4 13.8 1.0 O B:HOH206 2.4 9.9 1.0 O B:HOH210 2.4 8.5 1.0 H B:ASP6 3.3 9.2 1.0 H B:ASP3 3.3 5.0 1.0 H B:ASP9 3.3 4.9 1.0 C B:ASP9 3.4 4.1 1.0 C B:ASP3 3.4 4.7 1.0 HA B:PRO1 3.4 5.9 1.0 C B:ASP6 3.4 5.3 1.0 HA B:PRO4 3.5 6.2 1.0 HA B:PRO7 3.8 7.7 1.0 HB3 B:ASP6 4.0 4.8 1.0 CA B:PRO1 4.0 5.9 1.0 N B:ASP6 4.0 5.5 1.0 N B:ASP3 4.0 4.9 1.0 HB3 B:ASP3 4.1 6.1 1.0 CA B:PRO4 4.1 5.6 1.0 N B:PRO1 4.1 4.8 1.0 N B:ASP9 4.1 4.7 1.0 N B:PRO4 4.1 5.5 1.0 HB3 B:ASP9 4.2 4.2 1.0 CA B:ASP3 4.2 5.1 1.0 C B:PRO4 4.2 4.7 1.0 C B:PRO1 4.3 5.7 1.0 CA B:ASP6 4.3 5.2 1.0 CA B:ASP9 4.3 4.4 1.0 O B:PRO4 4.3 6.3 1.0 N B:PRO7 4.3 6.7 1.0 CA B:PRO7 4.3 7.8 1.0 O B:PRO1 4.5 7.0 1.0 C B:PRO7 4.5 6.6 1.0 CB B:ASP6 4.7 4.8 1.0 CB B:ASP3 4.7 6.1 1.0 CB B:ASP9 4.8 4.2 1.0 N B:ASP2 4.8 5.3 1.0 N B:ASP5 4.8 4.4 1.0 O B:PRO7 4.8 8.4 1.0 O I:HOH201 4.9 15.6 1.0 N B:ASP8 4.9 5.8 1.0 H B:ASP2 5.0 5.5 1.0

Sodium binding site 6 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:2.7 occ:1.00 O B:HOH203 1.9 4.8 1.0 O A:HOH202 1.9 4.3 1.0 O B:HOH204 1.9 4.8 1.0 O D:HOH203 1.9 4.7 1.0 O A:HOH204 1.9 4.6 1.0 O D:HOH201 1.9 4.5 1.0 OD2 B:ASP6 3.8 4.9 1.0 OD2 A:ASP6 3.8 5.3 1.0 OD2 D:ASP6 3.9 4.6 1.0 OD2 D:ASP3 4.0 7.4 1.0 OD2 B:ASP3 4.0 7.7 1.0 OD2 A:ASP3 4.0 6.7 1.0 OD2 B:ASP9 4.0 5.6 1.0 OD2 C:ASP3 4.0 5.5 1.0 OD2 D:ASP9 4.0 4.9 1.0 OD2 A:ASP9 4.1 4.4 1.0 OD2 C:ASP9 4.1 4.8 1.0 OD2 C:ASP6 4.1 5.5 1.0 HB2 D:ASP6 4.7 4.5 1.0 HB2 C:ASP9 4.7 4.2 1.0 HB2 C:ASP6 4.7 4.6 1.0 HB2 B:ASP3 4.7 6.0 1.0 HB2 C:ASP3 4.8 5.6 1.0 HB2 B:ASP6 4.8 4.8 1.0 HB2 D:ASP3 4.8 5.2 1.0 HB2 D:ASP9 4.8 4.2 1.0 HB2 B:ASP9 4.8 4.3 1.0 HB2 A:ASP3 4.8 5.3 1.0 CG D:ASP6 4.8 4.6 1.0 HB2 A:ASP9 4.8 4.1 1.0 CG B:ASP6 4.8 4.5 1.0 CG A:ASP6 4.9 4.7 1.0 HB2 A:ASP6 4.9 4.0 1.0 CD D:CD103 4.9 4.6 1.0 CD B:CD104 4.9 5.0 1.0 CD A:CD104 4.9 4.7 1.0 O D:HOH206 5.0 24.2 1.0 CG B:ASP3 5.0 6.6 1.0

Sodium binding site 7 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:20.0 occ:1.00 O B:HOH207 2.2 30.3 1.0 OD2 B:ASP3 2.4 7.7 1.0 OD1 B:ASP3 2.9 7.7 1.0 NA D:NA102 2.9 13.5 1.0 CG B:ASP3 3.0 6.6 1.0 NA A:NA103 3.2 13.3 1.0 HB2 B:ASP5 3.2 5.6 1.0 O D:HOH204 3.6 18.0 1.0 OD2 D:ASP3 4.1 7.4 1.0 CB B:ASP5 4.1 5.5 1.0 HB2 B:ASP6 4.2 4.8 1.0 O D:HOH206 4.3 24.2 1.0 H B:ASP5 4.3 4.5 1.0 HB3 B:ASP5 4.3 5.5 1.0 O B:HOH204 4.3 4.8 1.0 O A:HOH202 4.4 4.3 1.0 CB B:ASP3 4.5 6.1 1.0 OD2 A:ASP3 4.6 6.7 1.0 O A:HOH201 4.7 17.8 1.0 HB2 B:ASP3 4.8 6.0 1.0 OD2 B:ASP5 4.8 7.7 1.0 HB3 B:ASP3 5.0 6.1 1.0 CA B:ASP5 5.0 5.0 1.0 CG B:ASP5 5.0 6.1 1.0 CG D:ASP3 5.0 5.6 1.0

Sodium binding site 8 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:5.6 occ:1.00 O C:ASP6 2.3 5.0 1.0 O C:ASP9 2.4 5.4 1.0 O C:ASP3 2.4 5.0 1.0 O C:HOH204 2.4 9.2 1.0 O C:HOH203 2.5 8.8 1.0 O C:HOH205 2.6 9.2 1.0 H C:ASP9 3.3 4.8 1.0 H C:ASP3 3.3 5.1 1.0 H C:ASP6 3.3 4.7 1.0 C C:ASP6 3.4 4.4 1.0 C C:ASP9 3.4 4.7 1.0 C C:ASP3 3.4 5.0 1.0 HA C:PRO4 3.6 6.2 1.0 HA C:PRO7 3.6 6.8 1.0 HA C:PRO1 3.6 6.3 1.0 N C:ASP9 4.0 4.6 1.0 N C:ASP6 4.1 4.4 1.0 N C:ASP3 4.1 5.0 1.0 HB3 C:ASP6 4.1 4.6 1.0 HB3 C:ASP9 4.1 4.1 1.0 HB3 C:ASP3 4.1 5.7 1.0 CA C:PRO7 4.1 7.0 1.0 N C:PRO7 4.2 5.2 1.0 CA C:PRO1 4.2 6.3 1.0 N C:PRO1 4.2 4.8 1.0 CA C:PRO4 4.2 6.0 1.0 CA C:ASP6 4.2 4.3 1.0 N C:PRO4 4.2 5.3 1.0 CA C:ASP9 4.3 4.2 1.0 CA C:ASP3 4.3 5.0 1.0 C C:PRO7 4.4 7.4 1.0 C C:PRO1 4.4 6.3 1.0 C C:PRO4 4.5 6.8 1.0 CB C:ASP6 4.7 4.5 1.0 CB C:ASP9 4.7 4.2 1.0 CB C:ASP3 4.7 5.7 1.0 O C:PRO1 4.7 8.0 1.0 N C:ASP8 4.7 5.9 0.5 O C:PRO7 4.8 11.0 1.0 N C:ASP8 4.8 6.7 0.5 N C:ASP2 4.8 5.5 1.0 N C:ASP5 4.8 5.3 0.3 N C:ASP5 4.8 5.2 0.3 H C:ASP8 4.8 6.1 0.5 N C:ASP5 4.8 5.9 0.3 O C:PRO4 4.9 9.4 1.0 H C:ASP5 4.9 5.7 0.3 H C:ASP2 4.9 5.7 1.0 H C:ASP5 4.9 5.5 0.3 H C:ASP8 5.0 7.0 0.5 H C:ASP5 5.0 6.3 0.3

Sodium binding site 9 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:5.0 occ:1.00 O D:ASP3 2.4 4.4 1.0 O D:ASP6 2.4 5.8 1.0 O D:ASP9 2.4 3.7 1.0 O D:HOH211 2.4 12.6 1.0 O D:HOH209 2.4 7.6 1.0 O D:HOH207 2.5 10.7 1.0 H D:ASP6 3.3 5.0 1.0 H D:ASP3 3.3 4.3 1.0 C D:ASP9 3.3 3.4 1.0 C D:ASP3 3.3 4.3 1.0 HA D:PRO4 3.4 5.2 1.0 C D:ASP6 3.5 4.5 1.0 H D:ASP9 3.5 4.5 1.0 HA D:PRO1 3.5 4.4 1.0 HA D:PRO7 3.9 6.5 1.0 HB3 D:ASP6 3.9 4.7 1.0 CA D:PRO4 4.0 5.1 1.0 N D:ASP6 4.0 4.9 1.0 N D:ASP3 4.0 4.3 1.0 CA D:PRO1 4.1 4.4 1.0 HB3 D:ASP9 4.1 4.1 1.0 N D:PRO4 4.1 5.0 1.0 N D:ASP9 4.1 4.1 1.0 N D:PRO1 4.1 3.6 1.0 HB3 D:ASP3 4.1 5.2 1.0 C D:PRO4 4.2 4.8 1.0 CA D:ASP9 4.2 4.5 1.0 CA D:ASP6 4.2 4.6 1.0 CA D:ASP3 4.3 4.9 1.0 C D:PRO1 4.3 4.0 1.0 O D:PRO4 4.3 5.9 1.0 N D:PRO7 4.4 5.4 1.0 CA D:PRO7 4.4 6.8 1.0 O D:PRO1 4.5 5.2 1.0 O J:HOH204 4.5 13.8 1.0 CB D:ASP6 4.6 4.6 1.0 C D:PRO7 4.6 5.8 1.0 CB D:ASP9 4.7 4.2 1.0 CB D:ASP3 4.7 5.3 1.0 N D:ASP5 4.7 4.3 1.0 N D:ASP2 4.8 4.5 1.0 O D:HOH208 4.8 22.7 1.0 O J:HOH205 4.9 17.8 1.0 O D:PRO7 4.9 9.1 1.0 N D:ASP8 4.9 4.6 0.5 N D:ASP8 5.0 4.6 0.5 H D:ASP5 5.0 4.6 1.0

Sodium binding site 10 out of 26 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:13.5 occ:1.00 O D:HOH204 1.8 18.0 1.0 O D:HOH206 2.0 24.2 1.0 OD2 D:ASP3 2.4 7.4 1.0 OD1 D:ASP3 2.8 6.4 1.0 NA B:NA103 2.9 20.0 1.0 CG D:ASP3 3.0 5.6 1.0 HB2 D:ASP5 3.2 6.1 1.0 NA A:NA103 3.2 13.3 1.0 O A:HOH201 3.8 17.8 1.0 CB D:ASP5 4.1 6.2 1.0 OD2 A:ASP3 4.2 6.7 1.0 H D:ASP5 4.2 4.6 1.0 HB2 D:ASP6 4.3 4.5 1.0 O B:HOH204 4.3 4.8 1.0 HB3 D:ASP5 4.4 6.4 1.0 O D:HOH201 4.4 4.5 1.0 CB D:ASP3 4.4 5.3 1.0 OD2 B:ASP3 4.6 7.7 1.0 OD2 D:ASP5 4.7 9.0 1.0 HB2 D:ASP3 4.7 5.2 1.0 O B:HOH207 4.8 30.3 1.0 HB3 D:ASP3 4.9 5.2 1.0 CG D:ASP5 4.9 6.0 1.0 CA D:ASP5 5.0 5.6 1.0 N D:ASP5 5.0 4.3 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