Cadmium 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:

Sodium

(Na)

26 atoms

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

Cadmium binding site 1 out of 6 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd104 b:4.7 occ:1.00 OD2 A:ASP9 2.2 4.4 1.0 OD2 A:ASP2 2.2 9.4 1.0 OD2 C:ASP3 2.3 5.5 1.0 OD2 D:ASP6 2.3 4.6 1.0 OD1 C:ASP5 2.5 3.0 0.3 OD1 A:ASP2 2.6 9.2 1.0 OD1 D:ASP6 2.6 6.5 1.0 CG A:ASP2 2.7 7.5 1.0 CG D:ASP6 2.8 4.6 1.0 CG C:ASP3 3.0 6.3 1.0 CG A:ASP9 3.0 4.5 1.0 HB3 D:ASP8 3.0 7.7 0.5 OD1 C:ASP3 3.1 11.0 1.0 OD1 A:ASP9 3.1 5.7 1.0 HB2 D:ASP8 3.3 5.2 0.5 HB3 C:ASP5 3.4 5.7 0.3 CG C:ASP5 3.4 2.7 0.3 OD2 C:ASP5 3.6 3.3 0.3 HB2 C:ASP5 3.8 6.7 0.3 CB D:ASP8 3.9 7.3 0.5 HB2 D:ASP8 4.0 7.2 0.5 O D:HOH203 4.1 4.7 1.0 O A:HOH204 4.1 4.6 1.0 HB2 A:ASP3 4.1 5.3 1.0 H D:ASP8 4.1 4.6 0.5 H D:ASP8 4.2 4.8 0.5 O D:HOH201 4.2 4.5 1.0 HB2 D:ASP9 4.2 4.2 1.0 CB A:ASP2 4.2 6.0 1.0 CB D:ASP8 4.3 5.3 0.5 HB2 C:ASP6 4.3 4.6 1.0 CB D:ASP6 4.3 4.6 1.0 CB C:ASP5 4.3 5.8 0.3 OD2 D:ASP8 4.4 12.0 0.5 CB A:ASP9 4.5 4.0 1.0 CB C:ASP3 4.5 5.7 1.0 HB3 A:ASP2 4.5 6.0 1.0 O A:HOH207 4.5 25.3 1.0 H C:ASP5 4.5 6.3 0.3 H A:ASP2 4.5 4.7 1.0 H C:ASP5 4.6 5.5 0.3 H C:ASP5 4.6 5.7 0.3 HB2 D:ASP6 4.6 4.5 1.0 HB2 C:ASP5 4.6 5.6 0.3 HB2 A:ASP9 4.7 4.1 1.0 OD2 C:ASP5 4.7 7.1 0.3 HB3 D:ASP8 4.7 5.0 0.5 HB3 D:ASP6 4.7 4.7 1.0 OD2 D:ASP8 4.7 6.0 0.5 HB2 C:ASP3 4.7 5.6 1.0 CG D:ASP8 4.7 11.0 0.5 CG D:ASP8 4.7 4.2 0.5 HB2 A:ASP2 4.7 6.0 1.0 CB C:ASP5 4.8 7.1 0.3 HB3 A:ASP9 4.8 7.7 1.0 HB3 C:ASP3 4.8 5.7 1.0 HD2 D:PRO7 4.8 8.2 1.0 CB C:ASP5 4.9 4.1 0.3 CA D:ASP8 4.9 5.6 0.5 N D:ASP8 4.9 4.6 0.5 NA B:NA102 4.9 2.7 1.0 N D:ASP8 5.0 4.6 0.5

Cadmium binding site 2 out of 6 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd104 b:5.0 occ:1.00 OD2 B:ASP9 2.2 5.6 1.0 OD2 B:ASP2 2.3 8.2 1.0 OD2 C:ASP6 2.3 5.5 1.0 OD2 A:ASP6 2.3 5.3 1.0 OD1 B:ASP2 2.4 7.4 1.0 OD1 A:ASP6 2.6 6.0 1.0 CG B:ASP2 2.7 7.0 1.0 OD1 C:ASP8 2.7 9.0 0.5 CG A:ASP6 2.8 4.7 1.0 HB3 A:ASP8 3.0 7.7 1.0 CG B:ASP9 3.0 4.4 1.0 CG C:ASP6 3.1 5.3 1.0 OD1 B:ASP9 3.1 5.8 1.0 OD1 C:ASP6 3.2 8.3 1.0 HB2 C:ASP8 3.6 6.0 0.5 CG C:ASP8 3.7 10.8 0.5 CB A:ASP8 3.9 7.8 1.0 OD2 C:ASP8 4.0 13.5 0.5 HB2 A:ASP8 4.0 7.9 1.0 O A:HOH204 4.0 4.6 1.0 HB2 B:ASP3 4.1 6.0 1.0 HB2 A:ASP9 4.1 4.1 1.0 O B:HOH203 4.2 4.8 1.0 CB B:ASP2 4.2 7.0 1.0 O A:HOH202 4.2 4.3 1.0 H A:ASP8 4.3 5.1 1.0 CB A:ASP6 4.3 4.2 1.0 OD2 A:ASP8 4.4 13.6 1.0 H B:ASP2 4.4 5.5 1.0 HB2 C:ASP9 4.4 4.2 1.0 CB C:ASP6 4.5 4.5 1.0 CB B:ASP9 4.5 4.2 1.0 HB3 B:ASP2 4.5 6.9 1.0 CB C:ASP8 4.6 5.8 0.5 HB2 A:ASP6 4.6 4.0 1.0 HB2 B:ASP2 4.6 6.9 1.0 HB2 C:ASP6 4.7 4.6 1.0 HB3 A:ASP6 4.7 4.2 1.0 H C:ASP8 4.7 7.0 0.5 H C:ASP8 4.7 6.1 0.5 HB3 C:ASP8 4.7 5.8 0.5 HB2 B:ASP9 4.7 4.3 1.0 CG A:ASP8 4.8 12.1 1.0 HB3 B:ASP9 4.8 4.2 1.0 HB3 A:ASP9 4.9 7.7 1.0 HB3 C:ASP6 4.9 4.6 1.0 CA A:ASP8 4.9 6.4 1.0 NA B:NA102 4.9 2.7 1.0 CB A:ASP9 4.9 4.0 1.0 CB B:ASP3 4.9 6.1 1.0 N A:ASP8 5.0 4.9 1.0 CA B:ASP2 5.0 6.4 1.0 HB3 B:ASP3 5.0 6.1 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd103 b:4.6 occ:1.00 OD2 D:ASP9 2.2 4.9 1.0 OD2 C:ASP9 2.2 4.8 1.0 OD2 D:ASP2 2.2 8.4 1.0 OD2 B:ASP6 2.3 4.9 1.0 OD1 D:ASP2 2.4 8.4 1.0 OD1 B:ASP6 2.6 6.1 1.0 CG D:ASP2 2.7 7.6 1.0 CG B:ASP6 2.8 4.5 1.0 CG C:ASP9 3.0 4.8 1.0 CG D:ASP9 3.1 4.0 1.0 HB3 B:ASP8 3.1 9.4 1.0 OD1 C:ASP9 3.2 6.4 1.0 OD1 D:ASP9 3.2 5.1 1.0 HB2 C:ASP2 3.9 7.0 1.0 CB B:ASP8 4.0 9.3 1.0 HB2 D:ASP3 4.0 5.2 1.0 O B:HOH203 4.0 4.8 1.0 O D:HOH203 4.1 4.7 1.0 HB2 B:ASP9 4.2 4.3 1.0 HB2 B:ASP8 4.2 10.6 1.0 O B:HOH204 4.2 4.8 1.0 CB D:ASP2 4.2 5.9 1.0 H B:ASP8 4.3 6.1 1.0 CB B:ASP6 4.3 4.8 1.0 O D:HOH210 4.3 21.1 1.0 HB2 C:ASP3 4.4 5.6 1.0 H D:ASP2 4.5 4.4 1.0 CB D:ASP9 4.5 4.2 1.0 CB C:ASP9 4.5 4.2 1.0 OD2 B:ASP8 4.5 10.2 1.0 HB3 D:ASP2 4.6 5.4 1.0 HB2 B:ASP6 4.6 4.8 1.0 HB2 D:ASP2 4.6 6.0 1.0 HB2 C:ASP9 4.7 4.2 1.0 HB3 B:ASP6 4.7 4.8 1.0 HB2 D:ASP9 4.7 4.2 1.0 HB3 D:ASP9 4.8 4.1 1.0 H C:ASP2 4.8 5.7 1.0 CB C:ASP2 4.8 7.1 1.0 CG B:ASP8 4.8 10.0 1.0 HB3 C:ASP9 4.9 4.1 1.0 NA B:NA102 4.9 2.7 1.0 CA B:ASP8 4.9 6.7 1.0 CB D:ASP3 4.9 5.3 1.0 HB3 D:ASP3 4.9 5.2 1.0 HB3 B:ASP9 5.0 4.2 1.0 C B:ASP8 5.0 6.8 1.0 CA D:ASP2 5.0 4.7 1.0

Cadmium binding site 4 out of 6 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cd106 b:5.4 occ:1.00 OD2 E:ASP2 2.2 6.9 0.5 OD2 E:ASP9 2.2 4.5 1.0 OD2 G:ASP3 2.2 4.5 0.5 OD2 H:ASP6 2.2 5.6 1.0 OD2 G:ASP3 2.3 4.8 0.5 OD1 E:ASP2 2.5 6.4 0.5 OD1 G:ASP5 2.5 3.3 0.5 OD1 E:ASP2 2.6 8.0 0.5 CG E:ASP2 2.7 6.3 0.5 OD1 H:ASP6 2.7 7.3 1.0 CG H:ASP6 2.8 5.0 1.0 CG E:ASP9 3.0 4.3 1.0 CG G:ASP3 3.0 4.6 0.5 OD1 E:ASP9 3.1 5.7 1.0 OD1 G:ASP3 3.1 4.5 0.5 CG G:ASP3 3.1 4.3 0.5 OD1 G:ASP3 3.3 4.1 0.5 CG E:ASP2 3.3 4.8 0.5 HB2 H:ASP8 3.3 4.9 0.5 CG G:ASP5 3.4 3.7 0.5 HB3 H:ASP8 3.4 8.6 0.5 OD2 E:ASP2 3.4 5.6 0.5 OD2 G:ASP5 3.5 5.1 0.5 O G:HOH201 4.0 4.1 1.0 HB2 E:ASP3 4.1 4.7 1.0 O E:HOH202 4.1 4.3 1.0 CB E:ASP2 4.2 4.5 0.5 O E:HOH204 4.2 4.1 1.0 CB H:ASP8 4.2 4.5 0.5 HB2 G:ASP5 4.3 10.7 0.5 H H:ASP8 4.3 5.9 0.5 HB2 H:ASP9 4.3 3.9 1.0 H H:ASP8 4.3 6.4 0.5 CB H:ASP6 4.3 4.9 1.0 HB3 G:ASP5 4.3 10.5 0.5 CB H:ASP8 4.3 8.8 0.5 O E:HOH203 4.4 10.3 1.0 HB2 G:ASP6 4.4 4.8 1.0 HB3 E:ASP2 4.4 4.6 0.5 CB E:ASP9 4.4 3.9 1.0 OD2 H:ASP8 4.5 4.9 0.5 CB G:ASP3 4.5 4.9 0.5 H E:ASP2 4.6 4.2 0.5 CB G:ASP3 4.6 4.4 0.5 H E:ASP2 4.6 4.2 0.5 HB2 H:ASP6 4.6 4.8 1.0 CG H:ASP8 4.6 3.2 0.5 HB2 E:ASP9 4.6 3.8 1.0 HB2 G:ASP3 4.6 5.1 0.5 HB3 H:ASP8 4.6 4.7 0.5 H G:ASP5 4.6 6.6 0.5 H G:ASP5 4.7 7.4 0.5 HB2 E:ASP2 4.7 4.7 0.5 CB E:ASP2 4.7 4.9 0.5 HB2 H:ASP8 4.7 8.1 0.5 HB3 H:ASP6 4.7 5.0 1.0 CB G:ASP5 4.7 10.6 0.5 OD2 H:ASP8 4.8 9.0 0.5 HB3 E:ASP9 4.8 4.1 1.0 CB G:ASP5 4.8 4.7 0.5 HB3 G:ASP3 4.9 4.3 0.5 HB3 G:ASP3 4.9 4.8 0.5 O H:ASP8 4.9 7.0 0.5 HB2 G:ASP3 4.9 4.5 0.5 NA E:NA102 4.9 2.3 1.0 C H:ASP8 4.9 5.8 0.5 CB E:ASP3 5.0 4.7 1.0

Cadmium binding site 5 out of 6 in the C3 Symmetric Peptide Design Number 3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd103 b:4.3 occ:1.00 OD2 G:ASP6 2.2 4.8 1.0 OD2 F:ASP9 2.2 4.5 1.0 OD2 F:ASP2 2.2 5.8 1.0 OD2 E:ASP6 2.3 4.8 1.0 OD1 F:ASP2 2.4 5.5 1.0 OD1 E:ASP6 2.6 5.6 1.0 OD1 G:ASP8 2.6 7.3 0.3 CG F:ASP2 2.7 5.1 1.0 CG E:ASP6 2.8 4.2 1.0 CG G:ASP6 3.0 4.8 1.0 CG F:ASP9 3.0 3.9 1.0 OD1 G:ASP6 3.1 6.4 1.0 HB2 E:ASP8 3.1 8.4 1.0 OD1 F:ASP9 3.1 5.5 1.0 HB3 G:ASP8 3.4 8.7 0.3 CG G:ASP8 3.5 7.9 0.3 HB3 E:ASP8 3.6 8.4 1.0 OD2 G:ASP8 3.7 9.6 0.3 HB2 G:ASP8 3.8 4.7 0.3 CB E:ASP8 3.8 8.4 1.0 HB2 F:ASP3 4.0 5.0 1.0 O E:HOH202 4.1 4.3 1.0 O F:HOH202 4.2 4.3 1.0 CB F:ASP2 4.2 5.3 1.0 HB2 E:ASP9 4.2 3.8 1.0 O E:HOH201 4.2 4.2 1.0 H E:ASP8 4.2 4.9 1.0 CB E:ASP6 4.3 4.2 1.0 CB G:ASP8 4.3 8.5 0.3 HB2 G:ASP8 4.4 8.7 0.3 HB2 G:ASP9 4.4 4.6 1.0 O F:HOH208 4.4 10.0 1.0 CB G:ASP6 4.5 4.9 1.0 CB F:ASP9 4.5 4.7 1.0 H F:ASP2 4.5 4.2 1.0 HB3 F:ASP2 4.6 5.2 1.0 HB2 E:ASP6 4.6 4.0 1.0 HB2 F:ASP2 4.6 5.4 1.0 HB2 G:ASP6 4.6 4.8 1.0 HB3 E:ASP6 4.7 4.3 1.0 OD2 G:ASP8 4.7 10.4 0.3 H G:ASP8 4.7 5.8 0.3 H G:ASP8 4.7 5.0 0.7 OD2 E:ASP8 4.7 17.2 1.0 HB2 F:ASP9 4.7 53.2 1.0 CB G:ASP8 4.8 4.6 0.3 CG E:ASP8 4.8 14.2 1.0 HB3 F:ASP9 4.8 4.0 1.0 HB3 G:ASP6 4.8 5.0 1.0 CA E:ASP8 4.8 5.8 1.0 HB3 F:ASP3 4.8 5.2 1.0 CB F:ASP3 4.9 5.2 1.0 HB3 E:ASP9 4.9 4.1 1.0 N E:ASP8 4.9 4.8 1.0 CB G:ASP8 4.9 7.4 0.3 NA E:NA102 4.9 2.3 1.0 C E:ASP8 5.0 5.5 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of C3 Symmetric Peptide Design Number 3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd103 b:5.2 occ:1.00 OD2 F:ASP6 2.2 5.3 1.0 OD2 G:ASP9 2.3 5.1 1.0 OD2 H:ASP9 2.3 5.1 1.0 OD2 H:ASP2 2.3 10.6 1.0 OD1 H:ASP2 2.4 7.0 1.0 OD1 F:ASP8 2.6 11.8 1.0 OD1 F:ASP6 2.6 7.5 1.0 CG H:ASP2 2.7 6.7 1.0 CG F:ASP6 2.8 4.6 1.0 CG H:ASP9 3.1 4.3 1.0 CG G:ASP9 3.1 4.9 1.0 OD1 H:ASP9 3.2 5.0 1.0 OD1 G:ASP9 3.2 6.8 1.0 CG F:ASP8 3.6 10.6 1.0 HB2 G:ASP2 3.8 11.7 1.0 OD2 F:ASP8 3.9 16.7 1.0 O F:HOH202 4.0 4.3 1.0 HB2 H:ASP3 4.1 4.8 1.0 HB2 F:ASP9 4.1 53.2 1.0 H F:ASP8 4.2 5.8 1.0 O F:HOH201 4.2 4.1 1.0 CB H:ASP2 4.2 7.4 1.0 O G:HOH201 4.2 4.1 1.0 CB F:ASP6 4.3 4.7 1.0 HB2 G:ASP3 4.3 4.5 0.5 H H:ASP2 4.4 4.7 1.0 O H:HOH206 4.4 14.6 1.0 CB H:ASP9 4.5 3.9 1.0 CB G:ASP9 4.5 4.7 1.0 HB2 G:ASP3 4.5 5.1 0.5 HB3 H:ASP2 4.6 6.8 1.0 HB2 F:ASP6 4.6 4.7 1.0 HB2 H:ASP2 4.7 6.9 1.0 HB2 G:ASP9 4.7 4.6 1.0 HB3 F:ASP6 4.7 4.7 1.0 HB2 H:ASP9 4.7 3.9 1.0 CB G:ASP2 4.7 11.8 1.0 HB3 H:ASP9 4.8 3.9 1.0 H G:ASP2 4.8 5.8 1.0 HB3 H:ASP3 4.9 4.5 1.0 CB F:ASP8 4.9 10.2 1.0 HB3 F:ASP9 4.9 4.0 1.0 CB H:ASP3 4.9 4.6 1.0 HB3 G:ASP9 4.9 4.8 1.0 HB3 G:ASP2 4.9 10.7 1.0 CB F:ASP9 4.9 4.7 1.0 NA E:NA102 4.9 2.3 1.0 N F:ASP8 4.9 5.4 1.0 CA H:ASP2 5.0 5.5 1.0 C F:ASP8 5.0 5.7 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