Sodium in PDB 6ugb: C3 Symmetric Peptide Design Number 2, Baby Basil

Protein crystallography data

The structure of C3 Symmetric Peptide Design Number 2, Baby Basil, PDB code: 6ugb 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) 21.41 / 0.95
Space group P -3
Cell size a, b, c (Å), α, β, γ (°) 24.720, 24.720, 19.590, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 16.2

Other elements in 6ugb:

The structure of C3 Symmetric Peptide Design Number 2, Baby Basil also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 6ugb

Go back to Sodium Binding Sites List in 6ugb
Sodium binding site 1 out of 3 in the C3 Symmetric Peptide Design Number 2, Baby Basil


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 2, Baby Basil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:10.1
occ:0.33
O A:ASP3 2.4 10.1 1.0
O A:HOH202 2.4 14.1 1.0
C A:ASP3 3.4 9.7 1.0
H A:ASP3 3.4 10.2 1.0
HA A:PRO1 3.6 12.8 1.0
HB3 A:ASP3 4.0 9.2 1.0
N A:ASP3 4.1 10.1 1.0
CA A:PRO1 4.2 12.7 1.0
N A:PRO1 4.2 11.4 1.0
CA A:ASP3 4.3 9.5 1.0
C A:PRO1 4.3 13.0 1.0
O A:PRO1 4.4 18.0 1.0
CB A:ASP3 4.6 9.0 1.0
N A:ARG2 4.9 11.4 1.0

Sodium binding site 2 out of 3 in 6ugb

Go back to Sodium Binding Sites List in 6ugb
Sodium binding site 2 out of 3 in the C3 Symmetric Peptide Design Number 2, Baby Basil


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 2, Baby Basil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:7.5
occ:0.33
OD2 A:ASP3 2.4 8.0 1.0
OD2 B:ASP3 2.4 7.9 1.0
ZN B:ZN101 3.4 8.1 1.0
HB2 B:ASP3 3.4 7.5 1.0
HB2 A:ASP3 3.4 8.8 1.0
CG A:ASP3 3.4 8.3 1.0
CG B:ASP3 3.5 7.6 1.0
HB3 A:ASP3 3.5 9.2 1.0
HB3 B:ASP3 3.5 7.6 1.0
CB A:ASP3 3.7 9.0 1.0
CB B:ASP3 3.7 7.6 1.0
OD1 A:ASP3 4.6 10.0 1.0
OD1 B:ASP3 4.6 9.0 1.0
CL B:CL102 4.8 10.3 1.0
CL B:CL103 4.9 10.2 1.0

Sodium binding site 3 out of 3 in 6ugb

Go back to Sodium Binding Sites List in 6ugb
Sodium binding site 3 out of 3 in the C3 Symmetric Peptide Design Number 2, Baby Basil


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 2, Baby Basil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na104

b:8.3
occ:0.33
O B:ASP3 2.4 8.3 1.0
O B:HOH201 2.4 13.0 1.0
H B:ASP3 3.5 7.7 1.0
C B:ASP3 3.5 7.6 1.0
HB3 B:ASP3 4.0 7.6 1.0
HA B:PRO1 4.0 10.2 1.0
N B:ASP3 4.1 7.7 1.0
CA B:ASP3 4.3 7.3 1.0
O B:PRO1 4.4 11.6 1.0
C B:PRO1 4.4 9.2 1.0
N B:PRO1 4.4 8.8 1.0
CA B:PRO1 4.4 10.3 1.0
CB B:ASP3 4.6 7.6 1.0
N B:ARG2 4.9 7.9 1.0

Reference:

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
Page generated: Tue Dec 15 14:31:47 2020

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