Zinc in PDB 7uid: Thyclotides Peptide Nucleic Acid in Complex with Dna

The structure of Thyclotides Peptide Nucleic Acid in Complex with Dna, PDB code: 7uid was solved by I.Botos, D.H.Appella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.286, 64.098, 71.244, 90, 90, 90
R / Rfree (%)	23.2 / 26.5

The structure of Thyclotides Peptide Nucleic Acid in Complex with Dna also contains other interesting chemical elements:

Iodine	(I)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Thyclotides Peptide Nucleic Acid in Complex with Dna (pdb code 7uid). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Thyclotides Peptide Nucleic Acid in Complex with Dna, PDB code: 7uid:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:18.2 occ:1.00 O A:HOH242 2.1 21.3 1.0 O A:HOH212 2.1 12.5 1.0 O A:HOH207 2.2 11.7 1.0 O A:HOH214 2.2 16.6 1.0 N7 A:DG6 2.2 10.1 1.0 O A:HOH205 2.4 18.7 1.0 C8 A:DG6 3.1 10.4 1.0 C5 A:DG6 3.3 10.0 1.0 O6 A:DG6 3.7 9.8 1.0 OP2 A:DG6 3.8 14.2 1.0 C6 A:DG6 3.8 9.6 1.0 O A:HOH218 4.1 15.2 1.0 N9 A:DG6 4.3 11.6 1.0 O A:HOH206 4.3 18.6 1.0 N7 A:DA7 4.4 18.4 1.0 C4 A:DG6 4.4 10.4 1.0 N3 A:DT5 4.6 10.9 1.0 C4 A:DT5 4.7 12.2 1.0 O A:HOH244 4.8 26.3 1.0 C2 A:DT5 4.8 10.5 1.0 C5 A:DT5 4.9 12.0 1.0 O5' A:DG6 5.0 15.2 1.0 O4 A:DT5 5.0 12.9 1.0

Zinc binding site 2 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:21.4 occ:0.98 O A:HOH241 1.9 19.4 1.0 O A:HOH217 2.0 19.4 1.0 N7 A:DG1 2.1 16.2 1.0 O A:HOH232 2.1 15.6 1.0 O A:HOH229 2.2 29.6 1.0 C8 A:DG1 3.0 16.2 1.0 C5 A:DG1 3.2 15.5 1.0 O6 A:DG1 3.6 15.3 1.0 C6 A:DG1 3.8 14.6 1.0 O A:HOH223 4.1 24.8 1.0 N9 A:DG1 4.2 16.8 1.0 C4 A:DG1 4.3 15.8 1.0 O A:HOH238 4.4 28.9 1.0

Zinc binding site 3 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:47.5 occ:0.64 O A:HOH230 2.0 38.5 1.0 N7 A:DG4 2.2 16.2 1.0 O A:HOH203 2.6 29.9 1.0 O A:HOH237 3.0 34.7 1.0 C8 A:DG4 3.1 16.6 1.0 C5 A:DG4 3.3 15.8 1.0 O6 A:DG4 3.6 14.0 1.0 O A:HOH211 3.7 30.6 1.0 C6 A:DG4 3.8 14.6 1.0 C4 A:DT3 4.2 23.4 1.0 N3 A:DT3 4.2 24.2 1.0 C7 A:DT5 4.3 12.6 1.0 N9 A:DG4 4.4 16.8 1.0 C4 A:DG4 4.4 15.9 1.0 C5 A:DT3 4.5 24.5 1.0 O4 A:DT3 4.5 22.4 1.0 C2 A:DT3 4.5 25.4 1.0 OP2 A:DG4 4.6 31.2 1.0 C6 A:DT3 4.8 25.6 1.0 N1 A:DT3 4.8 26.7 1.0

Zinc binding site 4 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:29.6 occ:0.71 O C:HOH214 2.2 25.8 1.0 N7 C:DG4 2.3 23.8 1.0 O C:HOH218 2.4 29.8 1.0 O C:HOH215 2.5 35.1 1.0 C8 C:DG4 3.2 24.6 1.0 C5 C:DG4 3.4 23.6 1.0 O6 C:DG4 3.7 23.0 1.0 C6 C:DG4 3.9 23.3 1.0 O D:HOH224 4.1 31.4 1.0 OP2 C:DG4 4.3 33.1 1.0 C7 C:DT5 4.4 19.7 1.0 N9 C:DG4 4.4 25.5 1.0 C4 C:DG4 4.5 24.2 1.0 O4 C:DT5 4.5 19.0 1.0 N3 C:DT3 4.7 25.6 1.0 C4 C:DT3 4.7 25.3 1.0 C2 C:DT3 4.8 26.5 1.0 C5 C:DT3 4.8 25.8 1.0 N1 C:DT3 4.9 27.6 1.0 C6 C:DT3 5.0 26.6 1.0

Zinc binding site 5 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:27.4 occ:0.82 N7 C:DG6 2.0 20.4 1.0 O C:HOH234 2.2 32.9 1.0 O C:HOH213 2.2 26.5 1.0 O C:HOH209 2.4 21.6 1.0 O C:HOH228 2.5 25.0 1.0 O C:HOH219 2.6 34.6 1.0 C8 C:DG6 2.8 22.0 1.0 C5 C:DG6 3.0 19.2 1.0 O6 C:DG6 3.6 17.0 1.0 C6 C:DG6 3.7 17.6 1.0 N9 C:DG6 4.0 23.1 1.0 O C:HOH220 4.1 27.1 1.0 C4 C:DG6 4.1 20.2 1.0 O C:HOH230 4.4 39.2 1.0 OP2 C:DG6 4.5 33.2 1.0 C5 C:DT5 4.5 20.0 1.0 C4 C:DT5 4.6 19.4 1.0 N7 C:DA7 4.6 15.6 1.0 N6 C:DA7 4.7 13.0 1.0 C6 C:DT5 4.7 21.0 1.0 N3 C:DT5 4.8 19.7 1.0 N1 C:DT5 4.9 22.2 1.0 O4 C:DT5 4.9 19.0 1.0 C2 C:DT5 4.9 20.9 1.0 N1 C:DG6 5.0 16.6 1.0

Zinc binding site 6 out of 6 in the Thyclotides Peptide Nucleic Acid in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Thyclotides Peptide Nucleic Acid in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:66.3 occ:0.69 N7 C:DG1 1.9 39.5 1.0 O6 C:DG1 1.9 39.6 1.0 C5 C:DG1 2.2 39.4 1.0 C6 C:DG1 2.3 39.4 1.0 O C:HOH225 2.8 35.4 1.0 O C:HOH201 3.1 38.5 1.0 C8 C:DG1 3.2 39.9 1.0 C4 C:DG1 3.6 39.5 1.0 O B:HOH227 3.6 36.3 1.0 N1 C:DG1 3.7 38.6 1.0 N9 C:DG1 4.0 40.2 1.0 C2 C:DG1 4.6 38.2 1.0 N3 C:DG1 4.7 39.0 1.0 O C:HOH227 4.8 44.3 1.0 O B:HOH226 4.8 33.3 1.0

H.Zheng, V.Clausse, I.Botos, H.Amarasekara, S.J.Mazur, D.H.Appella. Thyclotides, (R,R)-Trans-Tetrahydrofuran-Constrained Peptide Nucleic Acids Enhance Oligonucleotide Binding and Cellular Uptake to Target Microrna-21 To Be Published.