Zinc in PDB 6dy5: Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+

The structure of Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+, PDB code: 6dy5 was solved by C.Hou, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.567, 42.451, 49.212, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.4

The binding sites of Zinc atom in the Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+ (pdb code 6dy5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+, PDB code: 6dy5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:19.5 occ:1.00 O A:HOH221 2.0 21.6 1.0 O A:HOH227 2.0 21.1 1.0 O A:HOH204 2.0 19.5 1.0 O A:HOH223 2.0 20.7 1.0 O A:HOH242 2.0 22.2 1.0 N7 A:DG2 2.1 16.9 1.0 C8 A:DG2 3.0 17.6 1.0 C5 A:DG2 3.2 17.5 1.0 O6 A:DG2 3.6 17.6 1.0 C6 A:DG2 3.8 16.6 1.0 O A:HOH206 4.1 22.1 1.0 O A:HOH231 4.1 33.7 1.0 OP2 A:DG2 4.2 23.0 1.0 N9 A:DG2 4.2 17.1 1.0 O A:HOH245 4.3 43.1 1.0 C4 A:DG2 4.3 16.6 1.0 O A:HOH241 4.4 51.3 1.0 O B:HOH219 4.4 29.6 1.0 O6 A:DG3 4.5 16.5 1.0 N7 A:DG1 4.6 19.5 1.0 C5 A:DG1 4.6 18.2 1.0 C6 A:DG1 4.9 18.0 1.0 O A:HOH205 4.9 35.3 1.0 O A:HOH217 5.0 39.7 1.0 C8 A:DG1 5.0 19.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:28.7 occ:1.00 O B:HOH208 1.9 26.4 1.0 O B:HOH220 2.0 28.6 1.0 O B:HOH212 2.0 32.6 1.0 O B:HOH226 2.0 26.3 1.0 O B:HOH237 2.0 33.4 1.0 N7 B:DG9 2.1 26.0 1.0 C8 B:DG9 3.0 22.9 1.0 C5 B:DG9 3.2 24.6 1.0 O6 B:DG9 3.6 25.9 1.0 C6 B:DG9 3.8 24.9 1.0 O B:HOH204 4.0 29.0 1.0 O B:HOH244 4.2 46.8 1.0 N9 B:DG9 4.2 22.4 1.0 N7 B:DG10 4.3 27.9 1.0 C4 B:DG9 4.3 20.3 1.0 OP2 B:DG9 4.4 32.4 1.0 C8 B:DG10 4.8 21.4 1.0 C5 B:DA8 4.9 26.7 1.0 N7 B:DA8 5.0 29.7 1.0 C6 B:DA8 5.0 25.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Double-Stranded Dna Agggatccct in Complex with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:18.8 occ:0.20 O B:HOH222 2.1 30.6 1.0 O B:HOH243 2.2 48.0 1.0 N7 B:DG11 2.5 23.7 1.0 O B:HOH213 2.5 39.5 1.0 C8 B:DG11 3.3 25.5 1.0 C5 B:DG11 3.4 22.7 1.0 O6 B:DG11 3.7 23.4 1.0 O B:HOH234 3.8 37.2 1.0 C6 B:DG11 3.9 24.0 1.0 OP2 B:DG11 4.1 37.1 1.0 N9 B:DG11 4.4 24.0 1.0 N7 B:DA12 4.4 19.5 1.0 C4 B:DG11 4.5 23.1 1.0 O A:HOH241 4.5 51.3 1.0 O B:HOH223 4.7 43.1 1.0 O B:HOH219 4.7 29.6 1.0 O B:HOH244 4.7 46.8 1.0 N7 B:DG10 4.8 27.9 1.0 C5 B:DG10 4.9 25.0 1.0 O5' B:DG11 5.0 28.1 1.0 C6 B:DG10 5.0 26.6 1.0

C.Hou, O.V.Tsodikov. Utilizing Guanine Coordinated ZN2+ to Determine Dna Crystal Structures By Single-Wavelength Anomalous Diffraction Acta Crystallogr.,Sect.D V. 75 32 2019.
ISSN: ISSN 0907-4449