Zinc in PDB 6dxj: Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+

The structure of Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+, PDB code: 6dxj 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 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.174, 44.174, 24.281, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+ (pdb code 6dxj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+, PDB code: 6dxj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in 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 Gaggcctc; Crystals Grown in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:56.4 occ:1.00 O A:HOH205 2.0 47.0 1.0 O A:HOH209 2.0 55.2 1.0 N7 A:DG1 2.1 39.9 1.0 C8 A:DG1 3.0 40.0 1.0 C5 A:DG1 3.1 34.5 1.0 O6 A:DG1 3.5 34.5 1.0 C6 A:DG1 3.7 33.7 1.0 N9 A:DG1 4.2 37.5 1.0 C4 A:DG1 4.3 36.0 1.0 O A:HOH201 4.4 50.3 1.0 N7 A:DA2 4.5 40.6 1.0 O5' A:DG1 4.6 47.0 1.0 N6 A:DA2 4.6 38.0 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in 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 Gaggcctc; Crystals Grown in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:0.7 occ:1.00 N7 A:DG4 2.1 42.9 1.0 C8 A:DG4 2.9 39.5 1.0 C5 A:DG4 3.3 38.8 1.0 O6 A:DG4 3.8 37.2 1.0 ZN A:ZN103 3.9 0.1 1.0 C6 A:DG4 3.9 34.5 1.0 OP2 A:DG4 4.0 64.0 1.0 N7 A:DG3 4.0 50.5 1.0 N9 A:DG4 4.1 37.5 1.0 C5 A:DG3 4.2 40.5 1.0 C4 A:DG4 4.3 37.6 1.0 C8 A:DG3 4.4 45.6 1.0 C6 A:DG3 4.6 36.3 1.0 C5 A:DC5 4.7 34.4 1.0 O6 A:DG3 4.7 40.5 1.0 C4 A:DG3 4.7 40.7 1.0 O5' A:DG4 4.8 49.8 1.0 N9 A:DG3 4.9 45.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in 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 Gaggcctc; Crystals Grown in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:0.1 occ:1.00 N7 A:DG3 2.1 50.5 1.0 C8 A:DG3 3.0 45.6 1.0 C5 A:DG3 3.2 40.5 1.0 O6 A:DG3 3.6 40.5 1.0 C6 A:DG3 3.8 36.3 1.0 ZN A:ZN102 3.9 0.7 1.0 N7 A:DA2 4.1 40.6 1.0 N9 A:DG3 4.2 45.1 1.0 C4 A:DG3 4.3 40.7 1.0 C5 A:DA2 4.5 40.3 1.0 N7 A:DG4 4.6 42.9 1.0 C8 A:DA2 4.7 43.6 1.0 N6 A:DA2 4.7 38.0 1.0 C6 A:DA2 4.7 35.4 1.0 OP2 A:DG3 4.8 65.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:0.8 occ:1.00 OP2 A:DT7 2.9 36.3 1.0 O5' A:DT7 3.4 36.1 1.0 OP2 A:DC8 3.5 48.8 1.0 C5 A:DC8 3.6 31.6 1.0 P A:DT7 3.7 37.8 1.0 C7 A:DT7 3.9 29.5 1.0 C6 A:DT7 3.9 31.4 1.0 C5 A:DT7 4.0 30.7 1.0 C3' A:DT7 4.2 37.3 1.0 OP1 A:DT7 4.3 44.0 1.0 C6 A:DC8 4.3 34.0 1.0 ZN A:ZN105 4.4 0.2 1.0 C5' A:DT7 4.6 34.5 1.0 C4 A:DC8 4.6 31.9 1.0 N4 A:DC8 4.7 32.1 1.0 P A:DC8 4.7 41.6 1.0 N1 A:DT7 4.7 33.8 1.0 C4' A:DT7 4.9 33.1 1.0 O3' A:DT7 4.9 36.5 1.0 C2' A:DT7 4.9 36.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Double-Stranded Dna Gaggcctc; Crystals Grown in ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:0.2 occ:1.00 OP2 A:DT7 3.4 36.3 1.0 OP2 A:DC6 3.4 39.6 1.0 C7 A:DT7 3.6 29.5 1.0 O5' A:DC6 4.0 38.4 1.0 P A:DC6 4.1 41.3 1.0 ZN A:ZN104 4.4 0.8 1.0 OP1 A:DC6 4.5 43.8 1.0 P A:DT7 4.9 37.8 1.0 O A:HOH203 4.9 44.7 1.0 C3' A:DC6 4.9 34.8 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