Copper in PDB 8oe7: Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes

The structure of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes, PDB code: 8oe7 was solved by M.C.Lambert, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.92 / 1.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	18.282, 30.737, 42.557, 90.01, 89.95, 90.01
R / Rfree (%)	19.9 / 23.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes (pdb code 8oe7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 20 binding sites of Copper where determined in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes, PDB code: 8oe7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu101 b:68.8 occ:1.00 O A:HOH210 2.3 22.6 1.0 N7 A:DG2 2.5 11.3 1.0 H8 A:DG2 2.8 13.8 1.0 C8 A:DG2 3.0 11.5 1.0 O A:HOH227 3.6 25.9 1.0 O A:HOH214 3.7 17.1 0.8 H5' A:DC1 3.8 16.6 1.0 C5 A:DG2 3.8 10.4 1.0 N9 A:DG2 4.3 10.9 1.0 O A:HOH225 4.4 24.3 1.0 C5' A:DC1 4.6 13.9 1.0 O6 A:DG2 4.6 11.6 1.0 C6 A:DG2 4.6 11.6 1.0 O A:HOH228 4.7 20.0 1.0 C4 A:DG2 4.7 10.7 1.0 O5' A:DC1 4.8 14.6 1.0 H5'' A:DC1 4.9 16.6 1.0

Copper binding site 2 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu102 b:44.6 occ:1.00 O1 A:PEO104 1.8 24.0 0.8 O A:HOH201 1.8 25.0 0.9 N7 A:DG4 2.0 10.9 1.0 O A:HOH211 2.2 19.7 0.9 O A:HOH213 2.9 23.6 1.0 C5 A:DG4 2.9 9.0 1.0 C8 A:DG4 3.0 10.1 1.0 O6 A:DG4 3.2 9.9 1.0 O2 A:PEO104 3.2 23.1 0.8 H8 A:DG4 3.3 12.1 1.0 C6 A:DG4 3.4 8.8 1.0 O A:HOH223 3.8 16.2 0.9 H5' A:DC3 4.1 12.3 1.0 C4 A:DG4 4.1 8.9 1.0 N9 A:DG4 4.2 10.4 1.0 H41 A:DC5 4.4 14.4 0.4 H42 A:DC5 4.5 14.4 0.4 H41 A:DC5 4.6 14.3 0.6 N4 A:DC5 4.6 12.0 0.4 H6 A:DC3 4.7 12.5 1.0 N1 A:DG4 4.7 9.3 1.0 H42 B:DC3 4.8 10.9 0.6 H42 B:DC3 4.9 12.8 0.4 N4 A:DC5 5.0 11.9 0.6

Copper binding site 3 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu103 b:62.4 occ:1.00 O2 A:PEO105 1.9 31.5 1.0 N7 A:DG6 2.2 12.7 1.0 O1 A:PEO105 3.0 32.9 1.0 C8 A:DG6 3.1 11.2 1.0 H8 A:DG6 3.1 13.4 1.0 C5 A:DG6 3.3 11.7 1.0 O6 A:DG6 3.6 12.7 1.0 C6 A:DG6 3.8 10.9 1.0 OP1 A:DC5 4.0 17.3 0.4 H5' A:DC5 4.2 14.2 0.6 H5' A:DC5 4.3 16.5 0.4 N9 A:DG6 4.3 11.1 1.0 C4 A:DG6 4.4 9.7 1.0 O G:HOH215 4.5 16.2 1.0 H41 G:DC1 4.7 11.7 1.0 O A:HOH220 4.8 32.2 1.0 P A:DC5 5.0 16.0 0.4

Copper binding site 4 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu101 b:64.8 occ:1.00 N7 B:DG4 2.8 10.7 1.0 H8 D:DG2 3.5 15.0 1.0 H8 B:DG4 3.5 11.8 1.0 C8 B:DG4 3.6 9.8 1.0 CU D:CU102 3.6 51.7 0.8 N7 D:DG2 3.9 13.6 1.0 C5 B:DG4 3.9 9.6 1.0 C8 D:DG2 4.0 12.5 1.0 OP1 B:DC3 4.0 14.6 0.4 OP2 B:DC3 4.0 14.0 0.4 O6 B:DG4 4.2 11.4 1.0 H5' B:DC3 4.2 14.1 0.4 H5' B:DC3 4.3 15.8 0.6 H5'' D:DC1 4.3 18.3 1.0 C6 B:DG4 4.5 9.3 1.0 O D:HOH211 4.5 19.0 1.0 P B:DC3 4.5 13.9 0.4 O D:HOH215 4.6 23.9 1.0 H41 B:DC5 4.8 14.3 1.0 N9 B:DG4 4.8 10.0 1.0 OP1 B:DC3 4.8 18.6 0.6 HO5' D:DC1 4.9 21.8 1.0

Copper binding site 5 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu102 b:57.6 occ:0.94 N7 B:DG2 2.3 14.5 1.0 C8 B:DG2 3.2 14.3 1.0 H8 B:DG2 3.3 17.2 1.0 C5 B:DG2 3.4 12.7 1.0 O6 B:DG2 3.7 15.1 1.0 C6 B:DG2 3.9 13.9 1.0 N9 B:DG2 4.5 14.1 1.0 C4 B:DG2 4.6 13.5 1.0 O B:HOH202 4.8 20.2 0.6 H5'' B:DC1 4.8 18.7 1.0 H41 B:DC3 4.9 10.9 0.6

Copper binding site 6 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu101 b:64.3 occ:1.00 O2 C:PEO104 1.8 26.0 1.0 N7 C:DG2 2.1 11.1 1.0 H8 C:DG2 2.3 13.2 1.0 O1 C:PEO104 2.5 23.7 1.0 C8 C:DG2 2.5 11.0 1.0 C5 C:DG2 3.5 10.3 1.0 H5' C:DC1 3.6 18.1 1.0 O C:HOH210 3.7 19.6 1.0 N9 C:DG2 3.9 11.3 1.0 O C:HOH203 3.9 34.3 1.0 OP2 B:DG2 4.3 18.7 1.0 C4 C:DG2 4.3 11.8 1.0 OP1 B:DG2 4.3 18.0 1.0 HO5' C:DC1 4.4 20.2 1.0 C6 C:DG2 4.4 13.1 1.0 C5' C:DC1 4.5 15.1 1.0 O6 C:DG2 4.5 13.7 1.0 H5'' C:DC1 4.7 18.1 1.0 O C:HOH207 4.8 24.2 0.8 P B:DG2 4.8 16.1 1.0 O5' C:DC1 4.8 16.8 1.0 H1' C:DG2 4.8 13.4 1.0 C1' C:DG2 5.0 11.2 1.0

Copper binding site 7 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu102 b:45.5 occ:1.00 O2 C:PEO105 1.7 18.4 1.0 N7 C:DG4 1.7 11.8 1.0 O1 C:PEO105 1.8 18.7 1.0 O2 C:PEO106 2.0 20.2 0.7 O C:HOH205 2.3 19.2 0.9 O1 C:PEO106 2.5 17.1 0.7 C8 C:DG4 2.6 11.0 1.0 H8 C:DG4 2.8 13.2 1.0 C5 C:DG4 2.9 9.9 1.0 O6 C:DG4 3.5 9.6 1.0 C6 C:DG4 3.5 9.2 1.0 O C:HOH217 3.8 19.4 1.0 N9 C:DG4 3.8 11.8 1.0 C4 C:DG4 3.9 9.9 1.0 H5' C:DC3 4.0 13.7 1.0 H41 C:DC5 4.5 16.6 0.3 O C:HOH206 4.5 25.6 0.8 H41 C:DC5 4.5 14.9 0.7 H42 C:DC5 4.7 16.6 0.3 N4 C:DC5 4.7 13.8 0.3 N1 C:DG4 4.8 8.6 1.0 H6 C:DC3 4.9 13.7 1.0 N4 C:DC5 5.0 12.4 0.7 C5' C:DC3 5.0 11.4 1.0

Copper binding site 8 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu103 b:67.9 occ:0.77 O C:HOH204 2.0 27.1 1.0 N7 C:DG6 2.1 12.2 1.0 O C:HOH211 2.7 21.8 1.0 C8 C:DG6 3.1 10.1 1.0 C5 C:DG6 3.2 11.9 1.0 H8 C:DG6 3.3 12.1 1.0 O6 C:DG6 3.3 12.0 1.0 O C:HOH201 3.5 24.8 0.7 C6 C:DG6 3.6 11.4 1.0 N9 C:DG6 4.3 10.5 1.0 C4 C:DG6 4.3 9.6 1.0 OP1 C:DC5 4.4 17.7 0.3 H5' C:DC5 4.4 17.6 0.3 H5' C:DC5 4.6 14.7 0.7 N1 C:DG6 5.0 10.4 1.0

Copper binding site 9 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu101 b:59.9 occ:1.00 O D:HOH209 2.2 22.7 1.0 N7 D:DG4 2.8 11.3 1.0 O D:HOH214 3.0 21.0 1.0 H8 D:DG4 3.6 13.2 1.0 C8 D:DG4 3.6 11.0 1.0 OP1 D:DC3 3.9 24.8 1.0 C5 D:DG4 4.0 11.3 1.0 O6 D:DG4 4.2 12.0 1.0 H5' D:DC3 4.3 15.6 1.0 H41 D:DC5 4.4 14.2 0.5 OP2 D:DC3 4.5 18.9 1.0 C6 D:DG4 4.5 10.6 1.0 P D:DC3 4.7 21.4 1.0 O1 C:PEO104 4.7 23.7 1.0 H42 D:DC5 4.8 10.1 0.5 H41 D:DC5 4.8 10.1 0.5 O B:HOH208 4.9 26.8 0.7 H42 D:DC5 4.9 14.2 0.5 N9 D:DG4 4.9 11.4 1.0 N4 D:DC5 4.9 11.9 0.5

Copper binding site 10 out of 20 in the Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of the Z-Dna Duplex D(Cgcgcg) Containing Ordered Copper(II) and Soaked in Hydrogen Peroxide For 5 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu102 b:51.7 occ:0.83 O D:HOH215 1.9 23.9 1.0 N7 D:DG2 2.1 13.6 1.0 C5 D:DG2 3.0 12.2 1.0 C8 D:DG2 3.1 12.5 1.0 O6 D:DG2 3.2 13.8 1.0 H8 D:DG2 3.3 15.0 1.0 OP2 B:DC3 3.3 14.0 0.4 C6 D:DG2 3.5 12.2 1.0 CU B:CU101 3.6 64.8 1.0 OP1 B:DC3 3.8 18.6 0.6 C4 D:DG2 4.2 11.7 1.0 N9 D:DG2 4.3 11.7 1.0 O D:HOH204 4.4 21.4 1.0 P B:DC3 4.6 13.9 0.4 H41 D:DC3 4.6 13.4 1.0 H5'' D:DC1 4.7 18.3 1.0 N1 D:DG2 4.8 11.1 1.0 H42 C:DC5 4.9 14.9 0.7 OP1 B:DC3 5.0 14.6 0.4

M.C.Lambert, J.P.Hall. Structural Analysis of Peroxide-Soaked Dna Crystals Containing Ordered Copper Binding Sites: Towards Understanding Oxidative Damage at the Atomic Scale To Be Published.