Copper in PDB 4xqz: Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes, PDB code: 4xqz was solved by M.Rohner, A.Medina-Molner, B.Spingler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.87 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.340, 35.253, 47.643, 90.00, 98.28, 90.00
R / Rfree (%)	23.1 / 30

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Copper atom in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes (pdb code 4xqz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes, PDB code: 4xqz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu101 b:34.4 occ:1.00 O3S D:MES102 1.9 27.3 1.0 N7 D:DG2 2.0 28.3 1.0 N7 A:DG2 2.0 32.5 1.0 O1S D:MES102 2.3 28.0 1.0 S D:MES102 2.4 47.4 1.0 CL A:CL103 2.5 23.7 0.4 C8 D:DG2 2.8 25.6 1.0 O6 A:DG2 2.8 27.7 1.0 C5 A:DG2 2.8 30.1 1.0 CL D:CL104 3.1 25.1 0.6 C6 A:DG2 3.1 28.0 1.0 C8 A:DG2 3.2 26.3 1.0 C5 D:DG2 3.2 25.5 1.0 O2S D:MES102 3.2 42.7 1.0 O6 D:DG2 3.8 29.0 1.0 C8 D:MES102 3.9 30.4 1.0 C6 D:DG2 3.9 27.0 1.0 N4 A:DC3 4.0 30.6 1.0 N9 D:DG2 4.0 23.4 1.0 C4 A:DG2 4.1 26.6 1.0 C4 D:DG2 4.2 23.1 1.0 N9 A:DG2 4.3 30.2 1.0 C5' D:DC1 4.4 24.4 1.0 N1 A:DG2 4.5 29.1 1.0 O5' D:DC1 4.9 28.2 1.0 C4 A:DC3 5.0 29.0 1.0

Copper binding site 2 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu101 b:27.9 occ:1.00 N7 B:DG2 1.9 21.1 1.0 N7 C:DG2 2.0 20.0 1.0 O B:HOH108 2.3 23.4 1.0 O B:HOH105 2.8 21.9 1.0 C8 B:DG2 2.8 18.7 1.0 C5 C:DG2 2.9 21.7 1.0 C8 C:DG2 3.0 24.2 1.0 O6 C:DG2 3.0 22.6 1.0 C5 B:DG2 3.1 21.9 1.0 C6 C:DG2 3.3 20.6 1.0 CL C:CL102 3.3 29.0 1.0 O6 B:DG2 3.6 25.8 1.0 C6 B:DG2 3.7 27.3 1.0 N4 C:DC3 3.8 19.0 1.0 O5' C:DC1 3.9 31.1 1.0 N9 B:DG2 4.0 20.2 1.0 C4 C:DG2 4.2 21.5 1.0 C4 B:DG2 4.2 20.6 1.0 N9 C:DG2 4.2 20.7 1.0 C5' B:DC1 4.4 24.3 1.0 O5' B:DC1 4.6 24.1 1.0 N1 C:DG2 4.7 20.0 1.0 N4 B:DC3 4.9 21.3 1.0 C4 C:DC3 4.9 23.0 1.0

Copper binding site 3 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu101 b:33.1 occ:1.00 N7 D:DG6 1.9 28.6 1.0 O D:HOH203 2.1 31.4 1.0 C8 D:DG6 2.9 25.7 1.0 C5 D:DG6 3.1 25.9 1.0 O6 D:DG6 3.5 24.9 1.0 C6 D:DG6 3.6 25.1 1.0 OP1 D:DC5 3.8 21.8 0.4 N9 D:DG6 4.1 24.6 1.0 C4 D:DG6 4.2 28.4 1.0 P D:DC5 4.9 20.7 0.4 N1 D:DG6 5.0 24.8 1.0

Copper binding site 4 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu101 b:35.4 occ:1.00 N7 H:DG2 2.1 26.4 1.0 N7 E:DG2 2.2 31.4 1.0 O H:HOH208 2.3 28.3 1.0 CL H:CL104 2.6 32.5 1.0 C8 H:DG2 3.1 23.5 1.0 C5 H:DG2 3.1 25.9 1.0 C8 E:DG2 3.1 23.5 1.0 C5 E:DG2 3.2 31.6 1.0 O6 H:DG2 3.3 24.9 1.0 O6 E:DG2 3.4 35.6 1.0 C6 H:DG2 3.5 26.3 1.0 C6 E:DG2 3.7 30.2 1.0 N9 H:DG2 4.2 25.8 1.0 C4 H:DG2 4.3 23.6 1.0 N4 E:DC3 4.3 30.0 1.0 N9 E:DG2 4.3 29.9 1.0 C4 E:DG2 4.4 31.4 1.0 C5' H:DC1 4.6 27.6 1.0 O5' H:DC1 4.7 30.3 1.0 N4 H:DC3 4.8 28.2 1.0 O G:HOH204 4.9 29.6 1.0 N1 H:DG2 4.9 29.9 1.0

Copper binding site 5 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ G:Cu101 b:32.3 occ:1.00 N7 G:DG2 1.8 26.1 1.0 N7 F:DG2 2.0 31.8 1.0 O F:HOH206 2.6 31.3 1.0 CL F:CL101 2.7 40.5 1.0 C5 G:DG2 2.8 24.0 1.0 C8 G:DG2 2.9 26.3 1.0 C8 F:DG2 2.9 29.9 1.0 O6 G:DG2 3.0 20.6 1.0 C5 F:DG2 3.2 32.5 1.0 C6 G:DG2 3.2 22.4 1.0 O5' F:DC1 3.3 38.2 1.0 O6 F:DG2 3.6 34.6 1.0 C6 F:DG2 3.7 35.9 1.0 N4 G:DC3 3.9 20.9 1.0 C4 G:DG2 4.0 22.4 1.0 N9 G:DG2 4.1 24.6 1.0 N9 F:DG2 4.2 29.0 1.0 C4 F:DG2 4.3 29.9 1.0 C5' G:DC1 4.6 25.7 1.0 N1 G:DG2 4.6 20.5 1.0 C5' F:DC1 4.6 30.7 1.0 O G:HOH201 4.8 30.7 1.0 C4 G:DC3 4.9 22.8 1.0 N4 F:DC3 4.9 35.2 1.0

Copper binding site 6 out of 6 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range: probe atom residue distance (Å) B Occ H:Cu101 b:37.5 occ:1.00 N7 H:DG6 2.0 31.3 1.0 CL H:CL102 2.5 35.6 0.6 C8 H:DG6 2.9 28.1 1.0 CL H:CL103 3.0 31.7 0.4 C5 H:DG6 3.2 29.4 1.0 O6 H:DG6 3.6 24.7 1.0 C6 H:DG6 3.7 24.8 1.0 N9 H:DG6 4.2 27.6 1.0 C4 H:DG6 4.3 29.1 1.0

M.Rohner, A.Medina-Molner, B.Spingler. N,N,O and N,O,N Meridional Cis Coordination of Two Guanines to Copper(II) By D(Cgcgcg)2. Inorg.Chem. V. 55 6130 2016.
ISSN: ISSN 0020-1669
PubMed: 27266259
DOI: 10.1021/ACS.INORGCHEM.6B00672