Copper in PDB 5ihd: Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate, PDB code: 5ihd 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)	26.22 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.487, 35.576, 31.044, 90.00, 107.50, 90.00
R / Rfree (%)	16.1 / 19

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

Calcium

(Ca)

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

Copper binding site 1 out of 4 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate


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 L-Lactate and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu101 b:13.3 occ:1.00 OXT A:2OP103 1.9 13.1 1.0 N7 A:DG2 2.0 11.5 1.0 O4 D:SIN101 2.0 13.7 1.0 N7 D:DG2 2.0 10.2 1.0 OHN A:2OP103 2.2 15.6 1.0 C A:2OP103 2.8 15.9 1.0 C4 D:SIN101 2.8 14.1 1.0 C8 D:DG2 2.9 11.7 1.0 C5 A:DG2 2.9 10.1 1.0 O3 D:SIN101 2.9 14.8 1.0 CA A:2OP103 3.0 14.4 1.0 O6 A:DG2 3.0 11.8 1.0 C8 A:DG2 3.1 12.2 1.0 C5 D:DG2 3.1 11.6 1.0 C6 A:DG2 3.3 10.4 1.0 O6 D:DG2 3.6 13.0 1.0 C6 D:DG2 3.8 11.4 1.0 CB A:2OP103 3.9 20.0 1.0 O A:2OP103 4.0 17.6 1.0 N4 A:DC3 4.0 10.9 1.0 C4 A:DG2 4.1 12.8 1.0 N9 D:DG2 4.1 10.1 1.0 N9 A:DG2 4.2 13.5 1.0 C3 D:SIN101 4.2 15.2 1.0 C4 D:DG2 4.2 12.7 1.0 N1 A:DG2 4.7 10.7 1.0 C5' D:DC1 4.7 13.8 1.0 O A:HOH220 4.7 23.1 1.0 C4 A:DC3 4.9 10.3 1.0

Copper binding site 2 out of 4 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate


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 L-Lactate and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu101 b:13.3 occ:1.00 O1 D:SIN101 2.0 14.0 1.0 O B:2OP103 2.0 11.2 1.0 N7 B:DG2 2.0 11.5 1.0 N7 C:DG2 2.0 10.4 1.0 OHN B:2OP103 2.3 14.0 1.0 C1 D:SIN101 2.8 14.0 1.0 C8 B:DG2 2.8 11.1 1.0 C B:2OP103 2.9 14.5 1.0 C5 C:DG2 3.0 9.1 1.0 O2 D:SIN101 3.0 16.1 1.0 C8 C:DG2 3.0 11.1 1.0 CA B:2OP103 3.1 11.7 1.0 O6 C:DG2 3.1 11.6 1.0 C5 B:DG2 3.1 11.8 1.0 C6 C:DG2 3.4 8.8 1.0 O6 B:DG2 3.6 13.4 1.0 C6 B:DG2 3.8 11.1 1.0 N4 C:DC3 3.9 11.0 1.0 CB B:2OP103 4.0 16.8 1.0 OXT B:2OP103 4.0 15.4 1.0 N9 B:DG2 4.1 10.7 1.0 C4 C:DG2 4.2 8.9 1.0 N9 C:DG2 4.2 9.5 1.0 C2 D:SIN101 4.2 16.1 1.0 C4 B:DG2 4.2 11.6 1.0 O B:HOH220 4.5 23.6 1.0 C5' B:DC1 4.6 11.3 1.0 N1 C:DG2 4.8 9.3 1.0 C4 C:DC3 4.9 9.4 1.0 O5' B:DC1 4.9 11.5 1.0 O6 D:DG4 5.0 11.3 1.0 O4' B:DC1 5.0 11.8 1.0

Copper binding site 3 out of 4 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By L-Lactate and Succinate


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 L-Lactate and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu102 b:20.7 occ:0.49 O B:HOH208 1.8 20.0 1.0 N7 B:DG6 2.0 14.4 1.0 O B:HOH201 2.3 20.9 1.0 O B:HOH209 2.4 27.8 1.0 OP1 B:DC5 2.7 20.7 0.3 C8 B:DG6 2.9 15.5 1.0 C5 B:DG6 3.2 13.5 1.0 O6 B:DG6 3.6 12.7 1.0 C6 B:DG6 3.8 13.1 1.0 P B:DC5 3.9 17.8 0.3 N9 B:DG6 4.1 13.5 1.0 C4 B:DG6 4.3 12.4 1.0 OP2 B:DC5 4.3 19.4 0.3 O5' B:DC5 4.7 21.9 1.0 C5' B:DC5 4.8 17.1 1.0 OP1 B:DC5 4.8 19.2 0.7

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


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 L-Lactate and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu101 b:15.2 occ:1.00 N7 C:DG4 2.0 14.6 1.0 O C:HOH219 2.2 18.6 1.0 C8 C:DG4 2.9 16.1 1.0 C5 C:DG4 3.1 15.2 1.0 O6 C:DG4 3.6 15.8 1.0 C6 C:DG4 3.7 15.0 1.0 N9 C:DG4 4.1 16.7 1.0 C4 C:DG4 4.2 13.6 1.0 O D:HOH214 4.4 21.9 1.0 N4 C:DC5 5.0 14.6 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