Copper in PDB 1d39: Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2

The structure of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2, PDB code: 1d39 was solved by T.F.Kagawa, B.H.Geierstanger, A.H.-J.Wang, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	18.010, 31.030, 44.800, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Copper atom in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 (pdb code 1d39). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2, PDB code: 1d39:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu7 b:75.5 occ:0.07 O A:HOH15 2.1 74.3 1.0 O A:HOH14 2.2 69.7 1.0 N7 A:DG2 2.6 11.9 1.0 C8 A:DG2 3.3 9.5 1.0 C5 A:DG2 3.7 9.9 1.0 N4 A:DC3 4.0 8.7 1.0 O6 A:DG2 4.1 10.1 1.0 C6 A:DG2 4.3 9.8 1.0 N9 A:DG2 4.4 11.0 1.0 C4 A:DG2 4.6 9.5 1.0

Copper binding site 2 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu8 b:53.5 occ:0.20 O A:HOH16 2.2 50.0 1.0 N7 A:DG4 2.3 7.8 1.0 C8 A:DG4 3.1 7.3 1.0 C5 A:DG4 3.5 6.7 1.0 O6 A:DG4 3.9 8.6 1.0 C6 A:DG4 4.1 7.9 1.0 O A:HOH33 4.1 23.4 1.0 N9 A:DG4 4.4 6.7 1.0 O B:HOH22 4.5 58.8 1.0 C4 A:DG4 4.6 6.7 1.0 O A:HOH41 4.6 13.9 1.0 O B:HOH44 4.8 42.5 1.0

Copper binding site 3 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu9 b:19.1 occ:0.63 O A:HOH17 2.1 12.0 1.0 O A:HOH20 2.2 21.8 1.0 O A:HOH18 2.2 16.7 1.0 N7 A:DG6 2.2 6.8 1.0 O A:HOH21 2.2 18.8 1.0 O A:HOH19 2.4 17.6 1.0 C8 A:DG6 3.1 6.5 1.0 C5 A:DG6 3.2 6.4 1.0 O6 A:DG6 3.5 7.0 1.0 C6 A:DG6 3.8 6.5 1.0 O A:HOH46 4.0 31.5 1.0 OP1 A:DC5 4.0 12.6 1.0 N9 A:DG6 4.2 6.9 1.0 C4 A:DG6 4.4 6.4 1.0 P A:DC5 4.9 11.0 1.0 C5' A:DC5 5.0 7.3 1.0

Copper binding site 4 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu13 b:59.6 occ:0.23 O B:HOH23 2.0 60.3 1.0 O B:HOH24 2.1 58.9 1.0 O B:HOH22 2.1 58.8 1.0 N7 B:DG8 2.3 7.4 1.0 O B:HOH25 3.0 58.3 1.0 C8 B:DG8 3.2 7.1 1.0 C5 B:DG8 3.4 7.2 1.0 O6 B:DG8 3.7 7.6 1.0 O B:HOH56 3.8 34.5 1.0 O B:HOH37 3.9 26.2 1.0 C6 B:DG8 4.0 7.1 1.0 O B:HOH44 4.2 42.5 1.0 N9 B:DG8 4.4 6.8 1.0 C4 B:DG8 4.5 6.8 1.0 N4 B:DC9 4.8 6.3 1.0

Copper binding site 5 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu14 b:39.1 occ:0.39 O B:HOH76 0.7 12.6 1.0 O B:HOH79 1.8 14.3 1.0 O B:HOH78 2.0 38.3 1.0 O B:HOH77 2.2 38.4 1.0 N7 B:DG10 2.4 10.7 1.0 C8 B:DG10 3.3 11.9 1.0 C5 B:DG10 3.5 10.6 1.0 O6 B:DG10 3.5 9.9 1.0 O B:HOH26 3.8 34.9 1.0 OP1 B:DC9 3.8 13.9 1.0 C6 B:DG10 3.9 10.2 1.0 N9 B:DG10 4.5 11.2 1.0 C4 B:DG10 4.6 10.7 1.0 O A:HOH15 4.7 74.3 1.0 P B:DC9 4.9 12.9 1.0 N4 B:DC11 5.0 7.1 1.0

Copper binding site 6 out of 6 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu15 b:38.1 occ:0.39 O B:HOH27 2.0 21.2 1.0 N7 B:DG12 2.4 7.9 1.0 O B:HOH73 3.0 33.7 1.0 C8 B:DG12 3.3 7.1 1.0 C5 B:DG12 3.4 7.2 1.0 O6 B:DG12 3.7 8.5 1.0 C6 B:DG12 3.9 7.4 1.0 N9 B:DG12 4.5 7.5 1.0 C4 B:DG12 4.6 6.7 1.0

T.F.Kagawa, B.H.Geierstanger, A.H.Wang, P.S.Ho. Covalent Modification of Guanine Bases in Double-Stranded Dna. the 1.2-A Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2. J.Biol.Chem. V. 266 20175 1991.
ISSN: ISSN 0021-9258
PubMed: 1939078