Copper in PDB 1d40: Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2

The structure of Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2, PDB code: 1d40 was solved by B.H.Geierstanger, T.F.Kagawa, S.-L.Chen, G.J.Quigley, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	17.590, 30.580, 44.520, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Copper atom in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 (pdb code 1d40). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2, PDB code: 1d40:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) 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 Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu7 b:67.4 occ:0.16 O A:HOH14 2.0 64.9 1.0 O A:HOH15 2.1 65.1 1.0 O A:HOH17 2.1 66.0 1.0 O A:HOH13 2.2 65.7 1.0 O A:HOH16 2.2 66.4 1.0 N7 A:DG2 2.3 10.3 1.0 C8 A:DG2 3.2 10.1 1.0 C5 A:DG2 3.3 8.8 1.0 O6 A:DG2 3.4 8.8 1.0 C6 A:DG2 3.8 8.7 1.0 O4 A:DU3 4.1 7.3 1.0 O A:HOH39 4.3 22.4 1.0 N9 A:DG2 4.4 10.8 1.0 O A:HOH29 4.4 19.7 1.0 C4 A:DG2 4.5 9.9 1.0 N6 B:DA10 4.9 6.7 1.0

Copper binding site 2 out of 4 in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) 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 Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu8 b:30.2 occ:0.33 O A:HOH22 1.8 27.2 1.0 O A:HOH19 2.0 32.8 1.0 O A:HOH21 2.0 23.3 1.0 O A:HOH20 2.1 35.4 1.0 N7 A:DG6 2.1 5.8 1.0 O A:HOH18 2.3 21.0 1.0 C8 A:DG6 3.2 7.5 1.0 C5 A:DG6 3.2 5.5 1.0 O6 A:DG6 3.5 6.2 1.0 C6 A:DG6 3.7 5.1 1.0 OP1 A:5CM5 3.8 19.4 1.0 C4 A:DG6 4.4 5.6 1.0 N9 A:DG6 4.4 7.9 1.0 O5' A:5CM5 4.8 17.5 1.0 P A:5CM5 4.9 19.5 1.0

Copper binding site 3 out of 4 in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) 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 Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu13 b:63.4 occ:0.14 O B:HOH24 2.0 63.0 1.0 O B:HOH23 2.0 62.7 1.0 O B:HOH26 2.2 61.4 1.0 O B:HOH25 2.2 65.4 1.0 N7 B:DG8 2.4 5.3 1.0 C8 B:DG8 3.1 3.6 1.0 C5 B:DG8 3.5 5.1 1.0 O B:HOH77 3.8 32.6 1.0 O6 B:DG8 3.8 6.3 1.0 O B:HOH68 3.9 21.2 1.0 O B:HOH65 4.0 25.5 1.0 C6 B:DG8 4.2 4.1 1.0 N9 B:DG8 4.3 5.6 1.0 C4 B:DG8 4.6 4.3 1.0 O5' B:5CM7 4.6 16.0 1.0 O A:HOH44 4.7 28.8 1.0

Copper binding site 4 out of 4 in the Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) 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 Base Specific Binding of Copper(II) to Z-Dna: the 1.3- Angstroms Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu14 b:27.9 occ:0.18 CU B:CUL14 0.0 27.9 0.2 N7 B:DG12 2.1 7.7 1.0 O B:HOH27 2.3 25.4 1.0 CL2 B:CUL14 2.7 27.3 1.0 C8 B:DG12 2.9 6.3 1.0 CL1 B:CUL14 3.1 34.7 1.0 C5 B:DG12 3.3 6.7 1.0 O6 B:DG12 3.8 7.1 1.0 C6 B:DG12 3.9 6.5 1.0 N9 B:DG12 4.1 8.7 1.0 C4 B:DG12 4.4 6.3 1.0 OP1 B:5CM11 4.8 19.5 1.0 O B:HOH81 4.9 35.6 1.0

B.H.Geierstanger, T.F.Kagawa, S.L.Chen, G.J.Quigley, P.S.Ho. Base-Specific Binding of Copper(II) to Z-Dna. the 1.3-A Single Crystal Structure of D(M5CGUAM5CG) in the Presence of CUCL2. J.Biol.Chem. V. 266 20185 1991.
ISSN: ISSN 0021-9258
PubMed: 1939079