Sodium in PDB 2des: Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg)

The structure of Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg), PDB code: 2des was solved by M.Cirilli, F.Bachechi, G.Ughetto, F.P.Colonna, M.L.Capobianco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	18.010, 18.830, 26.750, 92.60, 100.50, 94.90
R / Rfree (%)	n/a / n/a

The structure of Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg) (pdb code 2des). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg), PDB code: 2des:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na17 b:39.9 occ:1.00 O A:HOH85 2.4 39.9 1.0 N7 A:DG6 2.6 7.7 1.0 O A:HOH87 2.6 40.2 1.0 O A:HOH81 2.7 39.4 1.0 O4 A:DMM14 3.0 9.4 1.0 O6 A:DMM14 3.0 10.9 1.0 O6 A:DG6 3.5 8.1 1.0 C8 A:DG6 3.5 7.7 1.0 C5 A:DG6 3.5 7.7 1.0 C21 A:DMM14 3.7 8.9 1.0 C4 A:DMM14 3.8 8.1 1.0 C6 A:DG6 3.9 7.1 1.0 C6 A:DMM14 3.9 8.4 1.0 C2' A:DC5 4.1 9.9 1.0 C5 A:DMM14 4.2 8.4 1.0 O A:HOH90 4.6 40.9 1.0 OP2 A:DG6 4.6 16.4 1.0 N9 A:DG6 4.7 8.2 1.0 C4 A:DG6 4.7 7.8 1.0 O A:HOH95 4.7 44.2 1.0 O8 A:DMM14 4.8 9.1 1.0 O3' A:DC5 4.9 14.0 1.0 C3 A:DMM14 4.9 8.9 1.0 O A:HOH73 4.9 37.6 1.0 C3' A:DC5 5.0 11.5 1.0 C7 A:DMM14 5.0 8.0 1.0

Sodium binding site 2 out of 2 in the Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Interactions Between Morpholinyl Anthracyclines and Dna: the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na16 b:32.5 occ:1.00 O B:HOH59 2.3 32.8 1.0 O B:HOH46 2.3 30.5 1.0 O4 A:DMM13 2.5 6.8 1.0 C21 A:DMM13 2.7 6.6 1.0 O B:HOH65 2.8 34.0 1.0 O6 A:DMM13 3.2 10.0 1.0 N7 B:DG12 3.2 10.1 1.0 O A:HOH80 3.4 38.9 1.0 C4 A:DMM13 3.5 6.9 1.0 O B:HOH44 3.9 30.3 1.0 O A:HOH64 3.9 33.3 1.0 C8 B:DG12 4.0 9.9 1.0 C6 A:DMM13 4.0 8.2 1.0 C2' B:DC11 4.0 10.1 1.0 C5 A:DMM13 4.1 7.5 1.0 C5 B:DG12 4.3 9.6 1.0 O6 B:DG12 4.4 9.9 1.0 C3 A:DMM13 4.5 6.2 1.0 OP2 B:DG12 4.6 17.6 1.0 C6 B:DG12 4.8 9.6 1.0 O3' B:DC11 4.8 15.1 1.0 C3' B:DC11 4.9 12.3 1.0

M.Cirilli, F.Bachechi, G.Ughetto, F.P.Colonna, M.L.Capobianco. Interactions Between Morpholinyl Anthracyclines and Dna. the Crystal Structure of A Morpholino Doxorubicin Bound to D(Cgtacg). J.Mol.Biol. V. 230 878 1993.
ISSN: ISSN 0022-2836
PubMed: 8478940
DOI: 10.1006/JMBI.1993.1208