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

Protein crystallography data

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

Other elements in 2des:

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

Sodium Binding Sites:

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 2des

Go back to Sodium Binding Sites List in 2des
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 2des

Go back to Sodium Binding Sites List in 2des
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

Reference:

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
Page generated: Tue Dec 15 05:47:31 2020

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