Magnesium in PDB 308d: Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph

The structure of Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph, PDB code: 308d was solved by Y.-G.Gao, H.Robinson, E.R.Wijsman, G.A.Van Der Marel, J.H.Vanboom, A.H.-J.Wang, 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 (°)	18.619, 20.096, 26.553, 69.09, 90.40, 108.03
R / Rfree (%)	17.5 / 22.1

The binding sites of Magnesium atom in the Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph (pdb code 308d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph, PDB code: 308d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg16 b:16.1 occ:1.00 O A:HOH116 1.9 14.4 1.0 O A:HOH117 1.9 15.1 1.0 O A:HOH115 1.9 17.1 1.0 O A:HOH113 2.0 13.9 1.0 O A:HOH114 2.0 16.2 1.0 OP1 A:DT3 2.2 17.2 1.0 P A:DT3 3.6 14.1 1.0 O A:HOH44 4.0 24.2 1.0 O3' A:DG2 4.2 13.7 1.0 O A:HOH50 4.2 16.9 1.0 O A:HOH71 4.3 25.2 1.0 OP2 A:DT3 4.3 15.2 1.0 O A:HOH31 4.4 24.3 1.0 O A:HOH34 4.4 48.3 1.0 O A:HOH24 4.4 35.3 1.0 C3' A:DG2 4.4 14.2 1.0 O A:HOH70 4.5 18.1 1.0 O5' A:DT3 4.6 15.8 1.0 C5' A:DT3 4.9 13.5 1.0

Magnesium binding site 2 out of 3 in the Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg17 b:20.5 occ:1.00 O A:HOH120 1.9 20.7 1.0 O A:HOH121 1.9 19.8 1.0 O A:HOH119 1.9 19.6 1.0 O A:HOH118 1.9 20.9 1.0 O A:HOH122 2.0 20.6 1.0 OP2 A:DA4 2.2 17.3 1.0 P A:DA4 3.4 16.1 1.0 O A:HOH32 3.6 25.6 1.0 OP1 A:DA4 3.8 18.9 1.0 O A:HOH25 4.2 19.7 1.0 O A:HOH92 4.2 47.8 1.0 O3' A:DT3 4.4 15.8 1.0 O A:HOH48 4.5 38.1 1.0 O5' A:DA4 4.5 17.5 1.0 C3' A:DT3 4.6 13.9 1.0

Magnesium binding site 3 out of 3 in the Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Binding of Daunomycin to B-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallograph within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg15 b:15.6 occ:1.00 O B:HOH111 1.9 17.5 1.0 O B:HOH110 1.9 15.5 1.0 O A:HOH107 1.9 15.4 1.0 O B:HOH109 1.9 15.7 1.0 O B:HOH112 2.0 16.3 1.0 O A:HOH108 2.0 16.5 1.0 O A:HOH106 3.9 41.5 1.0 O4 A:BGC7 4.0 13.8 1.0 O A:HOH38 4.2 43.2 1.0 O A:HOH60 4.2 16.1 1.0 O19 A:DM114 4.2 13.7 1.0 O5' B:DC7 4.3 22.0 1.0 O B:HOH79 4.3 35.0 1.0 C4 A:BGC7 4.4 14.7 1.0 O B:HOH82 4.4 40.4 1.0 N7 B:DG8 4.5 14.2 1.0 O6 B:DG8 4.5 13.7 1.0 C5' B:DC7 4.7 17.3 1.0 O3 A:BGC7 4.8 16.8 1.0 C1 A:DM114 4.8 12.5 1.0

Y.-G.Gao, H.Robinson, E.R.Wijsman, G.A.Van Der Marel, J.H.Van Boom, A.H.-J.Wang. Binding of Daunomycin to Beta-D-Glucosylated Dna Found in Protozoa Trypanosoma Brucei Studied By X-Ray Crystallography J.Am.Chem.Soc. V. 119 1496 1997.
ISSN: ISSN 0002-7863