Magnesium in PDB 5lit: Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution

The structure of Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution, PDB code: 5lit was solved by C.R.Millan, C.Dardonville, H.P.De Koning, N.Saperas, J.Lourdes Campos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 1.25
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	22.330, 40.250, 72.423, 90.00, 93.67, 90.00
R / Rfree (%)	12.1 / 16.7

The binding sites of Magnesium atom in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution (pdb code 5lit). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution, PDB code: 5lit:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:14.6 occ:0.50 O D:HOH231 1.8 26.6 1.0 O D:HOH246 2.0 37.8 1.0 O D:HOH207 2.1 20.5 1.0 O D:HOH228 2.2 25.7 1.0 O D:HOH222 2.2 22.2 1.0 O D:HOH248 3.9 26.5 1.0 N7 D:DA1 4.0 9.4 1.0 O D:HOH244 4.2 38.4 1.0 C8 D:DA1 4.3 9.5 1.0 O D:HOH229 4.4 31.1 1.0 N6 D:DA2 4.4 7.7 1.0 N7 D:DA2 4.4 9.2 1.0

Magnesium binding site 2 out of 4 in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:14.4 occ:0.50 O C:HOH220 2.0 14.2 1.0 O C:HOH206 2.0 13.9 1.0 O C:HOH212 2.1 14.7 1.0 O C:HOH214 4.2 8.5 0.5 O C:HOH218 4.2 15.5 1.0 O C:HOH208 4.2 12.9 1.0 OP2 C:DT4 4.5 10.9 1.0 OP2 C:DA3 4.6 13.4 1.0 O C:HOH207 4.8 15.5 1.0

Magnesium binding site 3 out of 4 in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:6.9 occ:0.50 O C:HOH215 2.0 15.9 1.0 O B:HOH210 2.1 15.9 1.0 O B:HOH233 2.1 15.8 1.0 O4' B:DA2 4.1 11.2 1.0 O B:HOH223 4.2 11.3 1.0 O A:HOH210 4.4 12.3 1.0 N3 B:DA1 4.4 10.9 1.0 C4' B:DA2 4.6 11.3 1.0 N3 C:DA1 4.6 10.7 1.0 C2' B:DA1 4.8 15.5 1.0 C2 C:DA1 4.9 9.1 1.0

Magnesium binding site 4 out of 4 in the Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Dna Duplex D(Aaattt)2 with the Potential Antiparasitic Drug 6XV at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:9.1 occ:1.00 O B:HOH247 2.0 9.4 1.0 O B:HOH208 2.1 11.9 1.0 O B:HOH209 2.1 11.2 1.0 O B:HOH249 2.1 9.3 1.0 O B:HOH235 2.1 9.0 1.0 O B:HOH246 2.1 9.8 1.0 O B:HOH212 4.0 9.8 1.0 OP2 B:DT5 4.1 11.2 1.0 OP1 B:DT5 4.2 11.3 1.0 O B:HOH238 4.4 23.7 1.0 P B:DT5 4.6 10.0 1.0

C.R.Millan, F.J.Acosta-Reyes, L.Lagartera, G.U.Ebiloma, L.Lemgruber, J.J.Nue Martinez, N.Saperas, C.Dardonville, H.P.De Koning, J.L.Campos. Functional and Structural Analysis of at-Specific Minor Groove Binders That Disrupt Dna-Protein Interactions and Cause Disintegration of the Trypanosoma Brucei Kinetoplast. Nucleic Acids Res. V. 45 8378 2017.
ISSN: ESSN 1362-4962
PubMed: 28637278
DOI: 10.1093/NAR/GKX521