Magnesium in PDB 5yty: Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex

The structure of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex, PDB code: 5yty was solved by M.H.Hou, P.C.Wu, Y.F.Kao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.60 / 1.58
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	46.362, 46.362, 48.005, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 26.3

The structure of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex (pdb code 5yty). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex, PDB code: 5yty:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:24.4 occ:1.00 N7 A:DG6 2.3 19.4 1.0 O A:HOH209 2.8 44.0 1.0 C8 A:DG6 3.1 22.8 1.0 C5 A:DG6 3.4 20.8 1.0 O F:HOH204 3.5 33.3 1.0 O6 A:DG6 3.9 19.4 1.0 C6 A:DG6 4.0 24.2 1.0 O A:HOH211 4.1 34.1 1.0 N9 A:DG6 4.4 21.5 1.0 C4 A:DG6 4.5 18.4 1.0 OP2 A:DG6 4.6 26.5 1.0 N4 F:QUI102 5.0 16.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:23.4 occ:1.00 N7 B:DG6 2.2 21.1 1.0 O B:HOH207 2.2 39.5 1.0 O B:HOH215 2.7 36.2 1.0 C8 B:DG6 3.0 26.3 1.0 C5 B:DG6 3.4 21.5 1.0 O B:HOH201 3.6 47.0 1.0 O6 B:DG6 3.8 17.1 1.0 O D:HOH203 3.8 31.3 1.0 C6 B:DG6 4.0 19.6 1.0 O B:HOH216 4.2 33.3 1.0 N9 B:DG6 4.3 18.1 1.0 O B:HOH227 4.4 50.1 1.0 C4 B:DG6 4.5 17.7 1.0 OP2 B:DG6 4.6 30.1 1.0 N4 D:QUI101 4.9 22.6 1.0 C3 D:QUI101 5.0 15.5 1.0

P.C.Wu, S.L.Tzeng, C.K.Chang, Y.F.Kao, M.J.Waring, M.H.Hou. Cooperative Recognition of T:T Mismatch By Echinomycin Causes Structural Distortions in Dna Duplex Nucleic Acids Res. V. 46 7396 2018.
ISSN: ESSN 1362-4962
PubMed: 29741655
DOI: 10.1093/NAR/GKY345