Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex, PDB code: 5yty:

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:11.5 occ:1.00 O B:HOH211 2.1 11.3 1.0 N7 B:DG3 2.2 11.0 1.0 C8 B:DG3 3.1 12.8 1.0 C5 B:DG3 3.3 13.0 1.0 O6 B:DG3 3.7 10.8 1.0 C6 B:DG3 3.9 10.0 1.0 O F:HOH202 4.2 20.9 1.0 N9 B:DG3 4.4 14.1 1.0 C4 B:DG3 4.5 15.3 1.0 OP2 B:DG3 4.5 14.9 1.0 N4 F:QUI101 4.9 15.4 1.0 C3 F:QUI101 5.0 14.1 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