Manganese in PDB 5ytz: Crystal Structure of Echinomycin-D(Acgtcgt)2 Complex

The structure of Crystal Structure of Echinomycin-D(Acgtcgt)2 Complex, PDB code: 5ytz 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)	27.16 / 1.55
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	41.759, 41.759, 138.415, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.5

The structure of Crystal Structure of Echinomycin-D(Acgtcgt)2 Complex also contains other interesting chemical elements:

Potassium	(K)	1 atom
Bromine	(Br)	2 atoms

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

Manganese binding site 1 out of 2 in the Crystal Structure of Echinomycin-D(Acgtcgt)2 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(Acgtcgt)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:7.4 occ:0.47 O A:HOH210 2.2 15.7 0.5 O A:HOH221 2.2 12.1 0.5 O A:HOH205 2.2 19.2 1.0 N7 A:DG3 2.3 9.0 1.0 C8 A:DG3 3.1 14.1 1.0 C5 A:DG3 3.5 8.7 1.0 O6 A:DG3 3.9 8.9 1.0 O A:HOH211 4.0 20.6 1.0 C6 A:DG3 4.1 8.7 1.0 OP2 A:DG3 4.1 14.3 1.0 O D:HOH204 4.3 13.4 1.0 N9 A:DG3 4.4 9.1 1.0 C4 A:DG3 4.6 8.7 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Echinomycin-D(Acgtcgt)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:9.6 occ:0.48 O B:HOH214 2.2 15.3 1.0 N7 B:DG3 2.2 12.6 1.0 O F:HOH206 2.3 12.4 1.0 C8 B:DG3 3.1 14.1 1.0 C5 B:DG3 3.4 12.1 1.0 O6 B:DG3 3.8 12.4 1.0 C6 B:DG3 4.0 12.0 1.0 O B:HOH233 4.1 17.2 1.0 O B:HOH211 4.2 19.2 1.0 N9 B:DG3 4.4 12.8 1.0 O B:HOH206 4.5 18.9 1.0 C4 B:DG3 4.5 11.7 1.0 N4 F:QUI101 4.7 12.3 1.0 C3 F:QUI101 4.8 11.0 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