Bromine 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
Manganese	(Mn)	2 atoms

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Echinomycin-D(Acgtcgt)2 Complex, PDB code: 5ytz:
Jump to Bromine binding site number: 1; 2;

Bromine 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 Bromine with other atoms in the Br 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:Br7 b:53.9 occ:1.00 BR A:BRU7 0.0 53.9 1.0 C5 A:BRU7 1.9 34.4 1.0 C6 A:BRU7 2.9 25.7 1.0 C4 A:BRU7 2.9 36.4 1.0 O4 A:BRU7 3.1 31.7 1.0 N1 A:BRU7 4.1 24.8 1.0 C2' A:DG6 4.1 26.9 1.0 N3 A:BRU7 4.1 28.6 1.0 O3' A:DG6 4.6 47.0 1.0 C2 A:BRU7 4.6 28.9 1.0 O1 F:QUI102 4.6 19.1 1.0 C3' A:DG6 4.8 33.9 1.0 O A:HOH229 5.0 44.8 1.0

Bromine 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 Bromine with other atoms in the Br 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:Br7 b:44.3 occ:1.00 BR B:BRU7 0.0 44.3 1.0 C5 B:BRU7 1.9 39.1 1.0 C4 B:BRU7 2.9 18.5 1.0 C6 B:BRU7 2.9 20.4 1.0 O4 B:BRU7 3.1 20.1 1.0 C2' B:DG6 3.8 17.1 1.0 N3 B:BRU7 4.1 20.2 1.0 N1 B:BRU7 4.2 19.5 1.0 O3' B:DG6 4.2 17.6 1.0 O B:HOH222 4.2 32.3 1.0 OP2 B:BRU7 4.3 26.2 1.0 C3' B:DG6 4.3 19.0 1.0 O1 D:QUI101 4.6 9.5 1.0 C2 B:BRU7 4.6 24.3 1.0 P B:BRU7 4.8 20.6 1.0 O B:HOH218 4.9 34.5 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