Chlorine in PDB 7xdj: Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex, PDB code: 7xdj was solved by C.M.Chien, R.B.Satange, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.84 / 2.44
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	132.522, 132.522, 49.595, 90, 90, 120
R / Rfree (%)	20.1 / 23.6

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Chlorine atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex (pdb code 7xdj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex, PDB code: 7xdj:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:88.3 occ:1.00 MG A:MG102 2.8 42.8 1.0 OP1 A:DC3 3.1 47.7 1.0 OP1 A:DG4 3.6 71.6 1.0 OP1 E:DC3 3.7 51.4 1.0 CG2 C:THR7 4.2 49.8 1.0 P A:DC3 4.3 52.7 1.0 O5' A:DC3 4.3 53.7 1.0 O A:HOH202 4.5 41.6 1.0 C4' A:DC3 4.5 61.7 1.0 C5' A:DC3 4.5 58.0 1.0 P E:DC3 4.8 50.1 1.0 P A:DG4 4.8 67.9 1.0 O3' A:DG2 4.8 51.5 1.0 CB C:THR7 4.9 42.9 1.0 O3' A:DC3 4.9 51.9 1.0 OP2 E:DC3 4.9 44.7 1.0 CB C:PRO3 4.9 66.7 1.0 CG C:PRO3 5.0 86.3 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Cl101 b:59.9 occ:1.00 MG J:MG102 3.2 53.9 1.0 OP2 J:DG3 4.0 72.5 1.0 O5' J:DG3 4.3 73.8 1.0 C5' J:DG3 4.4 57.6 1.0 C3' J:DC2 4.4 52.1 1.0 OP2 J:DC2 4.5 70.2 1.0 C2' J:DC2 4.6 48.9 1.0 P J:DG3 4.7 83.0 1.0 O5' J:DC2 4.8 60.7 1.0 O3' J:DC2 5.0 70.2 1.0 OP2 N:DC6 5.0 57.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl101 b:62.8 occ:1.00 MG N:MG102 3.2 49.0 1.0 O5' N:DG3 4.0 64.1 1.0 OP2 N:DG3 4.2 68.8 1.0 C3' N:DC2 4.7 50.6 1.0 P N:DG3 4.8 79.8 1.0 O3 O:PXZ6 4.8 57.2 1.0 C5' N:DG3 4.9 64.2 1.0 C2' N:DC2 4.9 47.6 1.0 OP2 N:DC2 4.9 64.0 1.0 O5' N:DC2 4.9 56.3 1.0 OP2 J:DC6 5.0 64.5 1.0 C6 J:DC6 5.0 49.3 1.0

R.Satange, S.H.Kao, C.M.Chien, S.H.Chou, C.C.Lin, S.Neidle, M.H.Hou. Staggered Intercalation of Dna Duplexes with Base-Pair Modulation By Two Distinct Drug Molecules Induces Asymmetric Backbone Twisting and Structure Polymorphism. Nucleic Acids Res. V. 50 8867 2022.
ISSN: ESSN 1362-4962
PubMed: 35871296
DOI: 10.1093/NAR/GKAC629