Cobalt in PDB 7x6r: Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex, PDB code: 7x6r was solved by S.H.Kao, 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)	27.72 / 1.89
Space group	P 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.225, 43.225, 65.839, 90, 90, 90
R / Rfree (%)	24.4 / 25.9

The binding sites of Cobalt atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex (pdb code 7x6r). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex, PDB code: 7x6r:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:28.1 occ:0.50 O A:HOH201 2.0 40.9 1.0 O D:HOH201 2.1 36.5 1.0 N7 A:DG6 2.1 25.3 1.0 C8 A:DG6 3.0 32.6 1.0 C5 A:DG6 3.2 29.4 1.0 O6 A:DG6 3.6 32.9 1.0 C6 A:DG6 3.8 24.2 1.0 O A:HOH203 4.0 42.0 0.5 N9 A:DG6 4.3 30.2 1.0 O A:HOH204 4.3 35.3 1.0 C4 A:DG6 4.4 34.3 1.0 N4 D:QUI102 4.4 32.4 1.0 O A:HOH206 4.5 47.9 1.0 C3 D:QUI102 4.7 32.0 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:38.5 occ:1.00 O B:HOH204 1.7 39.0 1.0 O B:HOH202 1.7 45.0 1.0 O B:HOH201 1.9 46.1 1.0 O B:HOH205 2.0 40.5 1.0 O B:HOH207 2.0 39.0 1.0 N7 B:DG4 2.1 29.8 1.0 C5 B:DG4 3.0 29.3 1.0 C8 B:DG4 3.1 32.3 1.0 O6 B:DG4 3.3 38.0 1.0 C6 B:DG4 3.5 31.1 1.0 OP2 B:DG4 4.1 37.6 1.0 C4 B:DG4 4.2 35.5 1.0 N9 B:DG4 4.2 35.5 1.0 O6 B:DG5 4.3 43.4 1.0 C2' B:DG3 4.6 33.4 1.0 O1 D:QUI101 4.8 38.7 1.0 N1 B:DG4 4.9 32.1 1.0 N7 B:DG5 5.0 36.7 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcacgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:73.3 occ:1.00 N7 B:DG3 2.1 50.7 1.0 C8 B:DG3 3.0 41.8 1.0 C5 B:DG3 3.2 43.6 1.0 O6 B:DG3 3.6 40.6 1.0 C6 B:DG3 3.8 39.9 1.0 N9 B:DG3 4.3 42.4 1.0 C4 B:DG3 4.4 40.5 1.0 N4 D:QUI101 4.7 36.4 1.0 C5 B:DC2 4.9 38.5 1.0 C3 D:QUI101 4.9 35.5 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