Zinc in PDB 7x97: Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex, PDB code: 7x97 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)	25.57 / 1.95
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.452, 43.452, 139.365, 90, 90, 120
R / Rfree (%)	22.9 / 28.2

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

Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex (pdb code 7x97). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex, PDB code: 7x97:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:54.9 occ:0.33 O A:HOH214 2.6 19.6 1.0 O A:HOH210 4.3 21.9 1.0 C5 A:DC4 4.5 14.1 1.0 C6 A:DC4 4.9 14.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:55.6 occ:1.00 N7 A:DA1 2.4 38.2 1.0 N6 A:DA1 3.3 37.7 1.0 C5 A:DA1 3.3 37.3 1.0 C8 A:DA1 3.5 38.4 1.0 C6 A:DA1 3.7 36.9 1.0 O6 A:DG2 4.1 23.0 1.0 C4 A:DA1 4.6 36.8 1.0 N9 A:DA1 4.6 37.8 1.0 N4 B:DC6 4.9 29.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:116.6 occ:1.00 N7 A:DG6 2.5 17.5 1.0 C5 A:DG6 3.5 16.1 1.0 C8 A:DG6 3.5 18.2 1.0 O6 A:DG6 3.5 15.3 1.0 C6 A:DG6 3.9 15.4 1.0 N4 G:QUI102 4.7 11.4 1.0 N9 A:DG6 4.7 18.1 1.0 C4 A:DG6 4.7 16.5 1.0 C3 G:QUI102 5.0 11.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:16.1 occ:1.00 O B:HOH205 2.1 13.5 1.0 O B:HOH206 2.1 7.2 1.0 N7 B:DG4 2.2 20.6 1.0 C8 B:DG4 3.1 23.6 1.0 C5 B:DG4 3.3 19.6 1.0 O6 B:DG4 3.7 20.1 1.0 C6 B:DG4 3.9 19.7 1.0 O B:HOH204 4.0 16.4 1.0 O6 B:DG5 4.2 20.5 1.0 OP2 B:DG4 4.4 27.6 1.0 N9 B:DG4 4.4 22.9 1.0 C4 B:DG4 4.5 19.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:16.6 occ:1.00 N7 B:DG3 2.0 20.5 1.0 CL B:CL103 2.2 28.2 1.0 C8 B:DG3 2.9 21.3 1.0 C5 B:DG3 3.1 19.7 1.0 O6 B:DG3 3.5 18.3 1.0 C6 B:DG3 3.7 20.6 1.0 O G:HOH201 4.1 13.8 1.0 N9 B:DG3 4.1 21.0 1.0 C4 B:DG3 4.2 20.0 1.0 C5 B:DC2 4.8 21.1 1.0 C6 B:DC2 4.8 22.2 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