Magnesium 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:

Chlorine	(Cl)	3 atoms
Bromine	(Br)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcgcgt/Acgagct) Complex, PDB code: 7xdj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg102 b:42.8 occ:1.00 OP1 A:DC3 2.1 47.7 1.0 OP1 E:DC3 2.1 51.4 1.0 O A:HOH202 2.6 41.6 1.0 CL A:CL101 2.8 88.3 1.0 O E:HOH103 2.8 54.2 1.0 P E:DC3 3.4 50.1 1.0 P A:DC3 3.4 52.7 1.0 OP2 E:DC3 4.0 44.7 1.0 C5' E:DC3 4.1 65.1 1.0 OP2 A:DC3 4.1 44.4 1.0 O5' E:DC3 4.2 53.0 1.0 O5' A:DC3 4.2 53.7 1.0 C5' A:DC3 4.4 58.0 1.0 O3' A:DG2 4.5 51.5 1.0 O3' E:DG2 4.5 45.5 1.0 OP1 A:DG4 4.6 71.6 1.0 OP1 E:DG4 4.7 73.5 1.0 C4' E:DC3 5.0 65.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg102 b:53.9 occ:1.00 OP2 J:DC2 2.6 70.2 1.0 CL J:CL101 3.2 59.9 1.0 O5' J:DC2 3.5 60.7 1.0 P J:DC2 3.5 67.5 1.0 C3' J:DA1 4.0 73.1 1.0 O3' J:DA1 4.3 80.2 1.0 C2' N:DC6 4.4 65.6 1.0 C6 N:DC6 4.4 41.0 1.0 C2' J:DA1 4.5 65.5 1.0 OP1 J:DA1 4.5 104.3 1.0 OP1 J:DC2 4.8 64.2 1.0 C3' N:DC6 4.8 58.7 1.0 C5' N:DC6 4.8 56.4 1.0 C3' J:DC2 4.8 52.1 1.0 C5' J:DC2 4.9 52.4 1.0 C6 J:DC2 4.9 45.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg102 b:49.0 occ:1.00 O3' N:DA1 2.5 87.6 1.0 OP2 N:DC2 2.9 64.0 1.0 P N:DC2 3.1 66.4 1.0 CL N:CL101 3.2 62.8 1.0 O5' N:DC2 3.4 56.3 1.0 C3' N:DA1 3.7 71.5 1.0 OP2 N:DA1 3.8 113.1 1.0 O5' N:DA1 4.1 110.2 1.0 OP1 N:DC2 4.6 77.0 1.0 P N:DA1 4.6 122.5 1.0 C2' N:DA1 4.7 69.3 1.0 C5' N:DC2 4.7 51.1 1.0 C4' N:DA1 4.8 77.4 1.0 C3' N:DC2 4.9 50.6 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