Magnesium in PDB 1g3x: Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer

The structure of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer, PDB code: 1g3x was solved by L.Malinina, M.Soler-Lopez, J.Aymami, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.471, 68.365, 77.362, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26.6

The binding sites of Magnesium atom in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer (pdb code 1g3x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer, PDB code: 1g3x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:61.3 occ:0.95 O B:HOH900 2.1 60.7 0.9 O B:HOH899 2.1 59.9 0.9 O A:HOH903 2.1 60.2 0.9 O B:HOH902 2.1 59.5 0.9 O A:HOH901 2.1 59.1 0.9 O A:HOH898 2.1 61.2 0.9 O6 A:DG104 3.8 37.2 1.0 N7 A:DG104 4.5 33.8 1.0 O4 B:DT120 4.7 25.9 1.0 C5 A:DC103 4.7 30.1 1.0 C6 A:DG104 4.7 36.3 1.0

Magnesium binding site 2 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:52.6 occ:1.00 O B:HOH883 2.1 40.0 0.0 O B:HOH881 2.1 54.8 1.0 O B:HOH885 2.1 55.7 1.0 O B:HOH884 2.1 55.8 1.0 O B:HOH882 2.1 53.6 1.0 O B:HOH880 2.1 58.6 1.0 OP1 B:DT120 2.2 36.3 1.0 P B:DT120 3.4 31.1 1.0 OP2 B:DT120 3.9 29.4 1.0 O5' B:DT120 4.1 31.2 1.0 C5' B:DT120 4.3 31.9 1.0 O3' B:DT119 4.6 31.5 1.0

Magnesium binding site 3 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg800 b:67.0 occ:1.00 O G:HOH870 2.1 65.9 1.0 O G:HOH873 2.1 66.4 1.0 O G:HOH871 2.1 66.5 1.0 O G:HOH869 2.1 64.8 1.0 O G:HOH872 2.1 66.9 1.0 O G:HOH868 2.1 65.2 1.0 O6 G:DG410 3.3 38.1 1.0 C6 G:DG410 4.4 38.6 1.0 N4 H:DC415 4.4 30.5 1.0 C5 G:DC409 4.7 35.2 1.0 N4 G:DC409 4.7 38.3 1.0 N7 G:DG410 4.9 38.9 1.0

Magnesium binding site 4 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg801 b:55.5 occ:0.50 O J:HOH878 2.1 55.8 0.5 O J:HOH877 2.1 55.1 0.5 O J:HOH875 2.1 55.1 0.5 O I:HOH879 2.1 55.4 0.5 O I:HOH874 2.1 55.2 0.5 O J:HOH876 2.1 55.0 0.5 O6 I:DG510 4.1 42.6 1.0 C5 J:DC513 4.2 42.1 1.0 O6 J:DG514 4.4 36.9 1.0 C6 J:DC513 4.6 43.3 1.0 C4 J:DC513 4.9 41.0 1.0 N7 I:DG510 4.9 39.9 1.0 N7 J:DG514 4.9 37.5 1.0 C6 I:DG510 5.0 41.0 1.0

Magnesium binding site 5 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg804 b:52.4 occ:1.00 O K:HOH893 2.1 57.9 1.0 O K:HOH895 2.1 55.7 1.0 O K:HOH896 2.1 56.0 1.0 O K:HOH892 2.1 51.6 1.0 O K:HOH894 2.1 53.8 1.0 OP1 K:DG602 2.2 35.2 1.0 O K:HOH897 2.2 40.0 0.0 P K:DG602 3.3 26.9 1.0 OP2 K:DG602 3.6 30.2 1.0 O3' K:DC601 3.9 28.5 1.0 O5' K:DG602 4.5 28.3 1.0 OP2 K:DC603 4.6 36.4 1.0 C3' K:DC601 4.7 28.4 1.0 C5' K:DG602 4.8 29.2 1.0

Magnesium binding site 6 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg806 b:61.5 occ:0.95 O K:HOH908 2.1 61.8 0.9 O L:HOH909 2.1 62.2 0.9 O K:HOH907 2.1 63.2 0.9 O L:HOH906 2.1 62.2 0.9 O K:HOH905 2.1 63.4 0.9 O L:HOH904 2.1 62.1 0.9 O6 K:DG610 3.7 42.2 1.0 O6 L:DG614 4.2 36.4 1.0 N7 K:DG610 4.4 43.0 1.0 C6 K:DG610 4.6 41.3 1.0 C5 K:DG610 4.9 42.2 1.0 N7 L:DG614 4.9 38.9 1.0

Magnesium binding site 7 out of 7 in the Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Intercalation of An 9ACRIDINE-Peptide Drug in A Dna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg803 b:53.6 occ:1.00 O L:HOH889 2.1 54.3 1.0 O L:HOH888 2.1 56.6 1.0 O L:HOH886 2.1 57.3 1.0 O L:HOH890 2.1 55.7 1.0 O L:HOH887 2.1 57.1 1.0 OP1 L:DG614 2.2 47.6 1.0 O L:HOH891 2.5 40.0 0.0 P L:DG614 3.2 46.1 1.0 OP2 L:DG614 3.5 46.4 1.0 O3' L:DC613 4.2 44.5 1.0 C3' L:DC613 4.4 43.1 1.0 O5' L:DG614 4.4 46.1 1.0

L.Malinina, M.Soler-Lopez, J.Aymami, J.A.Subirana. Intercalation of An Acridine-Peptide Drug in An Aa/Tt Base Step in the Crystal Structure of [D(Cgcgaattcgcg)](2) with Six Duplexes and Seven Mg(2+) Ions in the Asymmetric Unit. Biochemistry V. 41 9341 2002.
ISSN: ISSN 0006-2960
PubMed: 12135355
DOI: 10.1021/BI020135C