Magnesium in PDB 336d: Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex

The structure of Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex, PDB code: 336d was solved by H.Ohishi, N.Terasoma, I.Nakanishi, G.Van Der Marel, J.H.Vanboom, A.Rich, A.H.-J.Wang, T.Hakoshima, K.-I.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	17.980, 31.510, 44.380, 90.00, 90.00, 90.00
R / Rfree (%)	19 / n/a

The binding sites of Magnesium atom in the Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex (pdb code 336d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex, PDB code: 336d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg15 b:22.8 occ:1.00 O A:HOH83 1.9 36.2 1.0 O B:HOH80 2.2 18.7 1.0 O B:HOH82 2.2 24.0 1.0 O A:HOH81 2.3 29.2 1.0 O B:HOH84 2.4 32.4 1.0 O B:HOH73 2.7 30.3 1.0 MG B:MG16 3.0 35.9 1.0 O A:HOH85 3.1 31.6 1.0 O A:HOH41 3.7 48.2 1.0 O B:HOH38 4.1 17.5 1.0 O A:HOH53 4.1 27.8 1.0 O B:HOH72 4.2 43.7 1.0 O B:HOH71 4.4 28.4 1.0 O B:HOH57 4.4 25.1 1.0 O B:HOH88 4.6 18.3 1.0 O B:HOH86 4.9 40.8 1.0

Magnesium binding site 2 out of 2 in the Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Interaction Between Left-Handed Z-Dna and Polyamine-3 the Crystal Structure of the D(Cg)3 and Thermospermine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg16 b:35.9 occ:1.00 O B:HOH88 2.0 18.3 1.0 O A:HOH83 2.1 36.2 1.0 O B:HOH84 2.2 32.4 1.0 O B:HOH86 2.3 40.8 1.0 O A:HOH85 2.6 31.6 1.0 O B:HOH87 2.7 56.6 1.0 MG B:MG15 3.0 22.8 1.0 O A:HOH53 3.4 27.8 1.0 O A:HOH81 3.5 29.2 1.0 O6 B:DG10 3.6 8.7 1.0 O B:HOH70 3.8 26.3 1.0 N4 A:DC3 4.0 7.4 1.0 O B:HOH80 4.3 18.7 1.0 O B:HOH38 4.3 17.5 1.0 O A:HOH29 4.4 22.3 1.0 O B:HOH82 4.6 24.0 1.0 C5 B:DC9 4.7 10.8 1.0 C6 B:DG10 4.8 10.8 1.0 O A:HOH41 5.0 48.2 1.0

H.Ohishi, N.Terasoma, I.Nakanishi, G.Van Der Marel, J.H.Van Boom, A.Rich, A.H.Wang, T.Hakoshima, K.Tomita. Interaction Between Left-Handed Z-Dna and Polyamine - 3. the Crystal Structure of the D(Cg)3 and Thermospermine Complex. Febs Lett. V. 398 291 1996.
ISSN: ISSN 0014-5793
PubMed: 8977125
DOI: 10.1016/S0014-5793(96)01225-2