Magnesium in PDB 293d: Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex, PDB code: 293d was solved by H.Ohishi, I.Nakanishi, K.Inubushi, G.A.Van Der Marel, J.H.Vanboom, A.Rich, A.H.-J.Wang, T.Hakoshima, K.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 (°)	17.930, 31.230, 44.640, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex (pdb code 293d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex, PDB code: 293d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine 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 the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg15 b:35.7 occ:1.00 O A:HOH95 2.0 12.2 1.0 O B:HOH96 2.4 13.6 1.0 O A:HOH99 2.4 16.7 1.0 O B:HOH100 2.5 14.1 1.0 O A:HOH98 2.5 16.3 1.0 MG B:MG14 2.9 18.4 1.0 O A:HOH97 2.9 27.2 1.0 O A:HOH93 3.3 18.8 1.0 O A:HOH30 3.5 10.4 1.0 O A:HOH23 3.7 27.1 1.0 O A:HOH24 3.9 24.9 1.0 O6 B:DG10 4.0 4.4 1.0 O B:HOH47 4.1 12.0 1.0 O B:HOH92 4.2 18.6 1.0 N4 A:DC3 4.4 4.1 1.0 O B:HOH31 4.4 18.4 1.0 O A:HOH41 4.4 16.8 1.0 O B:HOH53 4.6 12.7 1.0 O B:HOH94 4.9 23.6 1.0

Magnesium binding site 2 out of 3 in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine 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 the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg14 b:18.4 occ:1.00 O A:HOH95 2.0 12.2 1.0 O B:HOH92 2.2 18.6 1.0 O B:HOH96 2.2 13.6 1.0 O A:HOH93 2.3 18.8 1.0 O B:HOH94 2.4 23.6 1.0 MG A:MG15 2.9 35.7 1.0 O A:HOH97 3.3 27.2 1.0 O B:HOH53 3.9 12.7 1.0 O A:HOH39 4.3 18.6 1.0 O A:HOH30 4.3 10.4 1.0 O B:HOH48 4.4 16.9 1.0 O B:HOH100 4.5 14.1 1.0 O A:HOH99 4.6 16.7 1.0 O B:HOH67 4.6 11.3 1.0 O A:HOH41 4.9 16.8 1.0 O B:HOH63 5.0 28.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg16 b:21.1 occ:1.00 O A:HOH104 2.2 19.2 1.0 O B:HOH103 2.2 22.8 1.0 O A:HOH101 2.2 18.7 1.0 O A:HOH105 2.3 28.1 1.0 O B:HOH102 2.3 22.7 1.0 O B:HOH106 2.3 36.1 1.0 O A:HOH64 4.0 22.6 1.0 O B:HOH90 4.4 56.9 1.0 N7 B:DG8 4.4 3.6 1.0 O B:HOH48 4.5 16.9 1.0 O B:HOH67 4.5 11.3 1.0 O6 B:DG8 4.5 5.8 1.0 O B:HOH53 4.6 12.7 1.0 O6 A:DG4 4.8 4.0 1.0 O A:HOH50 4.8 17.8 1.0

H.Ohishi, I.Nakanishi, K.Inubushi, G.Van Der Marel, J.H.Van Boom, A.Rich, A.H.Wang, T.Hakoshima, K.Tomita. Interaction Between the Left-Handed Z-Dna and Polyamine-2. the Crystal Structure of the D(Cg)3 and Spermidine Complex. Febs Lett. V. 391 153 1996.
ISSN: ISSN 0014-5793
PubMed: 8706905
DOI: 10.1016/0014-5793(96)00723-5