Magnesium in PDB 292d: Interaction Between the Left-Handed Z-Dna and Polyamine:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex, PDB code: 292d was solved by H.Ohishi, S.Kunisawa, G.Van Der Marel, J.H.Van Boom, A.Rich, A.H.-J.Wang, K.Tomita, T.Hakoshima, 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 (°)	17.940, 31.230, 44.550, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane 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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex (pdb code 292d). 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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex, PDB code: 292d:
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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane 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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg14 b:16.9 occ:1.00 O A:HOH82 1.8 11.9 1.0 O A:HOH80 2.1 16.5 1.0 O A:HOH83 2.1 11.6 1.0 O A:HOH81 2.2 19.8 1.0 O A:HOH79 2.2 16.9 1.0 N7 A:DG6 2.3 4.6 1.0 MG A:MG15 2.8 38.1 1.0 C8 A:DG6 3.3 5.8 1.0 C5 A:DG6 3.4 3.9 1.0 O A:HOH85 3.5 22.6 1.0 O6 A:DG6 3.5 5.9 1.0 C6 A:DG6 3.8 4.5 1.0 O A:HOH86 4.2 19.9 1.0 O A:HOH84 4.2 31.1 1.0 OP1 A:DC5 4.3 9.1 1.0 O A:HOH87 4.5 11.8 1.0 N9 A:DG6 4.5 4.7 1.0 C4 A:DG6 4.6 4.8 1.0

Magnesium binding site 2 out of 3 in the Interaction Between the Left-Handed Z-Dna and Polyamine:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane 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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg15 b:38.1 occ:1.00 O A:HOH82 1.9 11.9 1.0 O A:HOH87 2.1 11.8 1.0 O A:HOH86 2.1 19.9 1.0 O A:HOH83 2.1 11.6 1.0 O A:HOH84 2.2 31.1 1.0 O A:HOH85 2.3 22.6 1.0 MG A:MG14 2.8 16.9 1.0 O A:HOH79 3.6 16.9 1.0 O A:HOH80 3.8 16.5 1.0 O6 A:DG6 4.3 5.9 1.0 O A:HOH81 4.6 19.8 1.0 N7 A:DG6 4.8 4.6 1.0

Magnesium binding site 3 out of 3 in the Interaction Between the Left-Handed Z-Dna and Polyamine:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane 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:the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4- Diaminobutane Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg16 b:26.5 occ:1.00 O B:HOH91 2.0 15.2 1.0 O B:HOH88 2.0 23.5 1.0 O B:HOH90 2.1 18.6 1.0 O B:HOH89 2.1 19.2 1.0 O B:HOH92 2.1 26.3 1.0 O B:HOH63 4.0 31.5 1.0 N7 B:DG8 4.4 5.2 1.0 O B:HOH32 4.4 18.1 1.0 O B:HOH49 4.5 11.1 1.0 O6 B:DG8 4.5 5.8 1.0 O B:HOH38 4.8 12.0 1.0 O A:HOH33 4.8 15.1 1.0 O A:HOH71 4.8 30.3 1.0 O6 A:DG4 4.9 5.9 1.0

H.Ohishi, S.Kunisawa, G.Van Der Marel, J.H.Van Boom, A.Rich, A.H.Wang, K.Tomita, T.Hakoshima. Interaction Between the Left-Handed Z-Dna and Polyamine. the Crystal Structure of the D(Cg)3 and N-(2-Aminoethyl)-1,4-Diamino-Butane Complex. Febs Lett. V. 284 238 1991.
ISSN: ISSN 0014-5793
PubMed: 2060642
DOI: 10.1016/0014-5793(91)80694-X