Magnesium in PDB 2elg: The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius

The structure of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius, PDB code: 2elg was solved by H.Ohishi, Y.Tozuka, D.Y.Zhou, T.Ishida, K.Nakatani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	17.847, 30.988, 44.022, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 24.7

The structure of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius (pdb code 2elg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius, PDB code: 2elg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg92 b:6.1 occ:1.00 O A:HOH41 1.9 8.6 1.0 O A:HOH14 2.1 4.1 1.0 O A:HOH40 2.1 6.0 1.0 O A:HOH28 2.1 6.3 1.0 N7 A:DG6 2.2 2.1 1.0 H1 A:HOH41 2.6 15.0 1.0 H1 A:HOH14 2.8 15.0 1.0 H2 A:HOH14 2.8 15.0 1.0 H2 A:HOH41 2.8 15.0 1.0 H1 A:HOH40 2.8 15.0 1.0 H2 A:HOH40 2.8 15.0 1.0 H2 A:HOH28 2.9 15.0 1.0 H1 A:HOH28 2.9 15.0 1.0 MG A:MG94 3.1 14.2 1.0 C8 A:DG6 3.2 2.4 1.0 C5 A:DG6 3.3 2.0 1.0 O A:HOH114 3.4 11.6 1.0 O6 A:DG6 3.6 2.0 1.0 H1 A:HOH114 3.8 15.0 1.0 O A:HOH88 3.8 5.5 1.0 C6 A:DG6 3.9 2.0 1.0 O A:HOH80 4.2 5.0 1.0 H1 A:HOH88 4.2 15.0 1.0 OP1 A:DC5 4.3 3.8 1.0 H2 A:HOH114 4.3 15.0 1.0 O A:HOH115 4.4 11.1 1.0 N9 A:DG6 4.4 2.2 1.0 H2 A:HOH88 4.4 15.0 1.0 C4 A:DG6 4.5 2.1 1.0 O A:HOH36 4.6 7.4 1.0 H1 A:HOH80 4.8 15.0 1.0 H2 A:HOH115 4.9 15.0 1.0 H1 A:HOH36 4.9 15.0 1.0 H2 A:HOH80 4.9 15.0 1.0

Magnesium binding site 2 out of 3 in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg93 b:8.1 occ:1.00 O A:HOH54 1.8 10.5 1.0 O B:HOH86 2.1 10.6 1.0 O A:HOH33 2.1 11.4 1.0 O A:HOH47 2.1 10.4 1.0 H2 A:HOH54 2.5 15.0 1.0 H1 A:HOH54 2.6 15.0 1.0 H2 B:HOH86 2.7 15.0 1.0 H1 A:HOH33 2.7 15.0 1.0 H1 B:HOH86 2.7 15.0 1.0 H1 A:HOH47 2.8 15.0 1.0 H2 A:HOH47 2.9 15.0 1.0 H2 A:HOH33 2.9 15.0 1.0 OP2 B:DG10 3.9 3.8 1.0 O A:HOH62 4.0 11.2 1.0 OP2 A:DG6 4.1 4.5 1.0 O B:HOH97 4.3 7.9 1.0 O A:HOH20 4.4 3.8 1.0 H1 A:HOH62 4.5 15.0 1.0 H2 A:HOH62 4.6 15.0 1.0 O B:HOH57 4.7 15.1 1.0 H1 A:HOH20 4.8 15.0 1.0 H2 B:HOH97 4.9 15.0 1.0 H2 B:HOH57 5.0 15.0 1.0

Magnesium binding site 3 out of 3 in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg94 b:14.2 occ:1.00 O A:HOH115 1.7 11.1 1.0 O A:HOH14 2.1 4.1 1.0 O A:HOH114 2.4 11.6 1.0 H1 A:HOH115 2.5 15.0 1.0 H2 A:HOH115 2.5 15.0 1.0 H2 A:HOH14 2.5 15.0 1.0 H1 A:HOH14 2.5 15.0 1.0 H2 A:HOH114 2.7 15.0 1.0 MG A:MG92 3.1 6.1 1.0 H1 A:HOH114 3.4 15.0 1.0 O A:HOH16 3.4 8.3 1.0 H2 A:HOH16 3.7 15.0 1.0 O A:HOH28 3.8 6.3 1.0 O A:HOH40 3.8 6.0 1.0 H1 A:HOH28 4.0 15.0 1.0 H1 A:HOH16 4.3 15.0 1.0 H2 A:HOH40 4.3 15.0 1.0 O6 A:DG6 4.4 2.0 1.0 H2 A:HOH28 4.6 15.0 1.0 H1 A:HOH40 4.6 15.0 1.0 O A:HOH88 4.7 5.5 1.0 O A:HOH41 4.8 8.6 1.0 N7 A:DG6 4.9 2.1 1.0 H1 A:HOH88 4.9 15.0 1.0 H42 B:DC7 5.0 15.0 1.0

H.Ohishi, Y.Tozuka, Z.Da-Yang, T.Ishida, K.Nakatani. The Rare Crystallographic Structure of D(Cgcgcg)(2): the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)(2) at 10 Degrees C Biochem.Biophys.Res.Commun. V. 358 24 2007.
ISSN: ISSN 0006-291X
PubMed: 17467661
DOI: 10.1016/J.BBRC.2007.04.026