Magnesium in PDB 460d: A "Hydrat-Ion Spine" in A B-Dna Minor Groove

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 460d was solved by V.Tereshko, G.Minasov, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.111, 39.731, 65.829, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / n/a

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Rubidium	(Rb)	1 atom

The binding sites of Magnesium atom in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove (pdb code 460d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 460d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:19.3 occ:1.00 O A:HOH28 2.1 17.8 1.0 O B:HOH31 2.1 19.9 1.0 O B:HOH30 2.1 19.7 1.0 O B:HOH29 2.2 22.3 1.0 O B:HOH27 2.2 19.9 1.0 O A:HOH26 2.2 20.4 1.0 O B:HOH105 4.2 20.7 1.0 O A:HOH57 4.2 26.1 1.0 O6 B:DG22 4.2 18.4 1.0 O B:HOH128 4.3 27.2 1.0 O B:HOH109 4.3 20.4 1.0 C5 A:DC1 4.3 17.3 1.0 O A:HOH108 4.3 19.7 1.0 O B:HOH119 4.4 27.2 1.0 O6 A:DG2 4.4 16.5 1.0 N7 A:DG2 4.5 17.8 1.0 C6 A:DC1 4.7 18.5 1.0

Magnesium binding site 2 out of 3 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg32 b:22.0 occ:0.50 O B:HOH33 1.8 34.3 0.5 O B:HOH35 2.0 22.7 0.5 O B:HOH36 2.1 32.9 1.0 O B:HOH34 2.2 42.9 1.0 O B:HOH37 2.2 45.0 1.0 OP1 B:DG24 4.3 43.0 1.0 O3' B:DC23 4.8 23.8 1.0

Magnesium binding site 3 out of 3 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg38 b:24.9 occ:0.50 O A:HOH40 2.0 24.1 0.5 O B:HOH41 2.1 39.6 0.5 O B:HOH44 2.2 38.9 0.5 O A:HOH43 2.2 29.6 0.5 O B:HOH42 2.2 28.6 0.5 O A:HOH247 4.1 39.2 0.5 O A:HOH168 4.1 50.4 1.0 O A:HOH133 4.3 34.3 1.0 OP1 B:DA18 4.3 30.9 1.0 O B:HOH56 4.3 38.3 1.0 O B:HOH116 4.6 25.0 1.0 C5' A:DC11 4.9 26.1 1.0 O3' B:DA17 5.0 24.8 1.0

V.Tereshko, G.Minasov, M.Egli. A "Hydrat-Ion Spine" in A B-Dna Minor Groove J.Am.Chem.Soc. V. 121 3590 1999.
ISSN: ISSN 0002-7863