Magnesium in PDB 461d: 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: 461d 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 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.070, 39.720, 65.770, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 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 461d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 461d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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:24.7 occ:1.00 O A:HOH28 2.1 21.7 1.0 O B:HOH27 2.1 21.1 1.0 O B:HOH29 2.1 20.4 1.0 O B:HOH30 2.1 21.5 1.0 O B:HOH31 2.1 20.6 1.0 O A:HOH26 2.2 20.9 1.0 O A:HOH57 4.1 34.1 1.0 O B:HOH105 4.2 23.9 1.0 O6 B:DG22 4.2 19.5 1.0 O B:HOH128 4.3 30.6 1.0 O B:HOH119 4.3 25.2 1.0 O B:HOH109 4.3 22.8 1.0 C5 A:DC1 4.4 19.3 1.0 N7 A:DG2 4.4 20.7 1.0 O A:HOH108 4.4 21.6 1.0 O6 A:DG2 4.4 19.6 1.0 C6 A:DC1 4.7 18.1 1.0

Magnesium binding site 2 out of 2 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:31.6 occ:0.50 O B:HOH37 2.0 92.5 0.5 O B:HOH34 2.2 34.6 0.5 OP1 B:DG24 4.7 42.5 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