Magnesium in PDB 436d: The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution

The structure of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution, PDB code: 436d 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 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.640, 39.630, 65.530, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / n/a

The structure of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution (pdb code 436d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution, PDB code: 436d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:12.8 occ:1.00 O B:HOH30 2.1 14.3 1.0 O A:HOH26 2.1 14.0 1.0 O B:HOH27 2.1 13.6 1.0 O B:HOH31 2.1 14.1 1.0 O A:HOH28 2.1 12.7 1.0 O B:HOH29 2.1 15.5 1.0 O B:HOH105 4.1 15.0 1.0 O A:HOH57 4.1 20.9 1.0 O6 B:DG22 4.2 13.0 1.0 C5 A:DC1 4.2 13.6 1.0 O B:HOH119 4.3 18.5 1.0 O A:HOH108 4.3 14.6 1.0 O B:HOH128 4.3 23.6 1.0 O B:HOH109 4.3 14.5 1.0 N7 A:DG2 4.4 12.0 1.0 O6 A:DG2 4.4 11.3 1.0 C6 A:DC1 4.6 13.6 1.0 C4 A:DC1 5.0 13.1 1.0

Magnesium binding site 2 out of 5 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg51 b:23.9 occ:0.50 O A:HOH122 1.9 26.4 1.0 O A:HOH179 2.1 34.0 1.0 O A:HOH54 2.1 27.3 0.5 O A:HOH55 2.2 19.9 0.5 O A:HOH52 2.4 25.2 0.5 O A:HOH53 2.7 29.7 0.5 O A:HOH220 4.2 24.7 0.5 OP1 A:DA5 4.3 26.4 1.0 O A:HOH236 4.3 24.5 0.5 OP2 A:DA6 4.5 14.1 1.0 C3' A:DA5 4.8 13.8 1.0 O A:HOH226 4.8 32.1 0.5 O A:HOH61 4.9 30.8 1.0

Magnesium binding site 3 out of 5 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg32 b:18.0 occ:1.00 O B:HOH37 2.0 20.3 1.0 O B:HOH33 2.0 20.5 1.0 O B:HOH35 2.0 19.9 1.0 O B:HOH36 2.1 20.4 1.0 O B:HOH34 2.1 19.3 1.0 OP1 B:DG24 4.0 17.7 1.0 O B:HOH281 4.2 46.8 0.5 O3' B:DC23 4.6 14.3 1.0 P B:DG24 4.9 14.8 1.0

Magnesium binding site 4 out of 5 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg38 b:21.6 occ:1.00 O B:HOH44 1.9 21.2 1.0 O B:HOH41 2.0 25.8 1.0 O A:HOH43 2.1 26.8 1.0 O A:HOH40 2.1 23.1 1.0 O B:HOH39 2.1 24.9 1.0 O B:HOH42 2.2 27.9 1.0 O A:HOH168 4.1 29.0 1.0 O B:HOH56 4.1 26.1 1.0 OP1 B:DA18 4.1 19.0 1.0 O A:HOH247 4.2 36.3 0.5 O A:HOH133 4.2 25.1 1.0 O B:HOH116 4.5 18.3 1.0 C5' A:DC11 4.8 16.4 1.0 O3' B:DA17 4.9 14.3 1.0

Magnesium binding site 5 out of 5 in the The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg45 b:25.4 occ:0.50 O B:HOH49 2.0 43.6 0.5 O B:HOH46 2.1 22.5 0.5 O B:HOH50 2.1 24.9 0.5 OP1 B:DA17 2.2 19.9 1.0 O B:HOH48 2.2 30.2 0.5 O B:HOH47 2.2 28.6 0.5 P B:DA17 3.6 17.0 1.0 OP2 B:DA17 4.2 18.2 1.0 O5' B:DA17 4.4 16.4 1.0 O B:HOH228 4.5 27.5 0.5 O3' B:DG16 4.5 16.1 1.0 C5' B:DA17 4.7 15.3 1.0

V.Tereshko, G.Minasov, M.Egli. The Dickerson-Drew B-Dna Dodecamer Revisited-at Atomic Resolution J.Am.Chem.Soc. V. 121 470 1999.
ISSN: ISSN 0002-7863