Magnesium in PDB 1puy: 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker

The structure of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker, PDB code: 1puy was solved by M.Egli, V.Tereshko, G.Murshudov, R.Sanishvili, X.Liu, F.D.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.890, 41.860, 51.100, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.9

The binding sites of Magnesium atom in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker (pdb code 1puy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker, PDB code: 1puy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:21.5 occ:1.00 O A:HOH203 2.0 26.2 1.0 O A:HOH202 2.1 25.7 1.0 O A:HOH207 2.1 29.7 1.0 O A:HOH205 2.1 26.4 1.0 O A:HOH206 2.1 28.8 1.0 O A:HOH204 2.2 23.5 1.0 O A:HOH422 4.2 29.1 1.0 O A:HOH442 4.2 27.0 1.0 O4' A:DA12 4.2 15.4 1.0 O2 A:DT5 4.3 14.3 1.0 O4' A:DG6 4.4 14.4 1.0 C4' A:DA12 4.5 16.3 1.0 O A:HOH470 4.5 43.0 1.0 O A:HOH462 4.5 35.5 1.0 O A:HOH509 4.6 46.5 1.0 C4' A:DG6 4.6 13.8 1.0 N3 A:DA11 4.6 14.1 1.0 C5' A:DG6 4.6 14.8 1.0 C5' A:DA12 4.7 19.5 1.0 O4' A:DA11 4.9 22.4 1.0

Magnesium binding site 2 out of 5 in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:29.8 occ:1.00 O A:HOH307 1.9 35.3 1.0 O A:HOH302 2.0 35.0 1.0 O A:HOH305 2.1 37.7 1.0 O A:HOH303 2.1 36.7 1.0 O A:HOH304 2.2 31.2 1.0 O A:HOH306 2.4 38.4 1.0 OP2 A:DC9 3.9 27.1 1.0 O A:HOH492 4.1 43.2 1.0 O A:HOH469 4.4 43.2 1.0 O5' A:DC9 4.5 26.2 1.0 P A:DC9 4.9 25.4 1.0

Magnesium binding site 3 out of 5 in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:34.8 occ:1.00 O A:HOH314 1.9 54.6 1.0 O A:HOH309 2.0 48.2 1.0 O A:HOH311 2.1 24.9 1.0 O A:HOH310 2.2 27.1 1.0 O A:HOH312 2.4 42.3 1.0 O A:HOH313 2.7 48.3 1.0 O A:HOH407 3.8 22.9 1.0 O A:HOH438 4.0 40.5 1.0 OP2 A:DA13 4.3 16.0 1.0 O A:HOH459 4.3 41.0 1.0

Magnesium binding site 4 out of 5 in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg208 b:22.3 occ:1.00 O B:HOH213 2.0 22.5 1.0 O B:HOH210 2.0 25.8 1.0 O B:HOH212 2.0 29.5 1.0 O B:HOH211 2.0 29.1 1.0 O B:HOH209 2.1 25.1 1.0 O B:HOH214 2.1 31.8 1.0 O B:HOH429 4.0 24.2 1.0 O B:HOH430 4.1 29.7 1.0 N2 B:DG6 4.2 11.6 1.0 N3 B:DA10 4.3 14.2 1.0 O B:HOH408 4.4 25.1 1.0 N3 B:DG6 4.4 11.4 1.0 O B:HOH455 4.4 43.4 1.0 C2 B:DA10 4.5 13.4 1.0 O4' B:DA11 4.7 21.4 1.0 C2 B:DG6 4.8 11.4 1.0

Magnesium binding site 5 out of 5 in the 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 1.5 A Resolution Structure of A Synthetic Dna Hairpin with A Stilbenediether Linker within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg315 b:28.5 occ:1.00 O B:HOH319 1.9 47.5 1.0 O B:HOH318 2.0 32.1 1.0 O B:HOH317 2.0 23.9 1.0 O B:HOH321 2.1 30.6 1.0 O B:HOH316 2.1 32.6 1.0 O B:HOH320 2.3 38.0 1.0 O A:HOH453 4.0 46.2 1.0 OP2 B:DA10 4.1 16.3 1.0 O B:HOH409 4.2 32.1 1.0 O B:HOH443 4.3 29.1 1.0 N7 B:DA10 4.3 16.0 1.0 O B:HOH427 4.4 28.9 1.0 O A:HOH480 4.4 36.8 1.0 C2' B:DC9 4.7 14.8 1.0 C8 B:DA10 4.9 16.7 1.0

M.Egli, V.Tereshko, G.N.Mushudov, R.Sanishvili, X.Liu, F.D.Lewis. Face-to-Face and Edge-to-Face Pi-Pi Interactions in A Synthetic Dna Hairpin with A Stilbenediether Linker J.Am.Chem.Soc. V. 125 10842 2003.
ISSN: ISSN 0002-7863
PubMed: 12952463
DOI: 10.1021/JA0355527