Magnesium in PDB 8q60: Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker.

The structure of Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker., PDB code: 8q60 was solved by P.K.Mandal, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.56 / 2.50
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	26.517, 30.04, 45.224, 105.62, 105.77, 94.34
R / Rfree (%)	27.8 / 32.8

The binding sites of Magnesium atom in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker. (pdb code 8q60). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker., PDB code: 8q60:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:38.3 occ:1.00 O D:HOH241 2.0 32.6 1.0 O D:HOH230 2.0 38.1 1.0 O E:HOH236 2.0 35.2 1.0 O D:HOH209 2.3 24.0 1.0 C7 D:DT3 2.9 34.2 1.0 O D:HOH228 3.7 35.9 1.0 O D:HOH232 4.1 28.2 1.0 O D:HOH243 4.2 42.4 1.0 OP2 D:DT3 4.3 24.4 1.0 O E:HOH218 4.3 20.5 1.0 O D:HOH217 4.3 51.5 1.0 C5 D:DT3 4.3 24.6 1.0 O D:HOH207 4.4 24.3 1.0

Magnesium binding site 2 out of 4 in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:28.1 occ:1.00 O B:HOH227 1.7 30.2 1.0 O B:HOH219 2.0 35.5 1.0 O B:HOH212 2.2 16.7 1.0 O B:HOH239 2.3 27.0 1.0 O A:HOH234 3.5 52.6 1.0 O B:HOH222 4.1 38.9 1.0 OP2 B:DA9 4.3 21.3 1.0 O A:HOH218 4.4 34.9 1.0 N7 B:DA9 4.4 20.9 1.0 O B:HOH216 4.4 35.8 1.0 O B:HOH213 4.7 28.4 1.0 O A:HOH249 4.7 70.8 1.0 C8 B:DA9 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:38.2 occ:1.00 O A:HOH243 2.7 50.6 1.0 O4' B:DA10 2.7 29.3 1.0 O A:HOH238 2.9 43.2 1.0 O B:HOH224 2.9 34.0 1.0 N3 B:DA9 3.0 23.5 1.0 O A:HOH203 3.0 52.4 1.0 O B:HOH201 3.1 58.3 1.0 O B:HOH234 3.3 46.1 1.0 C4' B:DA10 3.4 31.8 1.0 C2 B:DA9 3.5 23.9 1.0 O A:HOH205 3.6 41.8 1.0 C1' B:DA10 3.6 25.9 1.0 C5' B:DA10 4.0 29.4 1.0 N9 B:DA10 4.1 25.6 1.0 O B:HOH235 4.1 45.7 1.0 C4 B:DA9 4.2 23.4 1.0 N3 B:DA10 4.2 19.7 1.0 C4 B:DA10 4.4 21.7 1.0 C1' B:DA9 4.4 25.1 1.0 N2 A:DG6 4.6 21.1 1.0 C3' B:DA10 4.7 35.7 1.0 N9 B:DA9 4.7 24.4 1.0 N3 A:DG6 4.8 20.2 1.0 N1 B:DA9 4.8 23.1 1.0 O B:HOH209 4.9 18.8 0.8 C2' B:DA10 4.9 27.4 1.0 O4' B:DA9 4.9 27.5 1.0 O3' B:DA10 4.9 36.8 1.0

Magnesium binding site 4 out of 4 in the Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Racemic Crystal Structure of A Synthetic Dna Hairpin with Diquinoline Linker. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:58.6 occ:1.00 O D:HOH203 2.1 32.0 1.0 O E:HOH228 2.1 32.0 1.0 O D:HOH202 2.8 52.4 1.0 O4' E:DA11 3.4 31.1 1.0 C4' E:DA11 3.9 31.6 1.0 O2 D:DT4 3.9 50.5 1.0 O2 D:DT5 4.1 31.2 1.0 O E:HOH203 4.3 45.8 1.0 C1' E:DA11 4.4 34.9 1.0 N3 E:DA10 4.4 25.6 1.0 O4' D:DT5 4.4 40.5 1.0 O E:HOH227 4.5 42.8 1.0 O4' D:DG6 4.5 43.1 1.0 O E:HOH229 4.6 37.7 1.0 C2 E:DA10 4.6 43.4 1.0 C5' E:DA11 4.7 30.7 1.0 C4' D:DT5 4.7 41.7 1.0 C1' D:DT5 4.8 33.8 1.0 C5' D:DG6 4.8 45.8 1.0 O D:HOH211 4.8 38.8 1.0 O D:HOH239 4.8 66.2 1.0 N3 E:DA11 4.9 35.0 1.0 C4' D:DG6 4.9 43.9 1.0 C2 D:DT4 4.9 37.5 1.0 O3' E:DA11 4.9 32.4 1.0

P.K.Mandal, I.Huc. Interfacing Double Stranded B-Dna with Dna-Mimic Foldamers To Be Published.