Magnesium in PDB 5jzq: Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations

The structure of Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations, PDB code: 5jzq was solved by P.Drozdzal, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.93 / 0.78
Space group	C 1 2/c 1
Cell size a, b, c (Å), α, β, γ (°)	81.300, 17.610, 36.490, 90.00, 106.73, 90.00
R / Rfree (%)	13.9 / 14.3

The binding sites of Magnesium atom in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations (pdb code 5jzq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations, PDB code: 5jzq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:4.6 occ:0.52 MG A:MG101 0.0 4.6 0.5 MG A:MG101 0.3 20.0 0.5 O A:HOH234 1.5 10.8 0.2 OP2 A:DG6 2.0 6.7 1.0 O A:HOH218 2.0 4.5 0.4 O A:HOH235 2.1 10.9 0.8 O B:HOH229 2.1 7.0 0.5 O A:HOH234 2.1 8.2 0.8 O B:HOH229 2.2 17.0 0.5 O A:HOH218 2.3 16.0 0.6 O A:HOH237 3.0 11.2 0.2 P A:DG6 3.2 5.9 1.0 O3' A:DC5 3.7 5.6 1.0 O B:HOH269 3.8 11.3 0.6 OP1 A:DG6 4.0 8.0 1.0 O B:HOH269 4.2 27.0 0.4 O B:HOH233 4.3 6.3 0.4 O B:HOH217 4.4 7.9 0.5 O B:HOH233 4.4 29.8 0.6 O A:HOH238 4.5 28.1 0.5 O5' A:DG6 4.5 5.9 1.0 OP2 B:DG10 4.5 9.6 0.6 O A:HOH232 4.5 9.5 1.0 O B:HOH271 4.5 8.2 0.4 O A:HOH238 4.5 12.6 0.5 O B:HOH217 4.6 9.4 0.5 O B:HOH261 4.7 34.9 0.6 C5' A:DG6 4.8 5.3 1.0 O B:HOH223 4.8 13.2 0.8

Magnesium binding site 2 out of 4 in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:20.0 occ:0.48 MG A:MG101 0.0 20.0 0.5 MG A:MG101 0.3 4.6 0.5 O A:HOH234 1.7 10.8 0.2 O A:HOH218 1.8 4.5 0.4 O B:HOH229 2.0 7.0 0.5 O B:HOH229 2.0 17.0 0.5 OP2 A:DG6 2.1 6.7 1.0 O A:HOH218 2.1 16.0 0.6 O A:HOH235 2.2 10.9 0.8 O A:HOH234 2.3 8.2 0.8 O A:HOH237 2.9 11.2 0.2 P A:DG6 3.5 5.9 1.0 O B:HOH269 3.6 11.3 0.6 O3' A:DC5 3.9 5.6 1.0 O B:HOH269 4.0 27.0 0.4 O B:HOH233 4.2 6.3 0.4 OP1 A:DG6 4.2 8.0 1.0 O B:HOH233 4.3 29.8 0.6 O A:HOH232 4.5 9.5 1.0 OP2 B:DG10 4.5 9.6 0.6 O B:HOH217 4.6 7.9 0.5 O5' A:DG6 4.6 5.9 1.0 O B:HOH271 4.6 8.2 0.4 O B:HOH261 4.7 34.9 0.6 O A:HOH238 4.8 28.1 0.5 O B:HOH217 4.8 9.4 0.5 O A:HOH238 4.8 12.6 0.5 C5' A:DG6 4.8 5.3 1.0

Magnesium binding site 3 out of 4 in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:17.1 occ:0.30 O A:HOH209 2.0 18.4 0.7 O A:HOH254 2.0 24.3 0.5 O A:HOH239 2.1 18.9 0.5 O A:HOH239 2.5 18.1 0.5 O A:HOH254 2.8 30.4 0.5 O A:HOH209 2.8 7.9 0.3 O A:HOH223 3.4 12.0 0.3 O B:HOH280 3.8 30.5 0.4 O B:HOH284 4.1 47.9 0.6 O A:HOH233 4.2 7.5 0.9 O B:HOH228 4.3 17.2 1.0 N7 A:DG4 4.3 8.4 1.0 O B:HOH282 4.5 5.7 0.2 O A:HOH251 4.6 18.8 1.0 O B:HOH288 4.7 27.7 0.3 O A:HOH211 4.8 11.5 1.0 O A:HOH222 4.8 15.1 0.2

Magnesium binding site 4 out of 4 in the Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals Massive Presence of Multiple Conformations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:5.0 occ:0.34 O B:HOH235 1.4 25.7 0.6 O B:HOH254 2.1 15.3 0.9 O B:HOH235 2.1 6.9 0.4 O B:HOH239 2.1 7.7 0.4 OP1 B:DC9 2.4 11.4 0.8 O B:HOH201 2.6 15.5 0.2 O B:HOH259 2.7 17.6 0.5 O B:HOH262 3.1 9.3 0.3 P B:DC9 3.4 7.1 0.8 O B:HOH212 3.7 13.1 1.0 O B:HOH203 3.8 18.7 0.3 OP2 B:DC9 3.8 7.5 0.8 O3' B:DG8 4.0 7.7 0.7 O B:HOH215 4.0 12.6 0.3 O B:HOH278 4.1 18.5 0.4 O3' B:DG8 4.1 4.0 0.3 C2' B:DG8 4.1 6.3 0.7 C2' B:DG8 4.2 5.6 0.3 O B:HOH266 4.3 17.4 0.2 N7 B:DG10 4.6 11.0 0.4 C3' B:DG8 4.6 6.5 0.7 O B:HOH252 4.8 12.1 0.2 C3' B:DG8 4.8 4.5 0.3 O5' B:DC9 4.8 9.3 0.8 OP1 B:DC9 4.9 11.9 0.2 O B:HOH253 4.9 10.4 0.6

P.Drozdzal, M.Gilski, M.Jaskolski. Ultrahigh-Resolution Centrosymmetric Crystal Structure of Z-Dna Reveals the Massive Presence of Alternate Conformations. Acta Crystallogr D Struct V. 72 1203 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27841753
DOI: 10.1107/S205979831601679X