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- PDB-2lo8: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Reco... -
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Basic information
Entry | Database: PDB / ID: 2lo8 | ||||||||||||||||||||
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Title | Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA | ||||||||||||||||||||
![]() | DNA_(5'-D(*![]() DNA / thymine bulge / hairpin / Bifunctional Zn(II) Macrocyclic Complex | Function / homology | DNA | ![]() Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | Model details | fewest violations, model 1 | ![]() Morrow, J.R. / Fountain, M.A. / del Mundo, I.A. / Siter, K.E. | ![]() ![]() Title: Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Authors: Del Mundo, I.M. / Siters, K.E. / Fountain, M.A. / Morrow, J.R. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 91.1 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3045.993 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Structure determined using NOE distance restraints for the Zn(cy4q)DNA complex. Structure presented without the Zn(cy4q) ligand. | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 4 / NA beta-angle constraints total count: 4 / NA chi-angle constraints total count: 8 / NA delta-angle constraints total count: 6 / NA epsilon-angle constraints total count: 4 / NA gamma-angle constraints total count: 4 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 118 / NOE long range total count: 64 | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 2.05 ° Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 1000 / Conformers submitted total number: 18 / Maximum lower distance constraint violation: 0.28 Å / Maximum torsion angle constraint violation: 6.6 ° / Maximum upper distance constraint violation: 0.28 Å | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0202 Å / Distance rms dev error: 0.0047 Å |