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- PDB-2mwz: Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X... -
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Basic information
Entry | Database: PDB / ID: 2mwz | ||||||||||||||||||||
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Title | Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X O tetrad | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / xanthosine | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics | Model details | lowest energy, model1 | ![]() Cheong, V.V. / Heddi, B. / Lech, C.J. / Phan, A.T. | ![]() ![]() Title: Xanthine and 8-oxoguanine in G-quadruplexes: formation of a GGXO tetrad. Authors: Cheong, V.V. / Heddi, B. / Lech, C.J. / Phan, A.T. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 151.3 KB | Display | ![]() |
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PDB format | ![]() | 126.3 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 405.3 KB | Display | ![]() |
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Full document | ![]() | 470.9 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar 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: 7608.868 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: An intramolecular human telomeric G-quadruplex with xanthine and 8-oxoguanine modifications within a G-tetrad | ||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 90 / pH: 8.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA chi-angle constraints total count: 12 / NOE constraints total: 591 / NOE intraresidue total count: 280 / NOE long range total count: 83 / NOE sequential total count: 164 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.131 Å / Maximum upper distance constraint violation: 0.191 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.023 Å / Distance rms dev error: 0.002 Å |