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- PDB-5ihd: Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ihd | |||||||||||||||||||||||||||||||
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Title | Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by L-lactate and succinate | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() ![]() ![]() Function / homology | (2S)-2-HYDROXYPROPANOIC ACID / COPPER (II) ION / | ![]() ![]() ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() Rohner, M. / Medina-Molner, A. / Spingler, B. | Funding support | | ![]()
![]() ![]() Title: N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2. Authors: Rohner, M. / Medina-Molner, A. / Spingler, B. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.1 KB | Display | ![]() |
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PDB format | ![]() | 18.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xqzC ![]() 4xsnC ![]() 2dcgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA chain , 1 types, 4 molecules ABCD
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 142 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2OP.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2OP.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / ![]() #3: Chemical | #4: Chemical | ![]() #5: Chemical | ChemComp-SIN / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.48 % |
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Crystal grow![]() | Temperature: 296 K / Method: microbatch / pH: 6 Details: 1.2 mM d(CG)3, 1.2 mM di copper complex, 0.25 M MES pH 6, 25 mM Ca(lactate)2, 2.5% EtOAc |
-Data collection
Diffraction | Mean temperature: 183 K |
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Diffraction source | Source: SEALED TUBE / Type: Long fine focus / Wavelength: 1.54 Å |
Detector | Type: STOE / Detector: IMAGE PLATE / Date: Nov 7, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.57→26.215 Å / Num. obs: 7934 / % possible obs: 97.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.51 |
Reflection shell | Resolution: 1.57→1.7 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.1736 / Mean I/σ(I) obs: 3.77 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2DCG Resolution: 1.57→26.215 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→26.215 Å
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Refine LS restraints |
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LS refinement shell |
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