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(-) Description

Title :  THE ATOMIC STRUCTURE OF 5-HYDROXYMETHYL 2'-DEOXYCITIDINE BASE PAIRED WITH 2'-DEOXYGUANOSINE IN DICKERSON DREW DODECAMER
 
Authors :  B. Nocek, M. W. Szulik, A. Joachimiak, M. P. Stone
Date :  05 Dec 12  (Deposition) - 20 Nov 13  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  5-Hydroxymethyl 2' Deoxycitidine, 5-Hydroxymethyl-Dc Adduct, Modified Ddd, Dodecamer Of B-Dna, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Szulik, P. S. Pallan, B. Nocek, M. Voehler, S. Banerjee, S. Brooks A. Joachimiak, M. Egli, B. F. Eichman, M. P. Stone
Differential Stabilities And Sequence-Dependent Base Pair Opening Dynamics Of Watson-Crick Base Pairs With 5-Hydroxymethylcytosine, 5-Formylcytosine, Or 5-Carboxylcytosine.
Biochemistry V. 54 1294 2015
PubMed-ID: 25632825  |  Reference-DOI: 10.1021/BI501534X

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3')
    Chains: A, B
    Engineered: YES
    Organism Scientific: SYNTHETIC DNA
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2MG1Ligand/IonMAGNESIUM ION
3SPK2Ligand/IonSPERMINE (FULLY PROTONATED FORM)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:208 , HOH A:249 , HOH B:206 , HOH B:261 , HOH B:262 , HOH B:270BINDING SITE FOR RESIDUE MG A 101
2AC2SOFTWAREDG A:12 , HOH A:264 , HOH A:271 , DA B:18 , DT B:19 , DT B:20 , HOH B:250BINDING SITE FOR RESIDUE SPK B 101
3AC3SOFTWARE5HC A:9 , DG A:10 , HOH A:231 , DG B:14 , DC B:15 , DC B:23 , HOH B:219 , HOH B:257BINDING SITE FOR RESIDUE SPK B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I9V)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:DNA  Length:12
                                           
                  4i9v A  1 CGCGAATTcGCG 12
                                    10  
                                    9-5HC


Chain B from PDB  Type:DNA  Length:12
                                           
                  4i9v B 13 CGCGAATTcGCG 24
                                    22  
                                   21-5HC
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 Related Entries

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(-) Related Entries Specified in the PDB File

355d