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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA DUPLEX CONTAINING ZP BASE PAIR
 
Authors :  C. R. J. Agnew, R. L. Brady
Date :  17 Jul 16  (Deposition) - 03 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Synthetic Nucleotide, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. F. Reichenbach, A. A. Sobri, N. R. Zaccai, C. R. J. Agnew, N. Burton, L. P. Eperon, S. De Ornellas, I. C. Eperon, R. L. Brady, G. A. Burley
Structural Basis Of The Mispairing Of An Artificially Expanded Genetic Information System
Chem V. 1 946 2016
PubMed: search  |  Reference-DOI: 10.1016/J.CHEMPR.2016.11.009

(-) Compounds

Molecule 1 - ODN2
    Chains: A, B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
11W52Mod. Nucleotide(1R)-1-(6-AMINO-2-HYDROXY-5-NITROPYRIDIN-3-YL)-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL
21WA2Mod. Nucleotide2-AMINO-8-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-HYDROXY-1H-IMIDAZO[1,2-A][1,3,5]TRIAZINE-5,8-DIIUM
3CA4Ligand/IonCALCIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:12 , HOH A:202 , DG B:24binding site for residue CA A 101
2AC2SOFTWAREHOH A:203binding site for residue CA A 102
3AC3SOFTWAREDG A:12binding site for residue CA A 103
4AC4SOFTWAREDT A:8 , 1W5 A:9 , DG A:10 , DG B:14 , DA B:17 , DG B:24 , HOH B:201binding site for Di-nucleotide DC B 15 and 1WA B 16
5AC5SOFTWAREDT A:8 , 1W5 A:9 , DG A:10 , DC B:15 , DA B:18 , DG B:24 , HOH B:201binding site for Di-nucleotide 1WA B 16 and DA B 17
6AC6SOFTWARE1WA A:4 , DA A:5 , DA A:6 , DT B:19 , DG B:22binding site for Di-nucleotide DT B 20 and 1W5 B 21
7AC7SOFTWAREDG A:2 , DC A:3 , 1WA A:4 , DA A:5 , DG A:12 , DT B:20 , DC B:23 , HOH B:202binding site for Di-nucleotide 1W5 B 21 and DG B 22

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 5LJ4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA  Length:11
                                          
                  5lj4 A  2 GCxAATTxGCG 12
                              |    |11 
                              |    |   
                              4-1WA|   
                                   9-1W5


Chain B from PDB  Type:DNA  Length:11
                                          
                  5lj4 B 14 GCxAATTxGCG 24
                              |    |23 
                              |    |   
                             16-1WA|   
                                  21-1W5
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LJ4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5LJ4)

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  5lj4
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