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(-) Description

Title :  STRUCTURE OF 3'-FLUORO CYCLOHEXENYL NUCLEIC ACID HEPTAMER
 
Authors :  P. S. Pallan, M. Egli
Date :  08 May 12  (Deposition) - 30 May 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fluoro Cyclohexenyl Nucleic Acid, F-Cena, Modified Dna, B-Form Dna, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. P. Seth, J. Yu, A. Jazayeri, P. S. Pallan, C. R. Allerson, M. E. Ostergaard, F. Liu, P. Herdewijn, M. Egli, E. E. Swayze
Synthesis And Antisense Properties Of Fluoro Cyclohexenyl Nucleic Acid (F-Cena), A Nuclease Stable Mimic Of 2'-Fluoro Rna.
J. Org. Chem. V. 77 5074 2012
PubMed-ID: 22591005  |  Reference-DOI: 10.1021/JO300594B

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*(XTF)P*GP*CP*G)-3'
    Chains: A, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
    Chains: B, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
13CO6Ligand/IonCOBALT (III) ION
2NCO2Ligand/IonCOBALT HEXAMMINE(III)
3XTF2Mod. Nucleotide[(1R,4R,5S,6R)-5-FLUORO-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
13CO4Ligand/IonCOBALT (III) ION
2NCO2Ligand/IonCOBALT HEXAMMINE(III)
3XTF1Mod. Nucleotide[(1R,4R,5S,6R)-5-FLUORO-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
13CO2Ligand/IonCOBALT (III) ION
2NCO-1Ligand/IonCOBALT HEXAMMINE(III)
3XTF1Mod. Nucleotide[(1R,4R,5S,6R)-5-FLUORO-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:1 , DC A:2 , DG B:6 , DC B:7 , HOH B:205 , DG D:2 , DC D:3BINDING SITE FOR RESIDUE NCO A 101
2AC2SOFTWAREDC B:1 , DC B:3 , DA B:4 , HOH B:201 , HOH B:220 , DG C:1 , DG D:6 , DC D:7BINDING SITE FOR RESIDUE NCO B 101
3AC3SOFTWARE3CO B:103BINDING SITE FOR RESIDUE 3CO B 102
4AC4SOFTWARE3CO B:102BINDING SITE FOR RESIDUE 3CO B 103
5AC5SOFTWAREDG A:7 , 3CO B:105BINDING SITE FOR RESIDUE 3CO B 104
6AC6SOFTWARE3CO B:104BINDING SITE FOR RESIDUE 3CO B 105
7AC7SOFTWARE3CO C:102 , HOH C:201BINDING SITE FOR RESIDUE 3CO C 101
8AC8SOFTWAREDG C:7 , 3CO C:101 , HOH C:201BINDING SITE FOR RESIDUE 3CO C 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4F2X)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:7
                                     
                   4f2x A 1 GCGtGCG 7
                               |   
                               |   
                               4-XTF


Chain B from PDB  Type:DNA  Length:7
                                     
                   4f2x B 1 CGCACGC 7


Chain C from PDB  Type:DNA  Length:7
                                     
                   4f2x C 1 GCGtGCG 7
                               |   
                               4-XTF


Chain D from PDB  Type:DNA  Length:7
                                     
                   4f2x D 1 CGCACGC 7
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4F2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F2X)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

4f2y