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(-) Description

Title :  ALTERNATINGLY MODIFIED 2'FLUORO RNA OCTAMER F/RA2U2-P3
 
Authors :  P. S. Pallan, E. M. Greene, P. A. Jicman, R. K. Pandey, M. Manoharan, E. Ro M. Egli
Date :  06 Oct 10  (Deposition) - 05 Jan 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Rna, 2'-Fluoro-Rna, O2'-Modification, Octamer, 2'-Fluoro 2'- Deoxycytidine, 2'-Fluoro 2'-Deoxyadenosine, 2'-Fluoro 2'- Deoxyuridine, Sirna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Pallan, E. M. Greene, P. A. Jicman, R. K. Pandey, M. Manoharan, E. Rozners, M. Egli
Unexpected Origins Of The Enhanced Pairing Affinity Of 2'-Fluoro-Modified Rna.
Nucleic Acids Res. V. 39 3482 2011
PubMed-ID: 21183463  |  Reference-DOI: 10.1093/NAR/GKQ1270

(-) Compounds

Molecule 1 - 5'-R(*(CFZ)P*GP*(AF2)P*AP*(UFT)P*UP*(CFZ)P*G)-3'
    Chains: A, B, C, D, E, F
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED MODIFIED RNA OCTAMER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1AF26Mod. Nucleotide2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2BA2Ligand/IonBARIUM ION
3CFZ12Mod. Nucleotide2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4UFT6Mod. Nucleotide2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1AF22Mod. Nucleotide2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2BA-1Ligand/IonBARIUM ION
3CFZ4Mod. Nucleotide2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4UFT2Mod. Nucleotide2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1AF22Mod. Nucleotide2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2BA-1Ligand/IonBARIUM ION
3CFZ4Mod. Nucleotide2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4UFT2Mod. Nucleotide2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 3 (3, 8)
No.NameCountTypeFull Name
1AF22Mod. Nucleotide2'-DEOXY-2'-FLUOROADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2BA-1Ligand/IonBARIUM ION
3CFZ4Mod. Nucleotide2'-DEOXY-2'-FLUOROCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
4UFT2Mod. Nucleotide2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREUFT A:105 , HOH A:729 , HOH A:775BINDING SITE FOR RESIDUE BA A 701
2AC2SOFTWAREUFT D:405 , HOH D:734 , HOH D:825BINDING SITE FOR RESIDUE BA D 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P4B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P4B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric 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
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Chain A from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b A 101 cGaAxUcG 108
                            | | | | 
                            | | | | 
                          101-CFZ | 
                            103-AF2 
                              105-UFT
                                107-CFZ


Chain B from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b B 201 cGaAxUcG 208
                            | | | | 
                            | | | | 
                          201-CFZ | 
                            203-AF2 
                              205-UFT
                                207-CFZ


Chain C from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b C 301 cGaAxUcG 308
                            | | | | 
                            | | | | 
                          301-CFZ | 
                            303-AF2 
                              305-UFT
                                307-CFZ


Chain D from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b D 401 cGaAxUcG 408
                            | | | | 
                            | | | | 
                          401-CFZ | 
                            403-AF2 
                              405-UFT
                                407-CFZ


Chain E from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b E 501 cGaAxUcG 508
                            | | | | 
                            | | | | 
                          501-CFZ | 
                            503-AF2 
                              505-UFT
                                507-CFZ


Chain F from PDB  Type:DNA/RNA  Length:8
                                        
                 3p4b F 601 cGaAxUcG 608
                            | | | | 
                            | | | | 
                          601-CFZ | 
                            603-AF2 
                              605-UFT
                                607-CFZ
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3P4B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P4B)

(-) 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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3p4c 3p4d