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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMO-DNA AND NATURE'S CHOICE OF PENTOSE OVER HEXOSE IN THE GENETIC SYSTEM
 
Authors :  M. Egli, P. S. Pallan
Date :  11 Jun 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homo-Dna, Homo-Dna Crystal Structure, 2', 3'-Di-Deoxy-Beta- D-Glucopyranose, Hexose Nucleic Acid, Glucopyranosyl Nucleic Acid, Dideoxyglucopyranose Octamer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Egli, P. S. Pallan, R. Pattanayek, C. J. Wilds, P. Lubini, G. Minasov, M. Dobler, C. J. Leumann, A. Eschenmoser
Crystal Structure Of Homo-Dna And Nature'S Choice Of Pentose Over Hexose In The Genetic System.
J. Am. Chem. Soc. V. 128 10847 2006
PubMed-ID: 16910680  |  Reference-DOI: 10.1021/JA062548X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH) P*(XCT)P*(XGU))-3'
    Chains: A, B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2XAD4Mod. Nucleotide9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE
3XCT4Mod. Nucleotide4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE
4XGU4Mod. Nucleotide2-AMINO-9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE
5XTH4Mod. Nucleotide1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREXGU A:2 , HOH A:202 , HOH A:203 , HOH A:204 , HOH A:205BINDING SITE FOR RESIDUE MG A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H9S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H9S)

(-) Exons   (0, 0)

(no "Exon" information available for 2H9S)

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:8
                                       
                  2h9s A  1 cgaattcg  8
                            ||||||||
                            ||||||||
                            1-XCT|||
                             2-XGU||
                              3-XAD|
                               4-XAD
                                5-XTH
                                 6-XTH
                                  7-XCT
                                   8-XGU


Chain B from PDB  Type:DNA  Length:8
                                       
                  2h9s B  9 cgaattcg 16
                            ||||||||
                            ||||||||
                            9-XCT|||
                            10-XGU||
                             11-XAD|
                              12-XAD
                               13-XTH
                                14-XTH
                                 15-XCT
                                  16-XGU
   Legend:   → Mismatch (orange background)
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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 2H9S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H9S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H9S)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2H9S)

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  2h9s
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