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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DB921-D(CGCGAATTCGCG)2 COMPLEX.
 
Authors :  Y. Miao, M. P. Lee, G. N. Parkinson, A. Batista-Parra, M. A. Ismail, S. Neidle, D. W. Boykin, W. D. Wilson
Date :  14 Sep 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleic Acids, Dna, Double Helix, Minor Groove, Dna Minor Groove Binder, Dna Minor Groove-Ligand Complex, Db921, A2T2, Dickerson And Drew Dna, Crystal Structure Of B-Dna, Dna- Drug Complex, Magnesium-Water Complex, Hydrated Magnesium, Dna Hydration. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Miao, M. P. Lee, G. N. Parkinson, A. Batista-Parra, M. A. Ismail, S. Neidle, D. W. Boykin, W. D. Wilson
Out-Of-Shape Dna Minor Groove Binders: Induced Fit Interactions Of Heterocyclic Dications With The Dna Minor Groove.
Biochemistry V. 44 14701 2005
PubMed-ID: 16274217  |  Reference-DOI: 10.1021/BI051791Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    Chains: A, B
    Engineered: YES
    Other Details: AT-RICH REGION IN THE GENOME OF ORGANISMS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1D2A1Ligand/Ion2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:104 , HOH A:105 , HOH A:108 , HOH B:103 , HOH B:106 , HOH B:107BINDING SITE FOR RESIDUE MG A 26
2AC2SOFTWAREDA A:6 , DT A:7 , DT A:8 , DC A:9 , DA B:18 , DT B:19 , DT B:20 , DC B:21BINDING SITE FOR RESIDUE D2A A 25

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B0K)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric/Biological 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:12
                                           
                  2b0k A  1 CGCGAATTCGCG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  2b0k B 13 CGCGAATTCGCG 24
                                    22
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

2dbe DNA PART OF PDB ENTRY 2DBE