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(-) Description

Title :  CRYSTAL STRUCTURE OF [D(CGCGAA(Z3DU)(Z3DU)CGCG)]2, Z3DU:5-(3-AMINOPROPYL)-2'-DEOXYURIDINE, IN PRESENCE OF THALLIUM I.
 
Authors :  T. Moulaei, T. Maehigashi, G. T. Lountos, S. Komeda, D. Watkins, M. P. Stone, L. A. Marky, J. S. Li, B. Gold, L. D. Williams
Date :  19 Mar 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  B-Dna, Tl+, Thallium, Modified Dna, Cations, Modified Thymine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Moulaei, T. Maehigashi, G. T. Lountos, S. Komeda, D. Watkins, M. P. Stone, L. A. Marky, J. S. Li, B. Gold, L. D. Williams
Structure Of B-Dna With Cations Tethered In The Major Groove.
Biochemistry V. 44 7458 2005
PubMed-ID: 15895989  |  Reference-DOI: 10.1021/BI050128Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*(ZDU)P*(ZDU) P*CP*GP*CP*G)-3'
    Chains: A, B
    Engineered: YES
    Other Details: DICKERSON-DREW DODECAMER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1SPM2Ligand/IonSPERMINE
2TL8Ligand/IonTHALLIUM (I) ION
3ZDU4Mod. Nucleotide5-(3-AMINOPROPYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDG A:12 , HOH A:42 , DC B:13 , DG B:22 , TL B:28BINDING SITE FOR RESIDUE SPM A 25
02AC2SOFTWAREDC B:15 , DG B:16 , DA B:17 , TL B:34 , HOH B:52BINDING SITE FOR RESIDUE SPM B 26
03AC3SOFTWAREDA A:5 , DG A:12 , HOH A:38 , HOH A:71BINDING SITE FOR RESIDUE TL A 27
04AC4SOFTWARESPM A:25BINDING SITE FOR RESIDUE TL B 28
05AC5SOFTWAREDG A:10 , DC A:11 , HOH A:48 , DG B:16 , HOH B:55BINDING SITE FOR RESIDUE TL A 29
06AC6SOFTWAREZDU A:7 , ZDU A:8 , HOH A:44 , ZDU B:19 , ZDU B:20 , HOH B:40BINDING SITE FOR RESIDUE TL A 30
07AC7SOFTWAREHOH A:39 , HOH A:106 , DC B:21BINDING SITE FOR RESIDUE TL B 31
08AC8SOFTWAREDA A:6BINDING SITE FOR RESIDUE TL A 32
09AC9SOFTWAREZDU A:8BINDING SITE FOR RESIDUE TL A 33
10BC1SOFTWARESPM B:26 , HOH B:57BINDING SITE FOR RESIDUE TL B 34

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z5T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z5T)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z5T)

(-) 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:12
                                           
                  1z5t A  1 CGCGAAxxCGCG 12
                                  ||10  
                                  7-ZDU 
                                   8-ZDU


Chain B from PDB  Type:DNA  Length:12
                                           
                  1z5t B 13 CGCGAAxxCGCG 24
                                  ||22  
                                 19-ZDU 
                                  20-ZDU
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 1Z5T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z5T)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Z5T)

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