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(-) Description

Title :  STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS
 
Authors :  N. G. A. Abrescia, L. Malinina, L. F. Gonzaga, T. Huynh-Dinh, S. Neidle, J. A. Subirana
Date :  15 Jan 99  (Deposition) - 18 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Triple Helix, Nickel Binding, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. G. Abrescia, L. Malinina, L. G. Fernandez, T. Huynh-Dinh, S. Neidle, J. A. Subirana
Structure Of The Oligonucleotide D(Cgtatatacg) As A Site-Specific Complex With Nickel Ions.
Nucleic Acids Res. V. 27 1593 1999
PubMed-ID: 10075989  |  Reference-DOI: 10.1093/NAR/27.7.1593
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
    ChainsA, B, C, D
    EngineeredYES
    SyntheticYES

 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  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1NI9Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:10 , HOH A:15 , HOH A:16 , HOH A:17 , HOH A:18 , DG C:30BINDING SITE FOR RESIDUE NI A 11
2AC2SOFTWAREDG B:12 , HOH B:21 , HOH B:22 , HOH B:23 , HOH B:24 , HOH B:25BINDING SITE FOR RESIDUE NI B 7
3AC3SOFTWAREDG A:2 , HOH A:19 , HOH A:20 , HOH A:21 , HOH A:22 , HOH A:23BINDING SITE FOR RESIDUE NI A 12
4AC4SOFTWAREDG D:32 , HOH D:41 , HOH D:42 , HOH D:43 , HOH D:44 , HOH D:45BINDING SITE FOR RESIDUE NI D 9
5AC5SOFTWAREDG B:20 , HOH B:26 , HOH B:27 , HOH B:28 , HOH B:29 , HOH B:30BINDING SITE FOR RESIDUE NI B 5
6AC6SOFTWAREDG C:22 , HOH C:34 , HOH C:35 , HOH C:36 , HOH C:37 , HOH C:38BINDING SITE FOR RESIDUE NI C 1
7AC7SOFTWAREDG D:40 , HOH D:46 , HOH D:47 , HOH D:48 , HOH D:49 , HOH D:50BINDING SITE FOR RESIDUE NI D 2
8AC8SOFTWAREHOH A:24 , HOH A:25 , HOH A:26 , HOH A:27 , HOH A:28 , HOH A:29BINDING SITE FOR RESIDUE NI A 13
9AC9SOFTWAREHOH A:30 , HOH A:31 , HOH A:32 , HOH A:33 , HOH A:34 , HOH A:35BINDING SITE FOR RESIDUE NI A 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 446D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 446D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 446D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 446D)

(-) Exons   (0, 0)

(no "Exon" information available for 446D)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:10
                                         
                  446d A  1 CGTATATACG 10
                                    10

Chain B from PDB  Type:DNA  Length:9
                                        
                  446d B 12 GTATATACG 20

Chain C from PDB  Type:DNA  Length:10
                                         
                  446d C 21 CGTATATACG 30
                                    30

Chain D from PDB  Type:DNA  Length:10
                                         
                  446d D 31 CGTATATACG 40
                                    40

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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 446D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 446D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 446D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 446D)

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