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(-) Description

Title :  DNA HOLLIDAY JUNCTION STABILIZED BY CHLORINE HALOGEN BOND.
 
Authors :  M. Carter, P. S. Ho
Date :  22 Aug 12  (Deposition) - 31 Jul 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Dna Holliday Junction, Halogen Bond, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Carter, A. R. Voth, M. R. Scholfield, B. Rummel, L. C. Sowers, P. S. Ho
Enthalpy-Entropy Compensation In Biomolecular Halogen Bonds Measured In Dna Junctions.
Biochemistry V. 52 4891 2013
PubMed-ID: 23789744  |  Reference-DOI: 10.1021/BI400590H

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3')
    Chains: A, D
    Engineered: YES
    Other Details: SYNTHETICALLY ENGINEERED DNA SEQUENCE
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')
    Chains: B, C
    Engineered: YES
    Other Details: SYNTHETICALLY ENGINEERED DNA SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NA3Ligand/IonSODIUM ION
2UCL2Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2UCL4Mod. Nucleotide5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:3 , DG A:4 , DG C:23 , DA C:24 , HOH C:110BINDING SITE FOR RESIDUE NA A 101
2AC2SOFTWAREDC B:12 , DG B:13 , HOH B:210 , DC D:32 , DG D:33 , HOH D:128BINDING SITE FOR RESIDUE NA B 101
3AC3SOFTWAREDG B:19 , DG D:39 , HOH D:123BINDING SITE FOR RESIDUE NA B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GQD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GQD)

 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)
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Chain A from PDB  Type:DNA  Length:10
                                         
                  4gqd A  1 CCGGTAxCGG 10
                                  | 10
                                  7-UCL


Chain B from PDB  Type:DNA  Length:10
                                         
                  4gqd B 11 CCGATACCGG 20
                                    20


Chain C from PDB  Type:DNA  Length:10
                                         
                  4gqd C 21 CCGATACCGG 30
                                    30


Chain D from PDB  Type:DNA  Length:10
                                         
                  4gqd D 31 CCGGTAxCGG 40
                                  | 40
                                 37-UCL
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4GQD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GQD)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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  4gqd
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 Related Entries

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(-) Related Entries Specified in the PDB File

2orf 2org 2orh 3tok 4gre 4gs2 4gsg 4gsi