2AVJ | UD0063 - JenaLib

Title :   G4(BR)UTTG4 DIMERIC QUADRUPLEX

Authors :   P. Hazel, G. N. Parkinson, S. Neidle

Date :   30 Aug 05 (Deposition) - 28 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Quadruplex, Loop, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Hazel, G. N. Parkinson, S. Neidle
Topology Variation And Loop Structural Homology In Crystal And Simulated Structures Of A Bimolecular Dna Quadruplex.
J. Am. Chem. Soc. V. 128 5480 2006
PubMed-ID: 16620121 | Reference-DOI: 10.1021/JA058577+

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	BRU	6	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	CAC	2	Ligand/Ion	CACODYLATE ION
3	K	14	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BRU	2	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	CAC	-1	Ligand/Ion	CACODYLATE ION
3	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BRU	2	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	CAC	2	Ligand/Ion	CACODYLATE ION
3	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	BRU	2	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	CAC	-1	Ligand/Ion	CACODYLATE ION
3	K	-1	Ligand/Ion	POTASSIUM ION

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DG C:23 , DG C:33 , K C:69 , DG D:34 , DG D:44 , DG E:45 , DG E:55 , K E:68 , DG F:56 , DG F:66	BINDING SITE FOR RESIDUE K C 67
02	AC2	SOFTWARE	K C:67 , DG E:45 , DG E:46 , DG E:54 , DG E:55 , K E:70 , DG F:56 , DG F:57 , DG F:65 , DG F:66	BINDING SITE FOR RESIDUE K E 68
03	AC3	SOFTWARE	DG C:23 , DG C:24 , DG C:32 , DG C:33 , K C:67 , K C:74 , DG D:34 , DG D:35 , DG D:43 , DG D:44	BINDING SITE FOR RESIDUE K C 69
04	AC4	SOFTWARE	DG E:46 , DG E:47 , DG E:53 , DG E:54 , K E:68 , K E:71 , DG F:57 , DG F:58 , DG F:64 , DG F:65	BINDING SITE FOR RESIDUE K E 70
05	AC5	SOFTWARE	DG E:47 , DG E:48 , DG E:52 , DG E:53 , K E:70 , DG F:58 , DG F:59 , DG F:63 , DG F:64	BINDING SITE FOR RESIDUE K E 71
06	AC6	SOFTWARE	DG A:1 , DG A:2 , DG A:10 , DG A:11 , DG B:14 , DG B:15 , DG B:19 , DG B:20	BINDING SITE FOR RESIDUE K A 72
07	AC7	SOFTWARE	DG A:3 , DG A:4 , DG A:8 , DG A:9 , K A:75 , DG B:12 , DG B:13 , DG B:21 , DG B:22	BINDING SITE FOR RESIDUE K A 73
08	AC8	SOFTWARE	DG C:24 , DG C:25 , DG C:31 , DG C:32 , K C:69 , K C:76 , DG D:35 , DG D:36 , DG D:42 , DG D:43	BINDING SITE FOR RESIDUE K C 74
09	AC9	SOFTWARE	DG A:2 , DG A:3 , DG A:9 , DG A:10 , K A:73 , DG B:13 , DG B:14 , DG B:20 , DG B:21	BINDING SITE FOR RESIDUE K A 75
10	BC1	SOFTWARE	DG C:25 , DG C:26 , DG C:30 , DG C:31 , K C:74 , DG D:36 , DG D:37 , DG D:41 , DG D:42	BINDING SITE FOR RESIDUE K C 76
11	BC2	SOFTWARE	DG C:23 , DG C:32	BINDING SITE FOR RESIDUE K C 77
12	BC3	SOFTWARE	BRU F:60	BINDING SITE FOR RESIDUE K F 78
13	BC4	SOFTWARE	DG A:8 , HOH A:224 , DG B:21	BINDING SITE FOR RESIDUE K A 79
14	BC5	SOFTWARE	HOH E:128 , HOH E:195	BINDING SITE FOR RESIDUE K E 80

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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Chain A from PDB  Type:DNA  Length:11
                                          
                  2avj A  1 GGGGuTTGGGG 11
                                |   10 
                                |      
                                5-BRU

Chain B from PDB  Type:DNA  Length:11
                                          
                  2avj B 12 GGGGuTTGGGG 22
                                |   21 
                               16-BRU

Chain C from PDB  Type:DNA  Length:11
                                          
                  2avj C 23 GGGGuTTGGGG 33
                                |   32 
                               27-BRU

Chain D from PDB  Type:DNA  Length:11
                                          
                  2avj D 34 GGGGuTTGGGG 44
                                |   43 
                               38-BRU

Chain E from PDB  Type:DNA  Length:11
                                          
                  2avj E 45 GGGGuTTGGGG 55
                                |   54 
                               49-BRU

Chain F from PDB  Type:DNA  Length:11
                                          
                  2avj F 56 GGGGuTTGGGG 66
                                |   65 
                               60-BRU

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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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