1UB8 | UD0027 - JenaLib

Title :   CRYSTAL STRUCTURE OF D(GCGAAGC), BENDING DUPLEX WITH A BULGE-IN RESIDUE

Authors :   T. Sunami, J. Kondo, I. Hirao, K. Watanabe, K. Miura, A. Takenaka

Date :   31 Mar 03 (Deposition) - 09 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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 :   Dna, Sheared G:A Pair, Bulge-In Duplex, G:Axa:G Crossing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Sunami, J. Kondo, I. Hirao, K. Watanabe, K. Miura, A. Takenaka
Structures Of D(Gcgaagc) And D(Gcgaaagc) (Tetragonal Form): A Switching Of Partners Of The Sheared G. A Pairs To Form A Functional G. Axa. G Crossing.
Acta Crystallogr. , Sect. D V. 60 422 2004
PubMed-ID: 14993665 | Reference-DOI: 10.1107/S0907444903028415
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	NCO	9	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NCO	3	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	NCO	4	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	NCO	2	Ligand/Ion	COBALT HEXAMMINE(III)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DA A:5 , DG A:6 , HOH A:1430 , HOH B:11 , HOH B:37 , DC D:7 , HOH D:10 , HOH D:393	BINDING SITE FOR RESIDUE NCO D 400
2	AC2	SOFTWARE	DC A:2 , DG A:3 , HOH A:1405 , HOH A:1433 , HOH A:1443 , HOH A:1456 , DG B:3 , DA D:5	BINDING SITE FOR RESIDUE NCO A 1401
3	AC3	SOFTWARE	DG A:3 , DG C:1 , DC C:2 , DA D:5 , DG D:6 , DC D:7 , HOH D:59 , HOH D:65 , HOH D:68 , HOH D:159 , HOH D:209 , HOH D:377	BINDING SITE FOR RESIDUE NCO D 402
4	AC4	SOFTWARE	DG B:3 , HOH B:224 , DA E:5 , DG E:6 , DC E:7 , HOH E:39 , HOH E:87 , HOH E:93 , HOH E:94 , DG F:1 , HOH F:110	BINDING SITE FOR RESIDUE NCO E 403
5	AC5	SOFTWARE	HOH A:1406 , DA B:5 , DG B:6 , DC B:7 , HOH B:27 , HOH B:30 , HOH B:36 , HOH B:157 , DC E:7 , HOH E:89 , HOH E:129	BINDING SITE FOR RESIDUE NCO B 404
6	AC6	SOFTWARE	DG E:1 , HOH E:395 , DA F:5 , DG F:6 , DC F:7 , HOH F:187 , HOH F:268	BINDING SITE FOR RESIDUE NCO F 405
7	AC7	SOFTWARE	DA B:5 , HOH B:303 , DC E:2 , DG E:3 , HOH E:234 , DG F:3 , HOH F:394	BINDING SITE FOR RESIDUE NCO B 406
8	AC8	SOFTWARE	HOH A:1465 , DA C:5 , DG C:6 , HOH C:174 , DG D:1	BINDING SITE FOR RESIDUE NCO C 407
9	AC9	SOFTWARE	DA A:5 , DC C:2 , DG C:3 , HOH C:291 , DG D:3	BINDING SITE FOR RESIDUE NCO C 408

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:7
                                     
                   1ub8 A 1 GCGAAGC 7

Chain B from PDB  Type:DNA  Length:7
                                     
                   1ub8 B 1 GCGAAGC 7

Chain C from PDB  Type:DNA  Length:7
                                     
                   1ub8 C 1 GCGAAGC 7

Chain D from PDB  Type:DNA  Length:7
                                     
                   1ub8 D 1 GCGAAGC 7

Chain E from PDB  Type:DNA  Length:7
                                     
                   1ub8 E 1 GCGAAGC 7

Chain F from PDB  Type:DNA  Length:7
                                     
                   1ub8 F 1 GCGAAGC 7

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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