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Title :   A 1.9A CRYSTAL STRUCTURE OF THE HDV RIBOZYME PRECLEAVAGE SUGGESTS BOTH LEWIS ACID AND GENERAL ACID MECHANISMS CONTRIBUTE TO PHOSPHODIESTER CLEAVAGE

Authors :   J. -H. Chen, R. Yajima, D. M. Chadalavada, E. Chase, P. C. Bevilacqua, B.

Date :   18 Jun 10 (Deposition) - 01 Sep 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

Chains :   Asym./Biol. Unit : A,B

Keywords :   Catalytic Rna, Metal-Mediated Catalysis, Phosphodiester Cleavage, Dna, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Chen, R. Yajima, D. M. Chadalavada, E. Chase, P. C. Bevilacqua, B. L. Golden
A 1. 9 A Crystal Structure Of The Hdv Ribozyme Precleavage Suggests Both Lewis Acid And General Acid Mechanisms Contribute To Phosphodiester Cleavage.
Biochemistry V. 49 6508 2010
PubMed-ID: 20677830 | Reference-DOI: 10.1021/BI100670P

Compounds

*Molecule 1 - DNA/RNA (5'-D((DUR))-D(GPG)-R(PCPUPUPGPCPA)-3')**
	Chains	:	A
	Engineered	:	YES
	Other Details	:	NUCLEIC ACID WAS CHEMICALLY SYNTHESIZED
	Synthetic	:	YES

Molecule 2 - THE HEPATITIS DELTA VIRUS RIBOZYME
	Chains	:	B
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G B:35 , HOH B:522 , HOH B:615 , HOH B:635 , HOH B:656 , HOH B:661 , HOH B:663	BINDING SITE FOR RESIDUE MG B 201
02	AC2	SOFTWARE	HOH B:570 , HOH B:651 , HOH B:653	BINDING SITE FOR RESIDUE MG B 202
03	AC3	SOFTWARE	HOH B:510 , HOH B:511 , HOH B:513 , HOH B:514 , HOH B:515 , HOH B:555	BINDING SITE FOR RESIDUE MG B 203
04	AC4	SOFTWARE	G B:55 , U B:56 , HOH B:507 , HOH B:508 , HOH B:509 , HOH B:516	BINDING SITE FOR RESIDUE MG B 204
05	AC5	SOFTWARE	U B:56 , A B:57 , A B:58 , HOH B:502 , HOH B:504 , HOH B:506 , HOH B:543	BINDING SITE FOR RESIDUE MG B 205
06	AC6	SOFTWARE	HOH B:524 , HOH B:528 , HOH B:532 , HOH B:536 , HOH B:563 , HOH B:566	BINDING SITE FOR RESIDUE MG B 206
07	AC7	SOFTWARE	C B:32 , A B:64 , A B:65 , HOH B:600 , HOH B:613	BINDING SITE FOR RESIDUE MG B 207
08	AC8	SOFTWARE	U B:24 , HOH B:596 , HOH B:604 , HOH B:645 , HOH B:647 , HOH B:657	BINDING SITE FOR RESIDUE MG B 208
09	AC9	SOFTWARE	C B:25 , HOH B:544 , HOH B:573 , HOH B:623 , HOH B:650	BINDING SITE FOR RESIDUE MG B 209
10	BC1	SOFTWARE	G B:40 , HOH B:530 , HOH B:630 , HOH B:631	BINDING SITE FOR RESIDUE MG B 210

SS Bonds (0, 0)

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Chain A from PDB  Type:DNA/RNA  Length:8
                                       
                  3nkb A  2 GGCUUGCA  9

Chain B from PDB  Type:RNA  Length:64
                                                                                               
                  3nkb B 10 GGUCCGCAGCCUCCUCGCGGCGCAAGCUGGGCAACAUUCCGAAAGGUAAUGGCGAAUGCGGACC 73
                                    19        29        39        49        59        69

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Classification and Annotation

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