5EAO - JenaLib

Title :   TWO ACTIVE SITE DIVALENT ION IN THE CRYSTAL STRUCTURE OF THE HAMMERHEAD RIBOZYME BOUND TO A TRANSITION STATE ANALOG-MG2+

Authors :   A. Mir, B. L. Golden

Date :   16 Oct 15 (Deposition) - 24 Feb 16 (Release) - 24 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

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

Keywords :   Ribozyme, Hammerhead, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Mir, B. L. Golden
Two Active Site Divalent Ions In The Crystal Structure Of The Hammerhead Ribozyme Bound To A Transition State Analogue.
Biochemistry V. 55 633 2016
PubMed-ID: 26551631 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B01139
(for further references see the PDB file header)

Compounds

Molecule 1 - RNA (48-MER)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC19
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630

*Molecule 2 - RNA (5'-R(GPGPGPCPGPU(CVC) UPGPGPGPCPAPGPUPAPCPCPCPA)-3')*
	Chains	:	B
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CVC	1	Mod. Nucleotide	[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYLDIHYDROGEN PHOSPHATE
2	MG	8	Ligand/Ion	MAGNESIUM ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	A A:22 , G A:23	binding site for residue MG A 101
2	AC2	SOFTWARE	A A:41	binding site for residue MG A 102
3	AC3	SOFTWARE	G A:29 , G A:30 , MG B:102	binding site for residue MG A 103
4	AC4	SOFTWARE	U A:17 , U A:20	binding site for residue MG A 104
5	AC5	SOFTWARE	G A:39 , CVC B:7	binding site for residue MG A 105
6	AC6	SOFTWARE	A B:13 , G B:14	binding site for residue MG B 101
7	AC7	SOFTWARE	MG A:103	binding site for residue MG B 102
8	AC8	SOFTWARE	A B:16	binding site for residue MG B 103

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/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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Chain A from PDB  Type:RNA  Length:48
                                                                               
                  5eao A  1 GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACGAAACGCCCA 48
                                    10        20        30        40

Chain B from PDB  Type:RNA  Length:20
                                                   
                  5eao B  1 GGGCGUxUGGGCAGUACCCA 20
                                  | 10        20
                                  7-CVC

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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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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	Cis Peptide Bonds
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Still Images

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