4RGF - JenaLib

Title :   CRYSTAL STRUCTURE OF THE IN-LINE ALIGNED ENV22 TWISTER RIBOZYME SOAKED WITH MN2+

Authors :   A. Ren, K. R. Rajashankar, D. Simanshu, D. Patel

Date :   30 Sep 14 (Deposition) - 03 Dec 14 (Release) - 03 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Pseudoknot, Stems, Cleavage, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ren, M. Kosutic, K. R. Rajashankar, M. Frener, T. Santner, E. Westhof, R. Micura, D. J. Patel
In-Line Alignment And Mg(2+) Coordination At The Cleavage Site Of The Env22 Twister Ribozyme.
Nat Commun V. 5 5534 2014
PubMed-ID: 25410397 | Reference-DOI: 10.1038/NCOMMS6534

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 29)

Asymmetric Unit (4, 29)

No.	Name	Count	Type	Full Name
1	DU	3	Mod. Residue
2	K	14	Ligand/Ion	POTASSIUM ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	MN	11	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	DU	-1	Mod. Residue
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	DU	-1	Mod. Residue
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	DU	-1	Mod. Residue
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A A:6 , A A:7 , U A:8	BINDING SITE FOR RESIDUE MN A 101
02	AC2	SOFTWARE	G A:19 , C B:31 , U C:41 , MN C:102	BINDING SITE FOR RESIDUE MN A 102
03	AC3	SOFTWARE	G A:27 , HOH A:204	BINDING SITE FOR RESIDUE MN A 103
04	AC4	SOFTWARE	A A:42 , A A:43	BINDING SITE FOR RESIDUE MN A 104
05	AC5	SOFTWARE	A A:7 , U A:8	BINDING SITE FOR RESIDUE MN A 105
06	AC6	SOFTWARE	U A:3	BINDING SITE FOR RESIDUE K A 106
07	AC7	SOFTWARE	U A:4 , A A:6 , C A:31	BINDING SITE FOR RESIDUE K A 107
08	AC8	SOFTWARE	G A:48	BINDING SITE FOR RESIDUE K A 108
09	AC9	SOFTWARE	U A:24 , G A:25	BINDING SITE FOR RESIDUE K A 109
10	BC1	SOFTWARE	U A:30 , A A:35	BINDING SITE FOR RESIDUE K A 110
11	BC2	SOFTWARE	U A:30 , C A:31 , C A:32	BINDING SITE FOR RESIDUE K A 111
12	BC3	SOFTWARE	G A:52	BINDING SITE FOR RESIDUE K A 112
13	BC4	SOFTWARE	A B:6 , A B:7 , U B:8	BINDING SITE FOR RESIDUE MN B 101
14	BC5	SOFTWARE	A B:42 , A B:43	BINDING SITE FOR RESIDUE MN B 102
15	BC6	SOFTWARE	U B:24 , G B:25	BINDING SITE FOR RESIDUE K B 104
16	BC7	SOFTWARE	G B:53	BINDING SITE FOR RESIDUE K B 105
17	BC8	SOFTWARE	C B:31	BINDING SITE FOR RESIDUE K B 106
18	BC9	SOFTWARE	A C:6 , A C:7 , U C:8	BINDING SITE FOR RESIDUE MG C 101
19	CC1	SOFTWARE	G A:19 , MN A:102 , C B:31 , U C:41	BINDING SITE FOR RESIDUE MN C 102
20	CC2	SOFTWARE	A C:6 , C C:31	BINDING SITE FOR RESIDUE MN C 103
21	CC3	SOFTWARE	A C:42 , A C:43	BINDING SITE FOR RESIDUE MN C 104
22	CC4	SOFTWARE	U C:30	BINDING SITE FOR RESIDUE MN C 105
23	CC5	SOFTWARE	U C:24	BINDING SITE FOR RESIDUE K C 106
24	CC6	SOFTWARE	G C:27 , G C:28	BINDING SITE FOR RESIDUE K C 107

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

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:DNA/RNA  Length:56
                                                                                       
                  4rgf A  1 UUUUxAAUGAAGCCACAGGCCUGUGAGGGUCCUAAGCCCCUAAUUCAGAAGGGAAA 56
                                |   10        20        30        40        50      
                                5-DU

Chain B from PDB  Type:DNA/RNA  Length:56
                                                                                       
                  4rgf B  1 UUUUxAAUGAAGCCACAGGCCUGUGAGGGUCCUAAGCCCCUAAUUCAGAAGGGAAA 56
                                |   10        20        30        40        50      
                                5-DU

Chain C from PDB  Type:DNA/RNA  Length:55
                                                                                      
                  4rgf C  1 UUUUxAAUGAAGCCACAGGCCUGUGAGGGUCCUAAGCCCCUAAUUCAGAAGGGAA 55
                                |   10        20        30        40        50     
                                5-DU

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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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