4FRG - JenaLib

Title :   CRYSTAL STRUCTURE OF THE COBALAMIN RIBOSWITCH APTAMER DOMAIN

Authors :   F. E. Reyes, J. E. Johnson, J. T. Polaski, R. T. Batey

Date :   26 Jun 12 (Deposition) - 17 Oct 12 (Release) - 26 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : B,X
Biol. Unit 1: B  (1x)
Biol. Unit 2: X  (1x)

Keywords :   Cobalamin, Riboswitch, B12, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Johnson, F. E. Reyes, J. T. Polaski, R. T. Batey
B12 Cofactors Directly Stabilize An Mrna Regulatory Switch.
Nature V. 492 133 2012
PubMed-ID: 23064232 | Reference-DOI: 10.1038/NATURE11607

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 35)

Asymmetric Unit (3, 35)

No.	Name	Count	Type	Full Name
1	I2A	2	Ligand/Ion	HYDROXOCOBALAMIN
2	IR3	17	Ligand/Ion	IRIDIUM (III) ION
3	MG	16	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	I2A	1	Ligand/Ion	HYDROXOCOBALAMIN
2	IR3	9	Ligand/Ion	IRIDIUM (III) ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	I2A	1	Ligand/Ion	HYDROXOCOBALAMIN
2	IR3	8	Ligand/Ion	IRIDIUM (III) ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G B:19 , A B:20 , A B:21 , U B:44 , U B:54 , A B:55 , A B:70 , G B:72 , C B:73	BINDING SITE FOR RESIDUE I2A B 101
02	AC2	SOFTWARE	G B:57	BINDING SITE FOR RESIDUE IR3 B 103
03	AC3	SOFTWARE	G B:25 , A B:26	BINDING SITE FOR RESIDUE IR3 B 105
04	AC4	SOFTWARE	A B:14	BINDING SITE FOR RESIDUE IR3 B 109
05	AC5	SOFTWARE	U B:35 , U B:38	BINDING SITE FOR RESIDUE MG B 112
06	AC6	SOFTWARE	C B:46	BINDING SITE FOR RESIDUE MG B 113
07	AC7	SOFTWARE	A B:6 , A B:7 , A B:8 , G B:10	BINDING SITE FOR RESIDUE MG B 115
08	AC8	SOFTWARE	A B:14	BINDING SITE FOR RESIDUE MG B 116
09	AC9	SOFTWARE	U B:13 , A B:14	BINDING SITE FOR RESIDUE MG B 117
10	BC1	SOFTWARE	G X:19 , A X:20 , A X:21 , U X:44 , U X:54 , A X:55 , A X:70 , G X:72 , C X:73	BINDING SITE FOR RESIDUE I2A X 101
11	BC2	SOFTWARE	G X:57	BINDING SITE FOR RESIDUE IR3 X 102
12	BC3	SOFTWARE	C X:11	BINDING SITE FOR RESIDUE IR3 X 105
13	BC4	SOFTWARE	G X:81	BINDING SITE FOR RESIDUE IR3 X 106
14	BC5	SOFTWARE	A X:55 , C X:64	BINDING SITE FOR RESIDUE MG X 111
15	BC6	SOFTWARE	G B:28 , A X:32 , A X:33 , U X:60	BINDING SITE FOR RESIDUE MG X 112
16	BC7	SOFTWARE	U X:35 , U X:38	BINDING SITE FOR RESIDUE MG X 113
17	BC8	SOFTWARE	A X:14	BINDING SITE FOR RESIDUE MG X 114
18	BC9	SOFTWARE	A X:6 , U X:13 , A X:14	BINDING SITE FOR RESIDUE MG X 115
19	CC1	SOFTWARE	A X:6 , A X:7 , A X:8 , G X:10	BINDING SITE FOR RESIDUE MG X 116
20	CC2	SOFTWARE	A B:84 , A X:48	BINDING SITE FOR RESIDUE MG X 117

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 B from PDB  Type:RNA  Length:84
                                                                                                                   
                  4frg B  1 GGCCUAAAAGCAUAGUGGGAAAGUGACGUGAAAUUCGUCCAGAUGCGAAAGCAUACGGUUAUACUCCGAAUGCCACCUAGGCCA 84
                                    10        20        30        40        50        60        70        80

Chain X from PDB  Type:RNA  Length:84
                                                                                                                   
                  4frg X  1 GGCCUAAAAGCAUAGUGGGAAAGUGACGUGAAAUUCGUCCAGAUGCGAAAGCAUACGGUUAUACUCCGAAUGCCACCUAGGCCA 84
                                    10        20        30        40        50        60        70        80

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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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