3SKL - JenaLib

Title :   CRYSTAL STRUCTURE OF THE 2'- DEOXYGUANOSINE RIBOSWITCH BOUND TO 2'-DEOXYGUANOSINE, IRIDIUM HEXAMMINE SOAK

Authors :   O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov

Date :   22 Jun 11 (Deposition) - 17 Aug 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Three Way Junction, Riboswitch, Deoxyguanosine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Structural Principles Of Nucleoside Selectivity In A 2'-Deoxyguanosine Riboswitch.
Nat. Chem. Biol. V. 7 748 2011
PubMed-ID: 21841796 | Reference-DOI: 10.1038/NCHEMBIO.631

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 22)

Asymmetric Unit (5, 22)

No.	Name	Count	Type	Full Name
1	CCC	2	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GNG	2	Ligand/Ion	2'-DEOXY-GUANOSINE
3	GTP	2	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	IRI	10	Ligand/Ion	IRIDIUM HEXAMMINE ION
5	MG	6	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GNG	1	Ligand/Ion	2'-DEOXY-GUANOSINE
3	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	IRI	5	Ligand/Ion	IRIDIUM HEXAMMINE ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GNG	1	Ligand/Ion	2'-DEOXY-GUANOSINE
3	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
4	IRI	5	Ligand/Ion	IRIDIUM HEXAMMINE ION
5	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (17, 17)

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A A:29 , C A:30 , C A:55 , C A:56 , C A:57 , G A:58 , C A:79 , U A:80	BINDING SITE FOR RESIDUE GNG A 120
02	AC2	SOFTWARE	A B:29 , C B:30 , C B:55 , C B:56 , C B:57 , G B:58 , C B:79 , U B:80 , MG B:202	BINDING SITE FOR RESIDUE GNG B 120
03	AC3	SOFTWARE	GTP A:22	BINDING SITE FOR RESIDUE MG A 201
04	AC4	SOFTWARE	C B:30 , A B:31 , GNG B:120	BINDING SITE FOR RESIDUE MG B 202
05	AC5	SOFTWARE	GTP B:22 , G B:23 , C B:24 , G B:85 , U B:86	BINDING SITE FOR RESIDUE MG B 203
06	AC6	SOFTWARE	G B:32 , G B:33 , G B:34	BINDING SITE FOR RESIDUE MG B 205
07	AC7	SOFTWARE	C B:68 , U B:69	BINDING SITE FOR RESIDUE MG B 206
08	AC8	SOFTWARE	G A:44 , G A:45	BINDING SITE FOR RESIDUE IRI A 402
09	AC9	SOFTWARE	A A:31 , G A:32 , U A:61 , U A:62 , C A:63 , U A:73 , G A:74 , G A:75	BINDING SITE FOR RESIDUE IRI A 403
10	BC1	SOFTWARE	U B:51 , G B:52 , C B:54 , C B:56	BINDING SITE FOR RESIDUE IRI B 404
11	BC2	SOFTWARE	G A:32 , C A:47 , U A:48 , C A:59 , C A:60	BINDING SITE FOR RESIDUE IRI A 405
12	BC3	SOFTWARE	G B:58 , C B:59 , C B:60 , C B:63	BINDING SITE FOR RESIDUE IRI B 406
13	BC4	SOFTWARE	G B:44 , G B:45	BINDING SITE FOR RESIDUE IRI B 407
14	BC5	SOFTWARE	A B:31 , A B:76 , G B:77	BINDING SITE FOR RESIDUE IRI B 408
15	BC6	SOFTWARE	U A:51 , G A:52 , C A:54 , C A:55 , C A:56	BINDING SITE FOR RESIDUE IRI A 409
16	BC7	SOFTWARE	G B:32 , C B:47 , U B:48 , C B:59 , C B:60	BINDING SITE FOR RESIDUE IRI B 410
17	BC8	SOFTWARE	G A:34 , U A:35 , U A:72	BINDING SITE FOR RESIDUE IRI A 411

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:RNA  Length:66
                                                                                                 
                  3skl A 22 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 87
                            |       31        41        51        61        71        81     |
                            |                                                               87-CCC
                           22-GTP

Chain B from PDB  Type:RNA  Length:66
                                                                                                 
                  3skl B 22 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 87
                            |       31        41        51        61        71        81     |
                            |                                                               87-CCC
                           22-GTP

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Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (0, 0)

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