3SKR - JenaLib

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

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

Date :   23 Jun 11 (Deposition) - 17 Aug 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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, 19)

Asymmetric Unit (5, 19)

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	MG	4	Ligand/Ion	MAGNESIUM ION
5	NCO	9	Ligand/Ion	COBALT HEXAMMINE(III)

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	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NCO	5	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 2 (4, 7)

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	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NCO	4	Ligand/Ion	COBALT HEXAMMINE(III)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A A:30 , C A:31 , C A:56 , G A:59 , C A:80 , MG A:201	BINDING SITE FOR RESIDUE GNG A 120
02	AC2	SOFTWARE	A B:30 , C B:31 , C B:56 , C B:57 , C B:58 , G B:59 , C B:80 , U B:81	BINDING SITE FOR RESIDUE GNG B 120
03	AC3	SOFTWARE	A A:32 , A A:77 , G A:78	BINDING SITE FOR RESIDUE NCO A 401
04	AC4	SOFTWARE	C A:25 , U A:26 , U A:41 , A A:42	BINDING SITE FOR RESIDUE NCO A 402
05	AC5	SOFTWARE	G A:45 , G A:46	BINDING SITE FOR RESIDUE NCO A 403
06	AC6	SOFTWARE	G B:33 , C B:48 , U B:49 , C B:60 , C B:61	BINDING SITE FOR RESIDUE NCO B 404
07	AC7	SOFTWARE	G A:33 , C A:48 , U A:49 , C A:60 , C A:61	BINDING SITE FOR RESIDUE NCO A 405
08	AC8	SOFTWARE	G A:33 , U A:63 , U A:74 , G A:75 , G A:76 , A A:77	BINDING SITE FOR RESIDUE NCO A 406
09	AC9	SOFTWARE	GTP B:23 , G B:24 , C B:25 , G B:86 , U B:87	BINDING SITE FOR RESIDUE NCO B 407
10	BC1	SOFTWARE	G B:45 , G B:46	BINDING SITE FOR RESIDUE NCO B 408
11	BC2	SOFTWARE	G B:33 , U B:63 , U B:74 , G B:75 , G B:76	BINDING SITE FOR RESIDUE NCO B 409
12	BC3	SOFTWARE	C A:31 , A A:32 , GNG A:120	BINDING SITE FOR RESIDUE MG A 201
13	BC4	SOFTWARE	A B:40	BINDING SITE FOR RESIDUE MG B 203
14	BC5	SOFTWARE	G A:59 , C A:60	BINDING SITE FOR RESIDUE MG A 204

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
                                                                                                 
                  3skr A 23 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 88
                            |       32        42        52        62        72        82     |
                            |                                                               88-CCC
                           23-GTP

Chain B from PDB  Type:RNA  Length:66
                                                                                                 
                  3skr B 23 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 88
                            |       32        42        52        62        72        82     |
                            |                                                               88-CCC
                           23-GTP

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Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (0, 0)

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