3SKT - JenaLib

Title :   CRYSTAL STRUCTURE OF THE 2'- DEOXYGUANOSINE RIBOSWITCH BOUND TO 2'-DEOXYGUANOSINE, MANGANESE 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, 2'-Deoxy-Guanosine, 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, 25)

Asymmetric Unit (5, 25)

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	9	Ligand/Ion	MAGNESIUM ION
5	MN	10	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (3, 3)

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	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (3, 3)

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	MN	-1	Ligand/Ion	MANGANESE (II) ION

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A A:30 , C A:31 , C A:56 , C A:57 , C A:58 , G A:59 , C A:80 , U A:81	BINDING SITE FOR RESIDUE GNG A 89
02	AC2	SOFTWARE	G A:75 , MN A:208	BINDING SITE FOR RESIDUE MN A 201
03	AC3	SOFTWARE	G A:45	BINDING SITE FOR RESIDUE MN A 202
04	AC4	SOFTWARE	G A:34 , U A:73	BINDING SITE FOR RESIDUE MN A 207
05	AC5	SOFTWARE	G A:75 , G A:76 , MN A:201	BINDING SITE FOR RESIDUE MN A 208
06	AC6	SOFTWARE	G A:33 , C A:61	BINDING SITE FOR RESIDUE MN A 209
07	AC7	SOFTWARE	U A:41 , U A:70 , A A:71	BINDING SITE FOR RESIDUE MN A 210
08	AC8	SOFTWARE	A A:71	BINDING SITE FOR RESIDUE MG A 303
09	AC9	SOFTWARE	GTP A:23 , U A:83	BINDING SITE FOR RESIDUE MG A 308
10	BC1	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 89
11	BC2	SOFTWARE	GTP B:23	BINDING SITE FOR RESIDUE MN B 203
12	BC3	SOFTWARE	A B:32	BINDING SITE FOR RESIDUE MN B 204
13	BC4	SOFTWARE	G B:33 , U B:49 , C B:60 , C B:61 , MG B:309	BINDING SITE FOR RESIDUE MN B 205
14	BC5	SOFTWARE	G B:34 , G B:35 , U B:73	BINDING SITE FOR RESIDUE MN B 206
15	BC6	SOFTWARE	G B:53	BINDING SITE FOR RESIDUE MG B 302
16	BC7	SOFTWARE	U A:87 , GTP B:23	BINDING SITE FOR RESIDUE MG B 304
17	BC8	SOFTWARE	G B:33 , G B:34 , U B:73	BINDING SITE FOR RESIDUE MG B 305
18	BC9	SOFTWARE	G B:45	BINDING SITE FOR RESIDUE MG B 306
19	CC1	SOFTWARE	G B:33 , G B:75	BINDING SITE FOR RESIDUE MG B 307
20	CC2	SOFTWARE	G B:33 , C B:48 , C B:61 , MN B:205	BINDING SITE FOR RESIDUE MG B 309

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

Chain B from PDB  Type:RNA  Length:66
                                                                                                 
                  3skt 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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Gene Ontology (0, 0)

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