4YAZ - JenaLib

Title :   3',3'-CGAMP RIBOSWITCH BOUND WITH 3',3'-CGAMP

Authors :   A. M. Ren, D. J. Patel, R. K. Rajashankar

Date :   18 Feb 15 (Deposition) - 15 Apr 15 (Release) - 22 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Riboswitch, 3', 3'-Cgamp, Spinach, Rna Structure, C-Di-Gmp, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ren, X. C. Wang, C. A. Kellenberger, K. R. Rajashankar, R. A. Jones, M. C. Hammond, D. J. Patel
Structural Basis For Molecular Discrimination By A 3', 3'-Cgamp Sensing Riboswitch.
Cell Rep V. 11 1 2015
PubMed-ID: 25818298 | Reference-DOI: 10.1016/J.CELREP.2015.03.004

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	4BW	2	Ligand/Ion	2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE
2	GTP	2	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
3	K	3	Ligand/Ion	POTASSIUM ION
4	MG	5	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	4BW	1	Ligand/Ion	2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE
2	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	4BW	1	Ligand/Ion	2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9-(6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE
2	GTP	1	Mod. Nucleotide	GUANOSINE-5'-TRIPHOSPHATE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G R:44 , C R:45 , HOH R:216 , HOH R:232 , HOH R:259 , HOH R:281	binding site for residue MG R 101
02	AC2	SOFTWARE	G R:51 , HOH R:274 , HOH R:289	binding site for residue MG R 102
03	AC3	SOFTWARE	U R:81 , A R:82	binding site for residue MG R 103
04	AC4	SOFTWARE	HOH R:276 , HOH R:293	binding site for residue MG R 104
05	AC5	SOFTWARE	A R:48 , G R:51 , HOH R:247 , HOH R:284	binding site for residue K R 105
06	AC6	SOFTWARE	G R:8 , A R:11 , A R:12 , A R:14 , G R:40 , A R:41 , A R:42 , C R:75 , C R:76 , HOH R:228 , HOH R:239	binding site for residue 4BW R 106
07	AC7	SOFTWARE	A A:18 , A A:19 , HOH A:267 , A R:19	binding site for residue K R 107
08	AC8	SOFTWARE	U A:16 , G A:44 , C A:45	binding site for residue MG A 101
09	AC9	SOFTWARE	C A:58	binding site for residue K A 102
10	AD1	SOFTWARE	G A:8 , A A:11 , A A:12 , A A:14 , G A:40 , A A:41 , C A:75 , C A:76 , HOH A:225 , HOH A:233 , HOH A:260	binding site for residue 4BW A 103
11	AD2	SOFTWARE	U A:3 , A A:82 , U A:83 , C A:84 , HOH A:211 , HOH A:248 , HOH A:252	binding site for Di-nucleotide GTP A 1 and G A 2

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:84
                                                                                                                   
                  4yaz A  1 xGUACACGACAAUACUAAACCAUCCGCGAGGAUGGGGCGGAAAGCCUAAGGGUCUCCCUGAGACAGCCGGGCUGCCGAAAUAUC 84
                            |       10        20        30        40        50        60        70        80    
                            |                                                                                   
                            1-GTP

Chain R from PDB  Type:RNA  Length:84
                                                                                                                   
                  4yaz R  1 xGUACACGACAAUACUAAACCAUCCGCGAGGAUGGGGCGGAAAGCCUAAGGGUCUCCCUGAGACAGCCGGGCUGCCGAAAUAUC 84
                            |       10        20        30        40        50        60        70        80    
                            1-GTP

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Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (0, 0)

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