3OXM - JenaLib

Title :   CRYSTAL STRUCTURE OF GLYCINE RIBOSWITCH, TL-ACETATE SOAKED

Authors :   L. Huang, A. Serganov, D. J. Patel

Date :   21 Sep 10 (Deposition) - 29 Dec 10 (Release) - 29 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Gene Expression Regulator, Glycine Riboswitch, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, A. Serganov, D. J. Patel
Structural Insights Into Ligand Recognition By A Sensing Domain Of The Cooperative Glycine Riboswitch.
Mol. Cell V. 40 774 2010
PubMed-ID: 21145485 | Reference-DOI: 10.1016/J.MOLCEL.2010.11.026

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 42)

Asymmetric Unit (5, 42)

No.	Name	Count	Type	Full Name
1	CCC	2	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GDP	1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
3	GLY	2	Ligand/Ion	GLYCINE
4	MG	27	Ligand/Ion	MAGNESIUM ION
5	TL	10	Ligand/Ion	THALLIUM (I) 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	GDP	1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
3	GLY	1	Ligand/Ion	GLYCINE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	TL	-1	Ligand/Ion	THALLIUM (I) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GDP	-1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
3	GLY	1	Ligand/Ion	GLYCINE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	TL	-1	Ligand/Ion	THALLIUM (I) ION

Biological Unit 3 (3, 5)

No.	Name	Count	Type	Full Name
1	CCC	2	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	GDP	1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
3	GLY	2	Ligand/Ion	GLYCINE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	TL	-1	Ligand/Ion	THALLIUM (I) ION

Sites (34, 34)

Asymmetric Unit (34, 34)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G A:32 , A A:34 , G A:35 , G A:36 , C A:68 , U A:69 , A A:71 , MG A:102 , HOH A:115	BINDING SITE FOR RESIDUE GLY A 89
02	AC2	SOFTWARE	G B:32 , A B:34 , G B:35 , G B:36 , C B:68 , U B:69 , A B:71 , MG B:111 , HOH B:117	BINDING SITE FOR RESIDUE GLY B 89
03	AC3	SOFTWARE	G B:17 , U B:18 , U B:20 , A B:22 , U B:23	BINDING SITE FOR RESIDUE TL B 201
04	AC4	SOFTWARE	G B:25	BINDING SITE FOR RESIDUE TL B 202
05	AC5	SOFTWARE	G B:8 , G B:80	BINDING SITE FOR RESIDUE TL B 203
06	AC6	SOFTWARE	G A:8 , G A:80	BINDING SITE FOR RESIDUE TL A 204
07	AC7	SOFTWARE	U A:69 , C A:70 , A A:71 , G A:72	BINDING SITE FOR RESIDUE TL A 205
08	AC8	SOFTWARE	A A:41 , G A:42 , C A:43 , G A:60 , G A:62	BINDING SITE FOR RESIDUE TL A 206
09	AC9	SOFTWARE	G A:73	BINDING SITE FOR RESIDUE TL A 207
10	BC1	SOFTWARE	U B:6 , G B:8	BINDING SITE FOR RESIDUE TL B 208
11	BC2	SOFTWARE	G B:1 , G B:2	BINDING SITE FOR RESIDUE TL B 209
12	BC3	SOFTWARE	A A:78	BINDING SITE FOR RESIDUE TL A 210
13	BC4	SOFTWARE	A A:34 , G A:35 , HOH A:111 , HOH A:138 , HOH A:139 , HOH A:140	BINDING SITE FOR RESIDUE MG A 101
14	BC5	SOFTWARE	G A:32 , A A:33 , C A:66 , GLY A:89 , HOH A:115 , HOH A:141 , HOH A:142	BINDING SITE FOR RESIDUE MG A 102
15	BC6	SOFTWARE	A A:22 , A A:75	BINDING SITE FOR RESIDUE MG A 103
16	BC7	SOFTWARE	C A:74 , A A:75 , A A:76	BINDING SITE FOR RESIDUE MG A 104
17	BC8	SOFTWARE	A A:33	BINDING SITE FOR RESIDUE MG A 106
18	BC9	SOFTWARE	HOH A:119 , HOH A:120 , HOH A:121 , HOH A:122 , HOH A:123 , HOH A:143	BINDING SITE FOR RESIDUE MG A 109
19	CC1	SOFTWARE	C B:74 , A B:75 , A B:76 , HOH B:106 , HOH B:107 , HOH B:116	BINDING SITE FOR RESIDUE MG B 110
20	CC2	SOFTWARE	G B:32 , A B:33 , C B:66 , GLY B:89 , HOH B:109 , HOH B:117 , HOH B:118	BINDING SITE FOR RESIDUE MG B 111
21	CC3	SOFTWARE	HOH A:124 , HOH A:125 , HOH A:129 , HOH A:144 , HOH A:145 , HOH A:146	BINDING SITE FOR RESIDUE MG A 112
22	CC4	SOFTWARE	G A:50	BINDING SITE FOR RESIDUE MG A 113
23	CC5	SOFTWARE	A A:21	BINDING SITE FOR RESIDUE MG A 114
24	CC6	SOFTWARE	A B:34 , G B:35 , HOH B:114	BINDING SITE FOR RESIDUE MG B 115
25	CC7	SOFTWARE	HOH A:130 , HOH A:131 , HOH A:132 , HOH A:133 , HOH A:134 , HOH A:135	BINDING SITE FOR RESIDUE MG A 116
26	CC8	SOFTWARE	G A:10	BINDING SITE FOR RESIDUE MG A 117
27	CC9	SOFTWARE	U A:20 , A A:21	BINDING SITE FOR RESIDUE MG A 118
28	DC1	SOFTWARE	A B:75	BINDING SITE FOR RESIDUE MG B 120
29	DC2	SOFTWARE	U B:18 , U B:20	BINDING SITE FOR RESIDUE MG B 121
30	DC3	SOFTWARE	A B:52	BINDING SITE FOR RESIDUE MG B 122
31	DC4	SOFTWARE	U B:69 , C B:70 , A B:71 , G B:72	BINDING SITE FOR RESIDUE MG B 123
32	DC5	SOFTWARE	A B:78 , G B:79	BINDING SITE FOR RESIDUE MG B 124
33	DC6	SOFTWARE	G B:62	BINDING SITE FOR RESIDUE MG B 125
34	DC7	SOFTWARE	G A:62	BINDING SITE FOR RESIDUE MG A 126

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:88
                                                                                                                       
                  3oxm A  1 gGCUCUGGAGAGAACCGUUUAAUCGGUCGCCGAAGGAGCAAGCUCUGCGGAAACGCAGAGUGAAACUCUCAGGCAAAAGGACAGAGUc 88
                            |       10        20        30        40        50        60        70        80       |
                            |                                                                                     88-CCC
                            1-GDP

Chain B from PDB  Type:RNA  Length:88
                                                                                                                       
                  3oxm B  1 GGCUCUGGAGAGAACCGUUUAAUCGGUCGCCGAAGGAGCAAGCUCUGCGGAAACGCAGAGUGAAACUCUCAGGCAAAAGGACAGAGUc 88
                                    10        20        30        40        50        60        70        80       |
                                                                                                                  88-CCC

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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