3OXD - JenaLib

Title :   CRYSTAL STRUCTURE OF GLYCINE RIBOSWITCH WITH TWO MUTATIONS

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 :   3.00

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 (3, 37)

Asymmetric Unit (3, 37)

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	MG	34	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (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	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

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	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 3)

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	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:138 , HOH A:139 , HOH A:140 , HOH A:141 , HOH A:142 , HOH A:143	BINDING SITE FOR RESIDUE MG A 101
02	AC2	SOFTWARE	HOH A:146 , HOH A:147 , HOH A:148 , HOH A:149 , HOH A:150 , HOH A:151	BINDING SITE FOR RESIDUE MG A 109
03	AC3	SOFTWARE	A A:21 , HOH A:152 , HOH A:153 , HOH A:154 , HOH A:155 , HOH A:156	BINDING SITE FOR RESIDUE MG A 110
04	AC4	SOFTWARE	HOH A:157 , HOH A:158 , HOH A:159 , HOH A:160 , HOH A:161 , HOH A:162	BINDING SITE FOR RESIDUE MG A 111
05	AC5	SOFTWARE	U A:19 , U A:20 , HOH A:163 , HOH A:164 , HOH A:165 , HOH A:166 , HOH A:167	BINDING SITE FOR RESIDUE MG A 112
06	AC6	SOFTWARE	G A:50 , HOH A:168 , HOH A:169 , HOH A:170 , HOH A:171 , HOH A:172	BINDING SITE FOR RESIDUE MG A 130
07	AC7	SOFTWARE	A A:22 , A A:75	BINDING SITE FOR RESIDUE MG A 103
08	AC8	SOFTWARE	A A:75 , A A:76	BINDING SITE FOR RESIDUE MG A 104
09	AC9	SOFTWARE	G A:10	BINDING SITE FOR RESIDUE MG A 117
10	BC1	SOFTWARE	G A:62	BINDING SITE FOR RESIDUE MG A 118
11	BC2	SOFTWARE	A A:33 , C A:66 , U A:67	BINDING SITE FOR RESIDUE MG A 120
12	BC3	SOFTWARE	G A:8 , G A:80	BINDING SITE FOR RESIDUE MG A 123
13	BC4	SOFTWARE	A A:78 , G A:79 , G A:80	BINDING SITE FOR RESIDUE MG A 124
14	BC5	SOFTWARE	G A:17 , U A:19	BINDING SITE FOR RESIDUE MG A 125
15	BC6	SOFTWARE	A A:41	BINDING SITE FOR RESIDUE MG A 126
16	BC7	SOFTWARE	A A:81	BINDING SITE FOR RESIDUE MG A 137
17	BC8	SOFTWARE	HOH A:144 , HOH A:145 , HOH B:137 , HOH B:138 , HOH B:139 , HOH B:140	BINDING SITE FOR RESIDUE MG B 106
18	BC9	SOFTWARE	C B:39 , G B:62 , HOH B:141 , HOH B:142 , HOH B:143 , HOH B:144 , HOH B:145	BINDING SITE FOR RESIDUE MG B 113
19	CC1	SOFTWARE	C B:74 , A B:75 , A B:76 , HOH B:146 , HOH B:147 , HOH B:148	BINDING SITE FOR RESIDUE MG B 114
20	CC2	SOFTWARE	HOH B:149 , HOH B:150 , HOH B:151 , HOH B:152 , HOH B:153 , HOH B:154	BINDING SITE FOR RESIDUE MG B 131
21	CC3	SOFTWARE	C B:66 , U B:67 , HOH B:155 , HOH B:156 , HOH B:157 , HOH B:158 , HOH B:159 , HOH B:160	BINDING SITE FOR RESIDUE MG B 132
22	CC4	SOFTWARE	A B:34 , HOH B:161 , HOH B:162 , HOH B:163 , HOH B:164 , HOH B:165 , HOH B:166	BINDING SITE FOR RESIDUE MG B 133
23	CC5	SOFTWARE	U B:18 , U B:20	BINDING SITE FOR RESIDUE MG B 115
24	CC6	SOFTWARE	A B:78	BINDING SITE FOR RESIDUE MG B 116
25	CC7	SOFTWARE	A B:52	BINDING SITE FOR RESIDUE MG B 119
26	CC8	SOFTWARE	A B:81	BINDING SITE FOR RESIDUE MG B 121
27	CC9	SOFTWARE	G B:17 , U B:20 , A B:21	BINDING SITE FOR RESIDUE MG B 128
28	DC1	SOFTWARE	G B:70 , A B:71	BINDING SITE FOR RESIDUE MG B 129
29	DC2	SOFTWARE	A B:75	BINDING SITE FOR RESIDUE MG B 134
30	DC3	SOFTWARE	U A:20	BINDING SITE FOR RESIDUE MG B 135

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
                                                                                                                       
                  3oxd A  1 gGCUCUGGAGAGAACCGUUUAAUCGGUCGCCGAACGAGCAAGCUCUGCGGAAACGCAGAGUGAAACUCUGAGGCAAAAGGACAGAGUc 88
                            |       10        20        30        40        50        60        70        80       |
                            |                                                                                     88-CCC
                            1-GDP

Chain B from PDB  Type:RNA  Length:87
                                                                                                                      
                  3oxd B  1 GGCUCUGGAGAGAACCGUUUAUCGGUCGCCGAACGAGCAAGCUCUGCGGAAACGCAGAGUGAAACUCUGAGGCAAAAGGACAGAGUc 88
                                    10        20||      31        41        51        61        71        81      |
                                               21|                                                               88-CCC
                                                23

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