3OXE - JenaLib

Title :   CRYSTAL STRUCTURE OF GLYCINE RIBOSWITCH, MN2+ 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 :   2.90

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, 47)

Asymmetric Unit (5, 47)

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	10	Ligand/Ion	MAGNESIUM ION
5	MN	32	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	GDP	1	Mod. Nucleotide	GUANOSINE-5'-DIPHOSPHATE
3	GLY	1	Ligand/Ion	GLYCINE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MN	-1	Ligand/Ion	MANGANESE (II) 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	MN	-1	Ligand/Ion	MANGANESE (II) 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	MN	-1	Ligand/Ion	MANGANESE (II) ION

Sites (35, 35)

Asymmetric Unit (35, 35)

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 , MN A:102 , HOH A:160	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 , MN B:129 , HOH B:150	BINDING SITE FOR RESIDUE GLY B 89
03	AC3	SOFTWARE	A A:34 , G A:35 , HOH A:161	BINDING SITE FOR RESIDUE MN A 101
04	AC4	SOFTWARE	G A:32 , A A:33 , C A:66 , GLY A:89 , HOH A:158 , HOH A:159 , HOH A:160	BINDING SITE FOR RESIDUE MN A 102
05	AC5	SOFTWARE	A A:22 , A A:75	BINDING SITE FOR RESIDUE MN A 103
06	AC6	SOFTWARE	C A:74 , A A:75 , A A:76	BINDING SITE FOR RESIDUE MN A 104
07	AC7	SOFTWARE	U A:69 , C A:70 , A A:71	BINDING SITE FOR RESIDUE MN A 105
08	AC8	SOFTWARE	A A:33	BINDING SITE FOR RESIDUE MN A 106
09	AC9	SOFTWARE	GDP A:1	BINDING SITE FOR RESIDUE MN A 108
10	BC1	SOFTWARE	G A:8 , G A:80	BINDING SITE FOR RESIDUE MN A 109
11	BC2	SOFTWARE	A A:78	BINDING SITE FOR RESIDUE MN A 110
12	BC3	SOFTWARE	G A:10	BINDING SITE FOR RESIDUE MN A 111
13	BC4	SOFTWARE	G A:17 , U A:19	BINDING SITE FOR RESIDUE MN A 112
14	BC5	SOFTWARE	U A:20 , A A:21	BINDING SITE FOR RESIDUE MN A 113
15	BC6	SOFTWARE	G A:73	BINDING SITE FOR RESIDUE MN A 114
16	BC7	SOFTWARE	G A:62	BINDING SITE FOR RESIDUE MN A 115
17	BC8	SOFTWARE	G A:50	BINDING SITE FOR RESIDUE MN A 117
18	BC9	SOFTWARE	G B:1	BINDING SITE FOR RESIDUE MN B 118
19	CC1	SOFTWARE	G B:10	BINDING SITE FOR RESIDUE MN B 119
20	CC2	SOFTWARE	C B:74 , A B:75 , A B:76	BINDING SITE FOR RESIDUE MN B 120
21	CC3	SOFTWARE	A B:78 , G B:79	BINDING SITE FOR RESIDUE MN B 121
22	CC4	SOFTWARE	A B:34 , G B:35 , HOH B:151	BINDING SITE FOR RESIDUE MN B 122
23	CC5	SOFTWARE	G B:62	BINDING SITE FOR RESIDUE MN B 123
24	CC6	SOFTWARE	A B:21	BINDING SITE FOR RESIDUE MN B 124
25	CC7	SOFTWARE	U B:18 , U B:20	BINDING SITE FOR RESIDUE MN B 125
26	CC8	SOFTWARE	U B:23	BINDING SITE FOR RESIDUE MN B 126
27	CC9	SOFTWARE	U B:69 , C B:70 , A B:71	BINDING SITE FOR RESIDUE MN B 127
28	DC1	SOFTWARE	A B:14 , A B:75	BINDING SITE FOR RESIDUE MN B 128
29	DC2	SOFTWARE	G B:32 , A B:33 , C B:66 , GLY B:89 , HOH B:149 , HOH B:150	BINDING SITE FOR RESIDUE MN B 129
30	DC3	SOFTWARE	G B:50	BINDING SITE FOR RESIDUE MN B 130
31	DC4	SOFTWARE	HOH A:143 , HOH A:144 , HOH A:145 , HOH A:146 , HOH A:147 , HOH A:148	BINDING SITE FOR RESIDUE MG A 133
32	DC5	SOFTWARE	HOH A:149 , HOH B:142 , HOH B:143 , HOH B:144 , HOH B:145 , HOH B:146	BINDING SITE FOR RESIDUE MG B 134
33	DC6	SOFTWARE	A A:21 , HOH A:150 , HOH A:151 , HOH A:152 , HOH A:153 , HOH A:154	BINDING SITE FOR RESIDUE MG A 135
34	DC7	SOFTWARE	A B:52	BINDING SITE FOR RESIDUE MG B 136
35	DC8	SOFTWARE	A B:37	BINDING SITE FOR RESIDUE MG B 141

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

Chain B from PDB  Type:RNA  Length:88
                                                                                                                       
                  3oxe 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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