5VJB - JenaLib

Title :   GUANIDINE-II RIBOSWITCH P2 HAIRPIN DIMER WITH 5-BROMOU SUBSTITUTION FROM PSEUDOMONAS AERUGINOSA

Authors :   C. W. Reiss, S. A. Strobel

Date :   19 Apr 17 (Deposition) - 28 Jun 17 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Guanidine, Riboswitch, Kissing Loop, Hairpin, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. W. Reiss, S. A. Strobel
Structural Basis For Ligand Binding To The Guanidine-Ii Riboswitch.
Rna 2017
PubMed-ID: 28600356 | Reference-DOI: 10.1261/RNA.061804.117

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	5BU	4	Mod. Nucleotide	5-BROMO-URIDINE-5'-MONOPHOSPHATE
2	GAI	4	Ligand/Ion	GUANIDINE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SPM	4	Ligand/Ion	SPERMINE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	5BU	2	Mod. Nucleotide	5-BROMO-URIDINE-5'-MONOPHOSPHATE
2	GAI	2	Ligand/Ion	GUANIDINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SPM	2	Ligand/Ion	SPERMINE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	5BU	2	Mod. Nucleotide	5-BROMO-URIDINE-5'-MONOPHOSPHATE
2	GAI	2	Ligand/Ion	GUANIDINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SPM	2	Ligand/Ion	SPERMINE

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G A:6 , A A:7 , C A:8 , G A:9	binding site for residue GAI A 101
02	AC2	SOFTWARE	G A:5 , G A:6 , C A:8 , G A:9 , A A:10 , HOH A:201 , G C:15 , C C:16	binding site for residue SPM A 102
03	AC3	SOFTWARE	G B:6 , A B:7 , C B:8 , G B:9	binding site for residue GAI B 101
04	AC4	SOFTWARE	G B:3 , G B:4 , C B:12 , C B:13 , 5BU B:14	binding site for residue SPM B 102
05	AC5	SOFTWARE	C B:8 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:205	binding site for residue MG B 103
06	AC6	SOFTWARE	G C:6 , A C:7 , C C:8 , G C:9	binding site for residue GAI C 101
07	AC7	SOFTWARE	G A:15 , C A:16 , G C:5 , G C:6 , A C:7 , C C:8 , G C:9	binding site for residue SPM C 102
08	AC8	SOFTWARE	G D:6 , A D:7 , C D:8 , G D:9	binding site for residue GAI D 101
09	AC9	SOFTWARE	G B:5 , G D:5 , G D:6 , C D:8 , G D:9	binding site for residue SPM D 102
10	AD1	SOFTWARE	G B:3 , G B:4 , G B:5 , C B:12 , G B:15 , SPM B:102 , G D:9 , A D:10	binding site for Di-nucleotide C B 13 and 5BU B 14
11	AD2	SOFTWARE	C B:2 , G B:3 , G B:4 , C B:13 , C B:16 , SPM B:102 , G D:3 , G D:4 , G D:9	binding site for Di-nucleotide 5BU B 14 and G B 15
12	AD3	SOFTWARE	G C:3 , G C:4 , G C:5 , C C:12 , G C:15	binding site for Di-nucleotide C C 13 and 5BU C 14
13	AD4	SOFTWARE	G A:5 , G A:6 , SPM A:102 , C C:2 , G C:3 , G C:4 , C C:13 , C C:16	binding site for Di-nucleotide 5BU C 14 and G C 15
14	AD5	SOFTWARE	G D:3 , G D:4 , G D:5 , C D:12 , G D:15	binding site for Di-nucleotide C D 13 and 5BU D 14
15	AD6	SOFTWARE	C B:16 , C D:2 , G D:3 , G D:4 , C D:13 , C D:16	binding site for Di-nucleotide 5BU D 14 and G D 15

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:16
                                               
                  5vjb A  1 GCGGGGACGACCCxGC 16
                                    10   |  
                                        14-5BU

Chain B from PDB  Type:RNA  Length:16
                                               
                  5vjb B  1 GCGGGGACGACCCxGC 16
                                    10   |  
                                        14-5BU

Chain C from PDB  Type:RNA  Length:16
                                               
                  5vjb C  1 GCGGGGACGACCCxGC 16
                                    10   |  
                                        14-5BU

Chain D from PDB  Type:RNA  Length:16
                                               
                  5vjb D  1 GCGGGGACGACCCxGC 16
                                    10   |  
                                        14-5BU

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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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