5NDH - JenaLib

Title :   THE STRUCTURE OF THE G. VIOLACEUS GUANIDINE II RIBOSWITCH P2 STEM-LOOP

Authors :   L. Huang, J. Wang, D. M. J. Lilley

Date :   08 Mar 17 (Deposition) - 31 May 17 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

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

Keywords :   Guanidine Ii Riboswitch, Stem-Loop, Tetra Loop, Dimer, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Huang, J. Wang, D. M. J. Lilley
The Structure Of The Guanidine-Ii Riboswitch.
Cell Chem Biol V. 24 695 2017
PubMed-ID: 28529131 | Reference-DOI: 10.1016/J.CHEMBIOL.2017.05.014

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	CBV	4	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2	GAI	4	Ligand/Ion	GUANIDINE
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NA	4	Ligand/Ion	SODIUM ION
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CBV	2	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2	GAI	2	Ligand/Ion	GUANIDINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CBV	2	Mod. Nucleotide	5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2	GAI	2	Ligand/Ion	GUANIDINE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	2	Ligand/Ion	SULFATE ION

Sites (17, 17)

Asymmetric Unit (17, 17)

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	C A:8 , HOH C:220	binding site for residue NA A 102
03	AC3	SOFTWARE	G A:15 , C A:16 , HOH A:216 , HOH A:218 , G B:4	binding site for residue MG A 103
04	AC4	SOFTWARE	G B:6 , A B:7 , C B:8 , G B:9	binding site for residue GAI B 101
05	AC5	SOFTWARE	CBV B:2 , G B:3 , G B:4	binding site for residue NA B 102
06	AC6	SOFTWARE	G B:1	binding site for residue NA B 103
07	AC7	SOFTWARE	G C:6 , A C:7 , C C:8 , G C:9	binding site for residue GAI C 101
08	AC8	SOFTWARE	C A:11 , C C:8	binding site for residue NA C 102
09	AC9	SOFTWARE	G D:6 , A D:7 , C D:8 , G D:9	binding site for residue GAI D 101
10	AD1	SOFTWARE	A B:10 , G C:4 , G C:5 , A D:10 , HOH D:202 , HOH D:218	binding site for residue SO4 D 102
11	AD2	SOFTWARE	G D:4 , C D:13 , C D:14 , HOH D:205	binding site for residue SO4 D 103
12	AD3	SOFTWARE	G B:3 , G B:15 , C B:16 , NA B:102 , NA B:103 , HOH B:213 , G C:1 , C C:16	binding site for Di-nucleotide G B 1 and CBV B 2
13	AD4	SOFTWARE	G A:15 , HOH A:206 , HOH A:207 , G B:1 , G B:4 , C B:14 , G B:15 , C B:16 , NA B:102 , HOH B:213	binding site for Di-nucleotide CBV B 2 and G B 3
14	AD5	SOFTWARE	G B:1 , C B:16 , G C:3 , G C:15 , C C:16 , HOH C:201 , HOH C:207 , HOH C:213	binding site for Di-nucleotide G C 1 and CBV C 2
15	AD6	SOFTWARE	A B:10 , G C:1 , G C:4 , C C:14 , G C:15 , C C:16 , HOH C:201 , HOH C:212 , HOH C:213	binding site for Di-nucleotide CBV C 2 and G C 3
16	AD7	SOFTWARE	G A:1 , C A:16 , HOH A:211 , G D:3 , G D:15 , C D:16 , HOH D:222	binding site for Di-nucleotide G D 1 and CBV D 2
17	AD8	SOFTWARE	A A:10 , G D:1 , G D:4 , C D:14 , G D:15 , HOH D:208 , HOH D:222	binding site for Di-nucleotide CBV D 2 and G D 3

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
                                               
                  5ndh A  1 GxGGGGACGACCCCGC 16
                             |      10      
                             |              
                             2-CBV

Chain B from PDB  Type:RNA  Length:16
                                               
                  5ndh B  1 GxGGGGACGACCCCGC 16
                             |      10      
                             2-CBV

Chain C from PDB  Type:RNA  Length:16
                                               
                  5ndh C  1 GxGGGGACGACCCCGC 16
                             |      10      
                             2-CBV

Chain D from PDB  Type:RNA  Length:16
                                               
                  5ndh D  1 GxGGGGACGACCCCGC 16
                             |      10      
                             2-CBV

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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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