5KRG - JenaLib

Title :   RNA 15MER DUPLEX BINDING WITH PZG MONOMER

Authors :   W. Zhang, C. P. Tam, J. W. Szostak

Date :   07 Jul 16 (Deposition) - 07 Dec 16 (Release) - 18 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Zhang, C. P. Tam, J. Wang, J. W. Szostak
Unusual Base-Pairing Interactions In Monomer-Template Complexes.
Acs Cent Sci V. 2 916 2016
PubMed-ID: 28058281 | Reference-DOI: 10.1021/ACSCENTSCI.6B00278

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	LCC	12	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
2	LCG	4	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	PZG	4	Ligand/Ion	[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-(3-METHYL-1~{H}-PYRAZOL-4-YL)PHOSPHINICACID

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	LCC	6	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
2	LCG	2	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	PZG	2	Ligand/Ion	[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-(3-METHYL-1~{H}-PYRAZOL-4-YL)PHOSPHINICACID

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	LCC	6	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
2	LCG	2	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	PZG	2	Ligand/Ion	[(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-6-OXIDANYLIDENE-1~{H}-PURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-(3-METHYL-1~{H}-PYRAZOL-4-YL)PHOSPHINICACID

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LCC A:1 , LCC C:1 , LCC C:2 , G D:15	binding site for residue PZG A 101
2	AC2	SOFTWARE	G A:15 , HOH A:203 , LCC B:1 , LCC B:2 , LCC D:1	binding site for residue PZG A 102
3	AC3	SOFTWARE	LCC A:1 , LCC A:2 , G B:15 , HOH B:102 , LCC C:1	binding site for residue PZG C 101
4	AC4	SOFTWARE	U A:12 , C A:13 , LCC B:1 , G C:15 , LCC D:1 , LCC D:2 , HOH D:203	binding site for residue PZG D 101

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

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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Chain A from PDB  Type:RNA  Length:15
                                              
                  5krg A  1 xxxxACUUAAGUCGG 15
                            ||||    10     
                            ||||           
                            1-LCC          
                             2-LCC         
                              3-LCC        
                               4-LCG

Chain B from PDB  Type:RNA  Length:15
                                              
                  5krg B  1 xxxxACUUAAGUCGG 15
                            ||||    10     
                            1-LCC          
                             2-LCC         
                              3-LCC        
                               4-LCG

Chain C from PDB  Type:RNA  Length:15
                                              
                  5krg C  1 xxxxACUUAAGUCGG 15
                            ||||    10     
                            1-LCC          
                             2-LCC         
                              3-LCC        
                               4-LCG

Chain D from PDB  Type:RNA  Length:15
                                              
                  5krg D  1 xxxxACUUAAGUCGG 15
                            ||||    10     
                            1-LCC          
                             2-LCC         
                              3-LCC        
                               4-LCG

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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