2X2Q - JenaLib

Title :   CRYSTAL STRUCTURE OF AN 'ALL LOCKED' LNA DUPLEX AT 1.9 ANGSTROM RESOLUTION

Authors :   A. Eichert, K. Behling, J. P. Fuerste, C. Betzel, V. A. Erdmann, C. Foers

Date :   15 Jan 10 (Deposition) - 16 Feb 11 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Dna, Modified Nucleic Acid, Locked Nucleic Acid, Thermostability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Eichert, K. Behling, C. Betzel, V. A. Erdmann, J. P. Furste, C. Forster
The Crystal Structure Of An 'All Locked' Nucleic Acid Duplex.
Nucleic Acids Res. V. 38 6729 2010
PubMed-ID: 20530536 | Reference-DOI: 10.1093/NAR/GKQ505

Compounds

Molecule 1 - LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
	Chains	:	A, C
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Molecule 2 - LOCKED NUCLEIC ACID DERIVED FROM TRNA SER ACCEPTOR STEM MICROHELIX
	Chains	:	B, D
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 31)

Asymmetric Unit (7, 31)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	LCA	4	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	LCC	10	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4	LCG	10	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5	MG	1	Ligand/Ion	MAGNESIUM ION
6	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)
7	TLN	4	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE

Biological Unit 1 (5, 15)

No.	Name	Count	Type	Full Name
1	CAC	-1	Ligand/Ion	CACODYLATE ION
2	LCA	2	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	LCC	5	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4	LCG	5	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)
7	TLN	2	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE

Biological Unit 2 (5, 15)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	LCA	2	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3	LCC	5	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4	LCG	5	Mod. Nucleotide	[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NCO	-1	Ligand/Ion	COBALT HEXAMMINE(III)
7	TLN	2	OTHER	[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LCG B:6 , LCG B:7 , HOH B:210 , HOH B:216 , LCG D:6 , LCG D:7 , HOH D:212 , HOH D:213	binding site for residue NCO B 101
2	AC2	SOFTWARE	LCC C:72 , HOH C:201 , HOH C:207	binding site for residue MG C 101
3	AC3	SOFTWARE	LCG B:1 , LCG B:2 , HOH D:203	binding site for residue CAC D 101
4	AC4	SOFTWARE	TLN A:68 , HOH A:103 , HOH A:108 , LCG B:6 , LCG B:7 , LCC C:66 , LCG D:7 , HOH D:209	binding site for residues LCC A 66 and LCC A 67
5	AC5	SOFTWARE	LCA A:70 , HOH A:101 , HOH A:102 , HOH A:104 , HOH A:106 , HOH A:110 , HOH A:113 , HOH A:114 , LCG B:1 , LCG B:2 , TLN B:3 , LCG D:1	binding site for residues LCC A 71 and LCC A 72
6	AC6	SOFTWARE	LCC A:66 , LCG B:7 , TLN C:68 , HOH C:210 , LCG D:6 , LCG D:7	binding site for residues LCC C 66 and LCC C 67
7	AC7	SOFTWARE	LCG B:1 , LCA C:70 , MG C:101 , HOH C:201 , HOH C:203 , HOH C:205 , HOH C:206 , HOH C:207 , HOH C:209 , LCG D:1 , LCG D:2 , TLN D:3 , HOH D:201	binding site for residues LCC C 71 and LCC C 72

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:OTHER/RNA  Length:7
                                      
                  2x2q A 66 xxxxaxx 72
                            |||||||
                            |||||||
                           66-LCC||
                            67-LCC|
                             68-TLN
                              69-LCC
                               70-LCA
                                71-LCC
                                 72-LCC

Chain B from PDB  Type:OTHER/RNA  Length:7
                                      
                  2x2q B  1 ggxgagg  7
                            |||||||
                            |||||||
                            1-LCG||
                             2-LCG|
                              3-TLN
                               4-LCG
                                5-LCA
                                 6-LCG
                                  7-LCG

Chain C from PDB  Type:OTHER/RNA  Length:7
                                      
                  2x2q C 66 xxxxaxx 72
                            |||||||
                            |||||||
                           66-LCC||
                            67-LCC|
                             68-TLN
                              69-LCC
                               70-LCA
                                71-LCC
                                 72-LCC

Chain D from PDB  Type:OTHER/RNA  Length:7
                                      
                  2x2q D  1 ggxgagg  7
                            |||||||
                            |||||||
                            1-LCG||
                             2-LCG|
                              3-TLN
                               4-LCG
                                5-LCA
                                 6-LCG
                                  7-LCG

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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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