2GPM | UR0085 - JenaLib

Title :   CRYSTAL STRUCTURE OF AN RNA RACEMATE

Authors :   W. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, C. Betzel, V. A.

Date :   18 Apr 06 (Deposition) - 27 Jun 06 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : K,L,M,N  (2x)
Biol. Unit 1: K,L  (1x)
Biol. Unit 2: M,N  (1x)

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

Reference :   W. Rypniewski, M. Vallazza, M. Perbandt, S. Klussmann, L. J. Delucas, C. Betzel, V. A. Erdmann
The First Crystal Structure Of An Rna Racemate.
Acta Crystallogr. , Sect. D V. 62 659 2006
PubMed-ID: 16699193 | Reference-DOI: 10.1107/S090744490601359X

Compounds

*Molecule 1 - RNA (5'-R((0C)P(0U)P(0G)P(0G)P(0G)P(0C)P(0G)P(0G))- 3')*
	Chains	:	K, M
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE IS A 'SPIEGELMER' AND OCCURS IN 5S RNA FROM THERMUS FLAVUS
	Synthetic	:	YES

*Molecule 2 - RNA (5'-R((0C)P(0C)P(0G)P(0C)P(0C)P(0U)P(0G)P(0G))- 3')*
	Chains	:	L, N
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE IS A 'SPIEGELMER' AND OCCURS IN 5S RNA FROM THERMUS FLAVUS
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 38)

Asymmetric Unit (4, 38)

No.	Name	Count	Type	Full Name
1	0C	12	Mod. Residue	L-CYTIDINE-5'-MONOPHOSPHATE
2	0G	16	Mod. Residue	L-GUANOSINE-5'-MONOPHOSPHATE
3	0U	4	Mod. Residue	L-URIDINE-5'-MONOPHOSPHATE
4	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	0C	-1	Mod. Residue	L-CYTIDINE-5'-MONOPHOSPHATE
2	0G	-1	Mod. Residue	L-GUANOSINE-5'-MONOPHOSPHATE
3	0U	-1	Mod. Residue	L-URIDINE-5'-MONOPHOSPHATE
4	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	0C	-1	Mod. Residue	L-CYTIDINE-5'-MONOPHOSPHATE
2	0G	-1	Mod. Residue	L-GUANOSINE-5'-MONOPHOSPHATE
3	0U	-1	Mod. Residue	L-URIDINE-5'-MONOPHOSPHATE
4	CA	-1	Ligand/Ion	CALCIUM ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	0G L:97 , HOH L:336 , HOH L:355 , HOH L:362 , HOH M:336 , HOH M:342	BINDING SITE FOR RESIDUE CA L 310
2	AC2	SOFTWARE	HOH L:323 , 0G M:86 , HOH M:319 , HOH M:326 , HOH M:327 , HOH M:330 , HOH M:345	BINDING SITE FOR RESIDUE CA M 308
3	AC3	SOFTWARE	0G M:82 , HOH M:321 , HOH M:328 , HOH M:337 , HOH M:364	BINDING SITE FOR RESIDUE CA M 311
4	AC4	SOFTWARE	CA N:304 , HOH N:307 , HOH N:310 , HOH N:319 , HOH N:322 , HOH N:327 , HOH N:334 , HOH N:347	BINDING SITE FOR RESIDUE CA N 302
5	AC5	SOFTWARE	0G N:96 , CA N:302 , HOH N:310 , HOH N:319 , HOH N:324 , HOH N:327 , HOH N:345 , HOH N:350	BINDING SITE FOR RESIDUE CA N 304
6	AC6	SOFTWARE	HOH K:95 , 0G N:97 , HOH N:318 , HOH N:321 , HOH N:323 , HOH N:328 , HOH N:331	BINDING SITE FOR RESIDUE CA N 306

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 K from PDB  Type:OTHER  Length:8
                                       
                  2gpm K 79 xxxxxxxx 86
                            ||||||||
                            ||||||||
                           79-0C||||
                            80-0U|||
                             81-0G||
                              82-0G|
                               83-0G
                                84-0C
                                 85-0G
                                  86-0G

Chain L from PDB  Type:OTHER  Length:8
                                       
                  2gpm L 90 xxxxxxxx 97
                            ||||||||
                            ||||||||
                           90-0C||||
                            91-0C|||
                             92-0G||
                              93-0C|
                               94-0C
                                95-0U
                                 96-0G
                                  97-0G

Chain M from PDB  Type:OTHER  Length:8
                                       
                  2gpm M 79 xxxxxxxx 86
                            ||||||||
                            ||||||||
                           79-0C||||
                            80-0U|||
                             81-0G||
                              82-0G|
                               83-0G
                                84-0C
                                 85-0G
                                  86-0G

Chain N from PDB  Type:OTHER  Length:8
                                       
                  2gpm N 90 xxxxxxxx 97
                            ||||||||
                            ||||||||
                           90-0C||||
                            91-0C|||
                             92-0G||
                              93-0C|
                               94-0C
                                95-0U
                                 96-0G
                                  97-0G

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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)

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Pfam Domains (0, 0)

Gene Ontology (0, 0)

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