HL_4Y1M_001

3D structure

PDB id

4Y1M (explore in PDB, NAKB, or RNA 3D Hub)

Description

An Escherichia coli yybP-ykoY Mn riboswitch in the Mn2+-free state

Experimental method

X-RAY DIFFRACTION

Resolution

3 Å

Loop

Sequence

UUGAAAAA

Length

8 nucleotides

Bulged bases

4Y1M|1|A|A|60

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

HL_4Y1M_001 not in the Motif Atlas

Geometric match to HL_5J7L_142

Geometric discrepancy: 0.1812

The information below is about HL_5J7L_142

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_01609.3

Basepair signature

cWW-tWH-F-F-F

Number of instances in this motif group

18

Unit IDs

4Y1M|1|A|U|54
4Y1M|1|A|U|55
4Y1M|1|A|G|56
4Y1M|1|A|A|57
4Y1M|1|A|A|58
4Y1M|1|A|A|59
4Y1M|1|A|A|60
4Y1M|1|A|A|61

Current chains

Chain A

E. coli yybP-ykoY riboswitch

Nearby chains

Chain B

E. coli yybP-ykoY riboswitch