J4_5D8B_025

3D structure

PDB id

5D8B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch

Experimental method

X-RAY DIFFRACTION

Resolution

3.63 Å

Loop

Sequence

CGAUAAA*UC*GCGC*GG

Length

15 nucleotides

Bulged bases

5D8B|1|ZC|G|1271, 5D8B|1|ZC|A|1272, 5D8B|1|ZC|U|1273, 5D8B|1|ZC|A|1275, 5D8B|1|ZC|G|1647

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

J4_5D8B_025 not in the Motif Atlas

Homologous match to J4_9DFE_003

Geometric discrepancy: 0.1148

The information below is about J4_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_64571.6

Basepair signature

cWW-F-cWW-tSS-cWW-F-cWW

Number of instances in this motif group

4

Unit IDs

5D8B|1|ZC|C|1270
5D8B|1|ZC|G|1271
5D8B|1|ZC|A|1272
5D8B|1|ZC|U|1273
5D8B|1|ZC|A|1274
5D8B|1|ZC|A|1275
5D8B|1|ZC|A|1276
*
5D8B|1|ZC|U|1294
5D8B|1|ZC|C|1295
*
5D8B|1|ZC|G|1645
5D8B|1|ZC|C|1646
5D8B|1|ZC|G|1647
5D8B|1|ZC|C|1648
*
5D8B|1|ZC|G|2009
5D8B|1|ZC|G|2010

Current chains

Chain ZC

23S ribosomal RNA

Nearby chains

Chain HB

50S ribosomal protein L17

Chain MB

50S ribosomal protein L22

Chain UB

50S ribosomal protein L32