J4_9Q87_004

3D structure

PDB id

9Q87 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+

Experimental method

ELECTRON MICROSCOPY

Resolution

1.55 Å

Loop

Sequence

G(4SU)GG*CGU*AAGGUCG*CC

Length

16 nucleotides

Bulged bases

9Q87|1|Z|4SU|8, 9Q87|1|Z|U|47, 9Q87|1|Z|C|48

QA status

Modified nucleotides: 4SU

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_9Q87_004 not in the Motif Atlas

Homologous match to J4_9DFC_015

Geometric discrepancy: 0.139

The information below is about J4_9DFC_015

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_70449.29

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

54

Unit IDs

9Q87|1|Z|G|7
9Q87|1|Z|4SU|8
9Q87|1|Z|G|9
9Q87|1|Z|G|10
*
9Q87|1|Z|C|25
9Q87|1|Z|G|26
9Q87|1|Z|U|27
*
9Q87|1|Z|A|43
9Q87|1|Z|A|44
9Q87|1|Z|G|45
9Q87|1|Z|G|46
9Q87|1|Z|U|47
9Q87|1|Z|C|48
9Q87|1|Z|G|49
*
9Q87|1|Z|C|65
9Q87|1|Z|C|66

Current chains

Chain Z

P-site tRNA

Nearby chains

Chain A

Small subunit ribosomal RNA; SSU rRNA

Chain M

Small ribosomal subunit protein uS13

Chain a

Large subunit ribosomal RNA; LSU rRNA

Chain l

Large ribosomal subunit protein uL16