J4_5DQK_001

3D structure

PDB id

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

Description

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+

Experimental method

X-RAY DIFFRACTION

Resolution

2.71 Å

Loop

Sequence

AC*GAG*CGAAA*UCU

Length

13 nucleotides

Bulged bases

None detected

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_5DQK_001 not in the Motif Atlas

Homologous match to J4_2QUS_001

Geometric discrepancy: 0.158

The information below is about J4_2QUS_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_95838.1

Basepair signature

cWW-F-F-cWW-F-F-cWW-cWW-F

Number of instances in this motif group

2

Unit IDs

5DQK|1|A|A|15
5DQK|1|A|C|16
*
5DQK|1|A|G|21
5DQK|1|A|A|22
5DQK|1|A|G|23
*
5DQK|1|A|C|38
5DQK|1|A|G|39
5DQK|1|A|A|40
5DQK|1|A|A|41
5DQK|1|A|A|42
*
5DQK|1|B|U|6
5DQK|1|B|DC|7
5DQK|1|B|U|8

Current chains

Chain A

RNA (48-MER)

Chain B

RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')

Nearby chains