J4_5EAQ_001

3D structure

PDB id

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

Description

Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+

Experimental method

X-RAY DIFFRACTION

Resolution

3.2 Å

Loop

Sequence

AC*GAG*CGAAA*U(CVC)U

Length

13 nucleotides

Bulged bases

None detected

QA status

Modified nucleotides: CVC

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_5EAQ_001 not in the Motif Atlas

Homologous match to J4_5DH6_001

Geometric discrepancy: 0.2439

The information below is about J4_5DH6_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

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

Current chains

Chain A

RNA (48-MER)

Chain B

RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')

Nearby chains