HL_5DH7_002

3D structure

PDB id

5DH7 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mn2+

Experimental method

X-RAY DIFFRACTION

Resolution

3.06 Å

Loop

Sequence

CUGGGAUG

Length

8 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

HL_5DH7_002 not in the Motif Atlas

Geometric match to HL_5DH6_002

Geometric discrepancy: 0.0637

The information below is about HL_5DH6_002

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_13999.4

Basepair signature

cWW-tWH-F-F-F

Number of instances in this motif group

24

Unit IDs

5DH7|1|A|C|27
5DH7|1|A|U|28
5DH7|1|A|G|29
5DH7|1|A|G|30
5DH7|1|A|G|31
5DH7|1|A|A|32
5DH7|1|A|U|33
5DH7|1|A|G|34

Current chains

Chain A

RNA (48-MER)

Nearby chains

Chain B

5'-R(*GP*GP*GP*CP*GP*UP*DC*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'