SMTL ID : 7ndj.2 (1 other biounit)

Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x U- U- A- U- A- U: RNA (5'-R(*UP*UP*AP*UP*UP*AP*U)-3')(Non-covalent)

U-U-A-U-A-U.1: 6 residues within 4Å: Chain A: Y.177, C.181, T.182, Y.183, H.185, K.186 Protein-ligand interaction information (PLIP) not available

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: L.4, R.39, H.41, D.158, L.161, R.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.39, A:D.158, A:D.158, A:R.162 EDO.3: 3 residues within 4Å: Chain A: P.145, P.146, D.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.147 Water bridges: A:P.145 EDO.4: 7 residues within 4Å: Chain A: K.30, V.33, D.34, L.37, L.71, E.74, I.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.30, A:K.30, A:E.74 EDO.5: 7 residues within 4Å: Chain A: W.51, R.52, E.54, Q.55, A.60, I.62, Q.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.52 EDO.6: 6 residues within 4Å: Chain A: M.16, E.22, F.24, R.52, A.60, L.61 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.24, A:R.52, A:R.52, A:L.61 Water bridges: A:L.61

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: C.175, C.181, C.187, H.191 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.175, A:C.181, A:C.187, A:H.191

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 7 residues within 4Å: Chain A: A.15, M.16, S.17, H.18, N.20, V.23, S.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.16, A:V.23, A:S.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garg, A. et al., PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases. Nucleic Acids Res. (2021)

Release Date

2021-05-19

Peptides

Probable ribonuclease ZC3H12C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Probable ribonuclease ZC3H12C

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