SMTL ID : 5elh.1

Crystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bound to RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

U-U-A-U-U.1: 19 residues within 4Å: Chain B: D.86, R.89, R.90, Y.91, Y.95, Y.96, K.97, T.98, G.99, I.100, C.101, I.102, H.103, N.114, H.117, C.118, A.119, F.120 Ligands: SO4.10 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.16, F.19, C.24, C.32, H.36 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.16, A:C.24, A:C.32, A:H.36 ZN.3: 5 residues within 4Å: Chain A: C.61, Y.64, C.71, C.77, H.81 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.71, A:C.77, A:H.81 ZN.4: 7 residues within 4Å: Chain A: C.101, H.103, C.111, N.114, C.118, F.120, H.122 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.101, A:C.111, A:C.118, A:H.122 ZN.6: 5 residues within 4Å: Chain B: C.16, F.19, C.24, C.32, H.36 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.16, B:C.24, B:C.32, B:H.36 ZN.7: 5 residues within 4Å: Chain B: C.61, Y.64, C.71, C.77, H.81 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:C.71, B:C.77, B:H.81 ZN.8: 7 residues within 4Å: Chain B: C.101, H.103, C.111, N.114, C.118, F.120, H.122 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.101, B:C.111, B:C.118, B:H.122

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: R.48, R.49 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.49 Water bridges: A:R.48, A:R.48, A:D.50 Salt bridges: A:R.48, A:R.49 SO4.9: 3 residues within 4Å: Chain B: R.48, R.49, D.50 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.49, B:D.50, B:D.50 Water bridges: B:R.49 Salt bridges: B:R.49 SO4.10: 3 residues within 4Å: Chain B: G.85, R.90 Ligands: U-U-A-U-U.1 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.90, B:R.90 Salt bridges: B:R.90 SO4.11: 3 residues within 4Å: Chain B: Y.5, K.9, R.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.5 Salt bridges: B:K.9, B:R.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murn, J. et al., Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nat.Struct.Mol.Biol. (2016)

Release Date

2015-12-09

Peptides

RING finger protein unkempt homolog: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RING finger protein unkempt homolog