SMTL ID : 3v9s.1

Crystal structure of RNase T in complex with a product ssDNA (AAC) with one Mg in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x DA- DA- DC: DNA (5'-D(*TP*TP*AP*CP*AP*AP*C)-3')(Non-covalent)

DA-DA-DC.1: 17 residues within 4Å: Chain A: E.45, T.46, F.49, E.93, A.94, F.97, N.98, H.140, N.141, F.144, T.182, V.183, L.184 Chain B: R.35, H.164, F.166 Ligands: MG.3 Protein-ligand interaction information (PLIP) not available DA-DA-DC.2: 21 residues within 4Å: Chain A: R.35, F.37, H.164, F.166 Chain B: V.44, E.45, T.46, G.48, F.49, E.93, A.94, F.97, N.98, H.140, N.141, F.144, T.182, V.183, L.184, K.186 Ligands: MG.5 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.43, V.44 Ligands: DA-DA-DC.1, DA-DA-DC.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, H2O.1, H2O.3, H2O.4 MG.5: 6 residues within 4Å: Chain B: D.43, V.44, E.45, D.206 Ligands: DA-DA-DC.2, DA-DA-DC.2 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.43, H2O.12, H2O.16

1 x CO: COBALT (II) ION(Non-covalent)

CO.4: 2 residues within 4Å: Chain A: H.81, R.107 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsiao, Y.-Y. et al., How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes. Nucleic Acids Res. (2012)

Release Date

2012-07-11

Peptides

Ribonuclease T: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease T

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