SMTL ID : 3v9x.2 (1 other biounit)

Crystal structure of RNase T in complex with a preferred ssDNA (AAA) with two Mg in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

DA-DA-DA.1: 23 residues within 4Å: Chain A: D.43, V.44, 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, H.201, D.206 Chain B: R.35, F.37, H.164, F.166 Ligands: MG.3, MG.5 Protein-ligand interaction information (PLIP) not available DA-DA-DA.2: 23 residues within 4Å: Chain A: R.35, F.37, H.164, F.166 Chain B: D.43, V.44, 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, H.201, D.206 Ligands: MG.4, MG.6 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.43, E.45, D.206 Ligands: DA-DA-DA.1, MG.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.43, A:D.43, A:E.45, A:D.206 MG.4: 6 residues within 4Å: Chain B: D.43, E.45, H.201, D.206 Ligands: DA-DA-DA.2, MG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.45, B:D.206 MG.5: 4 residues within 4Å: Chain A: D.43 Ligands: DA-DA-DA.1, DA-DA-DA.1, MG.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, H2O.1, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.43, D.145 Ligands: DA-DA-DA.2, DA-DA-DA.2, MG.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.43, H2O.5, H2O.6, H2O.6

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
C

B
D

Ribonuclease T

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