SMTL ID : 3v9w.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

DT-DT-DA.1: 21 residues within 4Å: Chain A: D.43, V.44, E.45, T.46, F.49, A.94, F.97, N.98, H.140, N.141, F.144, T.182, V.183, L.184, H.201, D.206 Chain B: F.37, H.164, F.166 Ligands: CO.3, MG.7 Protein-ligand interaction information (PLIP) not available DT-DT-DA.2: 21 residues within 4Å: Chain A: 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: CO.5, MG.8 Protein-ligand interaction information (PLIP) not available

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

CO.3: 6 residues within 4Å: Chain A: D.43, E.45, H.201, D.206 Ligands: DT-DT-DA.1, MG.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.45, A:H.201, A:D.206 CO.4: 3 residues within 4Å: Chain A: G.112, A.152, R.155 No protein-ligand interaction detected (PLIP) CO.5: 6 residues within 4Å: Chain B: D.43, E.45, H.201, D.206 Ligands: DT-DT-DA.2, MG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.45, B:E.45, B:H.201, B:D.206 CO.6: 3 residues within 4Å: Chain B: F.85, G.112, R.155 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: D.43, D.145, D.206 Ligands: DT-DT-DA.1, DT-DT-DA.1, CO.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.8: 6 residues within 4Å: Chain B: D.43, D.145, D.206 Ligands: DT-DT-DA.2, DT-DT-DA.2, CO.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.43, H2O.10, H2O.10, H2O.10

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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