SMTL ID : 3va0.1

Crystal structure of RNase T in complex with a di-nucleotide product (GG) with one Mg in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x DG- DG: DNA (5'-D(*GP*G)-3')(Non-covalent)

DG-DG.1: 11 residues within 4Å: Chain A: E.45, T.46, G.48, F.49, Q.91, E.93, A.94, F.97, N.98, F.144 Chain B: F.166 Protein-ligand interaction information (PLIP) not available DG-DG.2: 13 residues within 4Å: Chain A: F.166 Chain B: E.45, T.46, G.48, F.49, Q.91, E.93, A.94, F.97, N.98, N.141, F.144 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.43, D.145 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.43, H2O.1, H2O.1, H2O.1, H2O.17, H2O.17 MG.4: 3 residues within 4Å: Chain B: D.43, D.145 Ligands: DG-DG.2 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.43, H2O.8, H2O.8, H2O.9, H2O.9, H2O.17

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

CO.5: 2 residues within 4Å: Chain B: 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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