SMTL ID : 4jzv.1 (1 other biounit)

Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - second guanosine residue in guanosine binding pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GCP- G: RNA (5'-R(*(GCP)P*G)-3')(Non-covalent)

GCP-G.1: 20 residues within 4Å: Chain A: D.6, V.12, H.27, H.43, R.46, G.52, G.53, K.54, E.68, E.72, Y.86, V.88, I.95, K.97, E.115, F.137, I.138, D.141 Ligands: MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.46, A:E.68, A:E.115, A:E.115 Salt bridges: A:H.43, A:R.46

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: G.52, G.53, E.68, E.72, E.115 Ligands: GCP-G.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.52, A:E.72, H2O.2, H2O.2 MG.3: 5 residues within 4Å: Chain A: E.68, E.72, E.115 Ligands: GCP-G.1, MG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.68, A:E.72, A:E.115, H2O.2

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 6 residues within 4Å: Chain A: K.37, E.42, Y.48, L.121, F.122, H.123 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.42, A:L.121, A:H.123 Water bridges: A:E.42 Salt bridges: A:K.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piton, J. et al., Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-08

Peptides

RNA PYROPHOSPHOHYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA PYROPHOSPHOHYDROLASE

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