SMTL ID : 4s2y.2 (1 other biounit)

Structure of E. coli RppH bound to RNA and three magnesium ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x APC- G: RNA (5'-R(*(APC)*GP*U)-3')(Non-covalent)

APC-G.1: 21 residues within 4Å: Chain A: R.9, N.11, R.28, Q.31, S.33, Q.38, G.39, G.40, E.54, E.58, Y.78, L.80, L.84, Q.96, E.121, V.138, F.140, K.141 Ligands: MG.2, MG.3, MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.9, A:N.11, A:Q.38, A:Q.38, A:G.40, A:E.54, A:Q.96 Water bridges: A:R.28, A:Q.35, A:Q.38, A:Q.38, A:R.53, A:R.53, A:E.121, A:E.121, A:E.121 Salt bridges: A:R.9 APC-G.7: 21 residues within 4Å: Chain B: R.9, N.11, R.28, Q.31, S.33, Q.38, G.39, G.40, E.54, E.58, Y.78, L.80, L.84, Q.96, E.121, V.138, F.140, K.141 Ligands: MG.8, MG.9, MG.12 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.9, B:N.11, B:Q.38, B:Q.38, B:G.40, B:E.54, B:Q.96 Water bridges: B:R.28, B:Q.35, B:Q.35, B:Q.38, B:Q.38, B:R.53, B:R.53 Salt bridges: B:R.9

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: E.54, E.57, E.58, E.121 Ligands: APC-G.1, MG.3, MG.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.54, A:E.58, A:E.121, H2O.1, H2O.5 MG.3: 5 residues within 4Å: Chain A: Q.38, E.58, E.121 Ligands: APC-G.1, MG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.38, A:E.58, A:E.121, H2O.1 MG.6: 5 residues within 4Å: Chain A: G.40, R.53, E.54 Ligands: APC-G.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.54, H2O.1, H2O.1, H2O.5, H2O.5 MG.8: 7 residues within 4Å: Chain B: E.54, E.57, E.58, E.121 Ligands: APC-G.7, MG.9, MG.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.54, B:E.58, B:E.121, H2O.5, H2O.9 MG.9: 5 residues within 4Å: Chain B: Q.38, E.58, E.121 Ligands: APC-G.7, MG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.38, B:E.58, B:E.121, H2O.5 MG.12: 5 residues within 4Å: Chain B: G.40, R.53, E.54 Ligands: APC-G.7, MG.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.54, H2O.6, H2O.6, H2O.9, H2O.10

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 6 residues within 4Å: Chain A: R.19, Q.20 Chain B: N.18, R.19, Q.20 Ligands: CL.10 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: N.18, R.19, Q.20 Chain B: R.19, Q.20 Ligands: CL.4 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: S.46, A.47, E.48, F.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.47, A:E.48, A:E.48 Water bridges: A:E.48 SO4.11: 4 residues within 4Å: Chain B: S.46, A.47, E.48, F.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.47, B:E.48 Water bridges: B:E.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vasilyev, N. et al., Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay. J.Biol.Chem. (2015)

Release Date

2015-02-11

Peptides

RNA pyrophosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RNA pyrophosphohydrolase

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