SMTL ID : 3bk2.1

Crystal Structure Analysis of the RNase J/UMP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.154, H.193 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.154, A:H.193 SO4.8: 3 residues within 4Å: Chain B: R.154, H.193 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.154, B:H.193

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.82, H.84, H.87, H.157, D.179 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.82, A:H.84, A:H.157, A:D.179 ZN.3: 6 residues within 4Å: Chain A: N.31, D.86, H.87, D.179, H.405 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.86, A:H.87, A:D.179, A:H.405 ZN.9: 6 residues within 4Å: Chain B: H.82, H.84, H.87, H.157, D.179 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.82, B:H.84, B:H.157, B:D.179 ZN.10: 6 residues within 4Å: Chain B: N.31, D.86, H.87, D.179, H.405 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.86, B:H.87, B:D.179, B:H.405

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.4: 13 residues within 4Å: Chain A: I.28, E.85, D.86, F.247, H.250, S.347, P.348, I.349, P.350, H.379, S.381, G.382, H.383 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.85, A:S.347, A:P.348, A:G.382 Water bridges: A:S.158, A:H.250, A:S.347, A:S.347, A:S.381 Salt bridges: A:H.379, A:H.383 pi-Stacking: A:F.247 U5P.11: 13 residues within 4Å: Chain B: I.28, E.85, D.86, F.247, H.250, S.347, P.348, I.349, P.350, H.379, S.381, G.382, H.383 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.85, B:S.347, B:P.348, B:G.382 Water bridges: B:S.158, B:H.250, B:S.347, B:S.347, B:S.381 Salt bridges: B:H.379, B:H.383 pi-Stacking: B:F.247

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: A.215, Q.386, N.413 Chain B: Y.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.386, A:N.413, A:N.413 GOL.6: 5 residues within 4Å: Chain A: M.225, K.229, D.232, W.259, K.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.232 GOL.7: 2 residues within 4Å: Chain A: H.193 Ligands: SO4.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.139 GOL.12: 4 residues within 4Å: Chain A: Y.376 Chain B: A.215, Q.386, N.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.386, B:N.413, B:N.413 GOL.13: 5 residues within 4Å: Chain B: M.225, K.229, D.232, W.259, K.263 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.232 GOL.14: 2 residues within 4Å: Chain B: H.193 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de la Sierra-Gallay, I.L. et al., Structural insights into the dual activity of RNase J. Nat.Struct.Mol.Biol. (2008)

Release Date

2008-01-22

Peptides

Metal dependent hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Metal dependent hydrolase

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