SMTL ID : 3bk1.1

Crystal Structure Analysis of RNase J

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.347, H.379, S.381, G.382, H.383 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.347, A:G.382 Water bridges: A:S.347, A:S.347 Salt bridges: A:H.379, A:H.383 SO4.2: 7 residues within 4Å: Chain A: Q.318, P.319, M.320, P.348, I.349, N.352, V.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.318, A:I.349, A:N.352 SO4.3: 2 residues within 4Å: Chain A: R.154, H.193 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.154, A:G.189, A:H.193 Salt bridges: A:R.154, A:H.193 SO4.8: 5 residues within 4Å: Chain B: S.347, H.379, S.381, G.382, H.383 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.347, B:G.382 Water bridges: B:S.347, B:S.347 Salt bridges: B:H.379, B:H.383 SO4.9: 7 residues within 4Å: Chain B: Q.318, P.319, M.320, P.348, I.349, N.352, V.356 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.318, B:I.349, B:N.352 SO4.10: 2 residues within 4Å: Chain B: R.154, H.193 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.154, B:G.189, B:H.193 Salt bridges: B:R.154, B:H.193

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: H.82, H.84, H.87, H.157, D.179 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.82, A:H.84, A:H.157, A:D.179, H2O.4 ZN.5: 6 residues within 4Å: Chain A: N.31, D.86, H.87, D.179, H.405 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.86, A:H.87, A:D.179, A:H.405, H2O.4 ZN.11: 6 residues within 4Å: Chain B: H.82, H.84, H.87, H.157, D.179 Ligands: ZN.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.82, B:H.84, B:H.157, B:D.179, H2O.194 ZN.12: 6 residues within 4Å: Chain B: N.31, D.86, H.87, D.179, H.405 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.86, B:H.87, B:D.179, B:H.405, H2O.194

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.216, Q.386, N.413, L.417 Chain B: Y.376 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.386, A:N.413, A:N.413, B:Y.376 GOL.7: 3 residues within 4Å: Chain A: T.185, M.225, K.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.185, A:K.229 GOL.13: 5 residues within 4Å: Chain A: Y.376 Chain B: E.216, Q.386, N.413, L.417 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.386, B:N.413, B:N.413, A:Y.376 GOL.14: 3 residues within 4Å: Chain B: T.185, M.225, K.229 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.185, B:K.229

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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