SMTL ID : 2bte.2 (1 other biounit)

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.439, C.442, C.484, C.487 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.439, A:C.442, A:C.484, A:C.487 ZN.2: 4 residues within 4Å: Chain A: C.159, C.162, C.176, H.179 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.159, A:C.162, A:C.176, A:H.179

1 x HG: MERCURY (II) ION(Non-covalent)

HG.3: 3 residues within 4Å: Chain A: Y.102, C.128, E.129 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.128

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

SO4.4: 4 residues within 4Å: Chain A: E.715, G.716, K.717, R.762 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.717 Salt bridges: A:R.762 SO4.5: 4 residues within 4Å: Chain A: G.707, R.769, R.773, W.795 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.707, A:W.795 Salt bridges: A:R.769, A:R.773 SO4.6: 5 residues within 4Å: Chain A: H.49, H.52, S.639, K.640 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.640 Salt bridges: A:H.49, A:H.52 SO4.7: 2 residues within 4Å: Chain A: R.759, P.763 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.759 SO4.8: 3 residues within 4Å: Chain A: R.187, E.188, K.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.188 Salt bridges: A:R.187, A:K.288 SO4.9: 4 residues within 4Å: Chain A: Y.43, S.45, R.178 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.45, A:S.45 Salt bridges: A:R.178 SO4.10: 3 residues within 4Å: Chain A: R.295, K.302, R.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.295 Salt bridges: A:K.302, A:R.346 SO4.11: 3 residues within 4Å: Chain A: E.208, K.217, R.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.208 Salt bridges: A:K.217, A:R.221 SO4.12: 3 residues within 4Å: Chain A: V.564, E.565, E.566 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.565, A:E.566 SO4.13: 5 residues within 4Å: Chain A: E.264, L.329, F.330, G.331, R.420 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.264, A:F.330, A:G.331 Salt bridges: A:R.420 SO4.14: 4 residues within 4Å: Chain A: E.298, G.299, R.300, E.301 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.300, A:E.301 Salt bridges: A:R.300 SO4.15: 1 residues within 4Å: Chain A: R.352 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.352 SO4.16: 3 residues within 4Å: Chain A: R.364, P.370, R.375 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.364, A:R.375

1 x LEU: LEUCINE(Non-covalent)

LEU.17: 10 residues within 4Å: Chain A: M.40, F.41, P.42, Y.43, D.80, S.504, Y.507, Y.535, H.541, H.545 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:F.41, A:Y.507 Hydrogen bonds: A:Y.43, A:D.80 Salt bridges: A:H.541

1 x NVA: NORVALINE(Non-covalent)

NVA.18: 10 residues within 4Å: Chain A: F.246, T.247, R.249, T.252, M.338, V.340, H.343, D.344, D.347 Ligands: 2AD.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.249, A:D.344 Hydrogen bonds: A:T.247, A:M.338, A:V.340, A:D.344

1 x 2AD: 2'-AMINO-2'-DEOXYADENOSINE(Non-covalent)

2AD.19: 11 residues within 4Å: Chain A: S.227, F.246, T.247, T.248, V.328, L.329, Y.332, I.337, R.346 Chain B: C.81 Ligands: NVA.18 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.227, A:S.227, A:T.247, A:T.248, A:T.248, A:L.329, A:L.329, A:Y.332, A:R.346 pi-Stacking: A:Y.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tukalo, M. et al., The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer- Editing Conformation. Nat.Struct.Mol.Biol. (2005)

Release Date

2005-09-15

Peptides

AMINOACYL-TRNA SYNTHETASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

AMINOACYL-TRNA SYNTHETASE

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