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

THERMUS THERMOPHILUS LEUCYL-TRNA SYNTHETASE COMPLEXED WITH 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

1 x LEU: LEUCINE(Non-covalent)

LEU.1: 11 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 Ligands: SO4.10 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.41, A:Y.507, A:H.545 Hydrogen bonds: A:Y.43, A:D.80, A:D.80 Salt bridges: A:H.541

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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.4: 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

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

SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: G.707, R.769, R.773, W.795 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.706, A:G.707, A:W.795 Salt bridges: A:R.769, A:R.773 SO4.7: 4 residues within 4Å: Chain A: H.49, H.52, S.639, K.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.640 Salt bridges: A:H.49, A:H.52 SO4.8: 1 residues within 4Å: Chain A: R.759 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.759 SO4.9: 4 residues within 4Å: Chain A: R.187, E.188, K.288, R.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.188 Salt bridges: A:K.288, A:R.289 SO4.10: 4 residues within 4Å: Chain A: Y.43, S.45, R.178 Ligands: LEU.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.45 Salt bridges: A:R.178 SO4.11: 4 residues within 4Å: Chain A: R.295, K.302, Y.327, R.346 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.295, A:K.302, A:R.346 SO4.12: 4 residues within 4Å: Chain A: L.207, 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 SO4.13: 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 SO4.14: 6 residues within 4Å: Chain A: K.186, E.264, L.329, F.330, G.331, R.420 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.264, A:F.330, A:G.331 Salt bridges: A:K.186, A:R.420 SO4.15: 3 residues within 4Å: Chain A: A.636, V.637, K.642 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.637 Salt bridges: A:K.634, A:K.642 SO4.16: 6 residues within 4Å: Chain A: H.438, E.474, K.492, R.493, D.494, T.495 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.494, A:T.495 Salt bridges: A:H.438, A:K.492

1 x NVA: NORVALINE(Non-covalent)

NVA.17: 9 residues within 4Å: Chain A: F.246, T.247, R.249, T.252, M.338, H.343, D.344, D.347 Ligands: 2AD.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.249, A:R.249 Hydrogen bonds: A:T.247, A:M.338

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

2AD.18: 12 residues within 4Å: Chain A: S.227, F.246, T.247, T.248, V.328, L.329, Y.332, G.335, I.337, R.346 Chain B: C.81 Ligands: NVA.17 9 PLIP interactions: 9 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:G.335, A:R.346

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
A

AMINOACYL-TRNA SYNTHETASE

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