SMTL ID : 6wrk.1

Crystal structure of 3rd-generation Mj 3-nitro-tyrosine tRNA synthetase ("A7") bound to 3-nitro-tyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.223, I.226, K.227, M.285, K.288, N.289, A.292, E.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.223, A:N.289 GOL.2: 4 residues within 4Å: Chain A: L.136, M.171, V.195, K.204 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.195 GOL.6: 5 residues within 4Å: Chain A: E.94, A.95, G.97, L.98, K.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.94 Water bridges: A:E.94 GOL.7: 8 residues within 4Å: Chain B: R.223, I.226, K.227, M.285, K.288, N.289, A.292, E.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.223, B:N.289, B:E.293 GOL.8: 4 residues within 4Å: Chain B: L.136, M.171, V.195, K.204 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.195 GOL.12: 5 residues within 4Å: Chain B: E.94, A.95, G.97, L.98, K.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.94 Water bridges: B:E.94, B:E.94

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: D.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.27 NA.9: 1 residues within 4Å: Chain B: D.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.27

4 x NIY: META-NITRO-TYROSINE(Non-covalent)

NIY.4: 13 residues within 4Å: Chain A: G.34, F.35, E.36, L.65, A.67, T.70, Q.109, I.137, Y.151, M.154, Q.155, H.158, Q.173 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.67, A:Q.155 Hydrogen bonds: A:G.34, A:E.36, A:Y.151, A:Q.155, A:Q.155, A:H.158, A:Q.173 Water bridges: A:H.32 NIY.5: 11 residues within 4Å: Chain A: K.76, E.135, L.136, I.137, A.138, R.139, E.140, K.204, S.206, S.208, K.209 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.135, A:E.140, A:S.206, A:S.208, A:S.208 Salt bridges: A:K.209 NIY.10: 13 residues within 4Å: Chain B: G.34, F.35, E.36, L.65, A.67, T.70, Q.109, I.137, Y.151, M.154, Q.155, H.158, Q.173 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.67, B:Q.155 Hydrogen bonds: B:G.34, B:E.36, B:Y.151, B:Q.155, B:Q.155, B:H.158, B:Q.173 Water bridges: B:H.32 NIY.11: 11 residues within 4Å: Chain B: K.76, E.135, L.136, I.137, A.138, R.139, E.140, K.204, S.206, S.208, K.209 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.135, B:S.206, B:S.208, B:S.208 Salt bridges: B:K.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beyer, J.N. et al., Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase. J.Mol.Biol. (2020)

Release Date

2020-07-01

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosine--tRNA ligase