SMTL ID : 6wrq.1

Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) S158C variant bound to 3-nitro-tyrosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: R.223, I.226, K.227, K.288, N.289, A.292, E.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.293 GOL.2: 5 residues within 4Å: Chain A: L.136, M.171, E.172, V.195, K.204 No protein-ligand interaction detected (PLIP) GOL.6: 7 residues within 4Å: Chain B: R.223, I.226, K.227, K.288, N.289, A.292, E.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.293, B:E.293 GOL.7: 5 residues within 4Å: Chain B: L.136, M.171, E.172, V.195, K.204 No protein-ligand interaction detected (PLIP)

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 Water bridges: A:D.27 NA.8: 1 residues within 4Å: Chain B: D.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.27 Water bridges: B:D.27

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

NIY.4: 15 residues within 4Å: Chain A: H.32, G.34, F.35, E.36, L.65, A.67, C.70, Q.109, I.137, Y.151, M.154, Q.155, C.158, Q.173, I.176 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.67, A:Q.155 Hydrogen bonds: A:G.34, A:E.36, A:Q.155, A:Q.173, A:Q.173 Water bridges: A:A.159 NIY.5: 11 residues within 4Å: Chain A: N.74, K.76, E.135, L.136, I.137, A.138, R.139, E.140, S.206, S.208, K.209 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.138, A:E.140, A:S.206, A:S.208, A:S.208 Water bridges: A:E.140 Salt bridges: A:K.209 pi-Cation interactions: A:K.209 NIY.9: 15 residues within 4Å: Chain B: H.32, G.34, F.35, E.36, L.65, A.67, C.70, Q.109, I.137, Y.151, M.154, Q.155, C.158, Q.173, I.176 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.67, B:Q.155 Hydrogen bonds: B:G.34, B:E.36, B:E.36, B:Q.155, B:Q.173, B:Q.173 Water bridges: B:A.159 NIY.10: 11 residues within 4Å: Chain B: N.74, K.76, E.135, L.136, I.137, A.138, R.139, E.140, S.206, S.208, K.209 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.138, B:S.206, B:S.208, B:S.208 Water bridges: B:E.140 Salt bridges: B:K.209 pi-Cation interactions: 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