SMTL ID : 4e2x.1

X-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and dTDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.18, A:C.56, A:C.59

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: L.95, D.98, F.99, Q.251, R.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.251, A:R.261 EDO.3: 3 residues within 4Å: Chain A: R.166, G.170, P.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.166, A:R.166 Water bridges: A:G.170 EDO.4: 8 residues within 4Å: Chain A: R.320, S.321, V.322, P.342, D.343, L.344, V.345, H.346 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.322, A:V.322 EDO.5: 3 residues within 4Å: Chain A: E.24, F.25, D.27 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.24, A:E.24, A:D.27 Water bridges: A:D.27, A:D.27, A:R.50

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.6: 20 residues within 4Å: Chain A: F.74, Y.78, Y.80, S.82, F.92, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:N.117 Hydrogen bonds: A:E.113, A:N.117, A:S.138, A:S.138, A:F.157, A:F.157, A:A.178, A:A.178, A:N.179, A:Y.186 Water bridges: A:Y.80, A:A.178 pi-Stacking: A:F.74

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.7: 18 residues within 4Å: Chain A: Y.80, H.256, Y.325, G.326, A.327, T.328, A.329, K.330, D.350, T.351, T.352, K.355, A.385, N.387, H.388, E.391, I.392, K.395 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:H.388, A:I.392 Hydrogen bonds: A:A.329, A:K.330, A:T.351, A:T.352, A:K.355, A:N.387, A:N.387, A:K.395 Water bridges: A:H.256, A:H.256, A:Y.325, A:Y.325, A:K.355 Salt bridges: A:H.256, A:K.330, A:K.330, A:K.355, A:H.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bruender, N.A. et al., Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose. Protein Sci. (2012)

Release Date

2012-04-25

Peptides

TcaB9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TcaB9