SMTL ID : 4dwr.3 (2 other biounits)

RNA ligase RtcB/Mn2+ complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain A: K.17, R.23, V.24, P.25, Y.57, K.58, V.339, D.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.58, A:K.17, A:R.23 Water bridges: A:K.17, A:I.56, A:D.340, A:K.17, A:K.17

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: C.98, H.234, H.329 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.98, A:H.234, A:H.329, H2O.1, H2O.2, H2O.9 MN.3: 4 residues within 4Å: Chain A: D.95, C.98, H.203 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.95, A:C.98, A:H.203

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

SO4.4: 6 residues within 4Å: Chain A: G.69, Y.70, I.74, G.93, Y.94, K.351 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.70, A:Y.94 Water bridges: A:D.95, A:N.330, A:N.330 Salt bridges: A:K.351 SO4.5: 7 residues within 4Å: Chain A: D.95, L.198, G.199, S.200, H.203, R.238, G.239 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.198, A:S.200, A:R.238 Water bridges: A:S.200, A:R.238, A:R.238, A:G.239, A:G.239 Salt bridges: A:H.203, A:R.238 SO4.6: 3 residues within 4Å: Chain A: Y.259, S.275, E.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.259, A:E.276 SO4.7: 2 residues within 4Å: Chain A: R.366, R.369 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.366, A:R.366, A:R.369 Salt bridges: A:R.366, A:R.369 SO4.8: 5 residues within 4Å: Chain A: D.95, C.98, H.203, N.330 Ligands: MN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.330 Water bridges: A:D.95, A:R.412 Salt bridges: A:H.203 SO4.9: 2 residues within 4Å: Chain A: K.212, R.472 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.472 Salt bridges: A:K.212, A:R.472 SO4.10: 2 residues within 4Å: Chain A: S.411, R.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.412 Water bridges: A:K.413 Salt bridges: A:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Englert, M. et al., Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-09-05

Peptides

tRNA-splicing ligase RtcB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

tRNA-splicing ligase RtcB

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