SMTL ID : 4it0.2 (1 other biounit)

Structure of the RNA ligase RtcB-GMP/Mn(II) complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 9 residues within 4Å: Chain A: K.17, R.23, V.24, P.25, Y.57, K.58, Y.59, V.339, D.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.58, A:K.58, A:K.17 Water bridges: A:D.340

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

MN.2: 6 residues within 4Å: Chain A: C.98, N.202, H.234, H.329, H.404 Ligands: MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.98, A:H.234, A:H.329, H2O.9 MN.3: 6 residues within 4Å: Chain A: D.95, C.98, N.202, H.203, G.236 Ligands: MN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:C.98, A:H.203, H2O.6

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

SO4.4: 5 residues within 4Å: Chain A: D.95, G.199, S.200, H.203, R.238 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.198, A:S.200 Water bridges: A:R.238, A:R.238, A:G.239, A:G.239 Salt bridges: A:H.203, A:R.238 SO4.5: 2 residues within 4Å: Chain A: R.366, R.369 7 PLIP interactions: 7 interactions with chain A Water bridges: A:E.362, A:R.366, A:R.366, A:R.369, A:R.369 Salt bridges: A:R.366, A:R.369 SO4.6: 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 SO4.7: 3 residues within 4Å: Chain A: S.411, R.412, K.413 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.412, A:K.413 Salt bridges: A:R.412, A:K.413 SO4.8: 6 residues within 4Å: Chain A: G.69, Y.70, I.74, G.93, Y.94, K.351 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.70, A:Y.94 Water bridges: A:N.330 Salt bridges: A:K.351 SO4.9: 4 residues within 4Å: Chain A: R.23, P.54, G.55, I.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.55, A:I.56 Salt bridges: A:R.23 SO4.10: 2 residues within 4Å: Chain A: R.254, K.258 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.254, A:R.254, A:R.254, A:R.254, A:R.254 Salt bridges: A:K.258 SO4.11: 3 residues within 4Å: Chain A: S.439, M.440, R.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.440, A:R.441 SO4.12: 2 residues within 4Å: Chain A: K.342, R.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.343 Salt bridges: A:R.343 SO4.13: 1 residues within 4Å: Chain A: K.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.220, A:K.220 Salt bridges: A:K.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desai, K.K. et al., Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation. Biochemistry (2013)

Release Date

2013-03-20

Peptides

tRNA-splicing ligase RtcB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

tRNA-splicing ligase RtcB

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