SMTL ID : 4isj.1 (2 other biounits)

RNA Ligase RtcB in complex with Mn(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 10 residues within 4Å: Chain A: K.17, R.23, V.24, P.25, I.56, Y.57, K.58, Y.59, V.339, D.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.58, A:K.17, A:R.23

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

MN.2: 4 residues within 4Å: Chain A: C.98, N.202, H.234, H.329 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.98, A:H.234, A:H.329, H2O.6

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

SO4.3: 7 residues within 4Å: Chain A: D.95, G.199, S.200, H.203, R.238, H.242 Ligands: SO4.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.95, A:S.200, A:R.238 Salt bridges: A:H.203, A:R.238, A:H.242 SO4.4: 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:D.95 Salt bridges: A:K.351 SO4.5: 2 residues within 4Å: Chain A: K.212, R.472 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.212 Salt bridges: A:K.212, A:R.472 SO4.6: 2 residues within 4Å: Chain A: R.366, R.369 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.366, A:R.369 SO4.7: 2 residues within 4Å: Chain A: S.184, Q.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.185 Water bridges: A:V.183 SO4.8: 6 residues within 4Å: Chain A: G.132, R.190, Q.194, R.238, G.239 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.194, A:R.238 Salt bridges: A:R.190 SO4.9: 3 residues within 4Å: Chain A: S.439, M.440, R.441 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.439, A:S.439, A:M.440, A:R.441

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
A

tRNA-splicing ligase RtcB

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