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

RNA ligase RtcB in complex with GTP alphaS and Mn(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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.58, A:K.17, A:R.23

1 x GAV: GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE(Non-covalent)

GAV.2: 27 residues within 4Å: Chain A: I.74, D.95, C.98, N.202, H.203, F.204, E.206, Q.208, H.234, H.329, N.330, P.378, G.379, S.380, M.381, G.382, T.383, S.385, H.404, G.405, A.406, G.407, Y.451, V.478, K.480 Ligands: MN.3, MN.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.202, A:N.202, A:Q.208, A:N.330, A:G.379, A:G.379, A:S.380, A:M.381, A:S.385, A:S.385, A:A.406, A:G.407, A:K.480 Water bridges: A:D.95, A:D.95, A:G.352 Salt bridges: A:H.203, A:E.206, A:H.234 pi-Stacking: A:F.204 pi-Cation interactions: A:F.204

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

MN.3: 5 residues within 4Å: Chain A: C.98, H.234, H.329 Ligands: GAV.2, MN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.98, A:H.234, A:H.329 MN.4: 5 residues within 4Å: Chain A: D.95, C.98, H.203 Ligands: GAV.2, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.95, A:C.98, A:H.203

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

SO4.5: 7 residues within 4Å: Chain A: D.95, L.198, G.199, S.200, H.203, T.235, R.238 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.200, A:S.200 Water bridges: A:R.238, A:R.238, A:R.238 Salt bridges: A:H.203, A:R.238 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: 3 residues within 4Å: Chain A: G.341, K.342, R.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.343 Salt bridges: A:R.343 SO4.8: 2 residues within 4Å: Chain A: K.212, R.472 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.212, A:R.472 SO4.9: 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 SO4.10: 2 residues within 4Å: Chain A: R.254, K.258 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.254, A:R.254 Salt bridges: A:R.254, A:K.258 SO4.11: 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 SO4.12: 1 residues within 4Å: Chain A: K.220 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.220 SO4.13: 3 residues within 4Å: Chain A: R.190, Q.194, G.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.194 Water bridges: A:G.132, A:R.238 Salt bridges: A:R.190

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

2013-04-10

Peptides

tRNA-splicing ligase RtcB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

tRNA-splicing ligase RtcB

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