SMTL ID : 8dc9.2 (1 other biounit)

RNA ligase RtcB from Pyrococcus horikoshii in complex with Mn2+ and GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 7 residues within 4Å: Chain A: K.37, R.43, P.45, Y.77, K.78, V.359, D.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.78, A:D.360, A:K.37

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 25 residues within 4Å: Chain A: D.115, C.118, N.222, H.223, F.224, E.226, Q.228, H.254, H.349, N.350, P.398, G.399, S.400, M.401, S.405, H.424, G.425, A.426, G.427, E.466, Y.471, K.500 Ligands: SO4.4, MN.11, MN.12 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.222, A:N.222, A:Q.228, A:N.350, A:G.399, A:S.405, A:A.426, A:G.427, A:E.466, A:K.500 Water bridges: A:D.115, A:R.428 Salt bridges: A:H.223, A:E.226, A:H.254, A:H.254, A:H.349, A:H.424 pi-Stacking: A:F.224, A:Y.471

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

SO4.3: 6 residues within 4Å: Chain A: D.115, L.218, G.219, S.220, H.223, R.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.220 Water bridges: A:R.258, A:R.258 Salt bridges: A:H.223, A:R.258 SO4.4: 7 residues within 4Å: Chain A: G.89, Y.90, I.94, G.113, Y.114, K.371 Ligands: GTP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.90, A:Y.114 Water bridges: A:D.115, A:N.350 Salt bridges: A:K.371 SO4.5: 3 residues within 4Å: Chain A: S.204, Q.205, R.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.205, A:Q.205, A:R.206 Salt bridges: A:R.206 SO4.6: 2 residues within 4Å: Chain A: K.232, R.492 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.232, A:R.492 SO4.7: 1 residues within 4Å: Chain A: R.47 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.47 SO4.8: 1 residues within 4Å: Chain A: K.240 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.240 SO4.9: 4 residues within 4Å: Chain A: W.182, E.183, R.184, E.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.183, A:R.184, A:E.336 SO4.10: 2 residues within 4Å: Chain A: R.386, R.389 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.389

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

MN.11: 5 residues within 4Å: Chain A: C.118, H.254, H.349 Ligands: GTP.2, MN.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.118, A:H.254, A:H.349 MN.12: 5 residues within 4Å: Chain A: D.115, C.118, H.223 Ligands: GTP.2, MN.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.115, A:C.118, A:H.223

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 2 residues within 4Å: Chain A: R.210, Q.214 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: K.306 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacewicz, A. et al., Structures of RNA ligase RtcB in complexes with divalent cations and GTP. Rna (2022)

Release Date

2022-10-12

Peptides

tRNA-splicing ligase RtcB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

tRNA-splicing ligase RtcB

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