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

RNA ligase RtcB-GMP/Mn(2+) complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Covalent)

5GP.1: 18 residues within 4Å: Chain A: I.74, N.202, F.204, E.206, H.234, H.329, P.378, G.379, S.380, M.381, S.385, H.404, G.405, A.406, G.407, Y.451, K.480 Ligands: MN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.208, A:G.379, A:S.385, A:A.406, A:G.407, A:K.480 Water bridges: A:N.330, A:M.381, A:M.381, A:R.408 Salt bridges: A:E.206, A:H.329, A:H.404 pi-Stacking: A:F.204

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

MN.2: 4 residues within 4Å: Chain A: C.98, H.234, H.329 Ligands: 5GP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.98, A:H.234, A:H.329, 5GP.1

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 8 residues within 4Å: Chain A: K.58, Y.59, E.338, M.395, K.396, E.397, T.398, F.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.338, A:F.399 Water bridges: A:E.338 Salt bridges: A:K.58

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.134, Q.189, R.190, P.193, Q.194 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.134, A:R.190, A:Q.194

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: R.104, R.168, A.221, Y.222, G.223, D.322, I.323, L.367, Y.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.323, A:Y.368 Salt bridges: A:R.168 PO4.6: 7 residues within 4Å: Chain A: V.131, G.132, R.190, Q.194, R.238, G.239 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132, A:Q.194 Water bridges: A:R.238 Salt bridges: A:R.190, A:R.238

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
B

tRNA-splicing ligase RtcB

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