SMTL ID : 5hr7.1 (1 other biounit)

X-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked in vitro transcribed tRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: U.8, C.9, C.12 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: C.39, G.40 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: G.23, A.46 No protein-ligand interaction detected (PLIP)

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.4: 8 residues within 4Å: Chain B: C.125, C.129, C.132, A.135, G.179, S.213 Ligands: 5AD.5, MET.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Metal complexes: MET.6, B:C.125, B:C.129, B:C.132 Salt bridges: B:E.180

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.5: 17 residues within 4Å: Chain B: F.131, C.132, M.176, S.211, S.233, H.235, E.278, V.280, I.309, P.310, W.311, N.312, R.344, C.355, G.356 Ligands: SF4.4, MET.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:M.176 Hydrogen bonds: B:S.211, B:S.233, B:S.233, B:N.312, B:N.312, B:N.312 pi-Stacking: B:F.131

1 x MET: METHIONINE(Non-covalent)

MET.6: 12 residues within 4Å: Chain B: M.175, M.176, G.177, G.179, E.180, P.181, S.211, T.212, S.213, S.233 Ligands: SF4.4, 5AD.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.180, B:S.211, B:S.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwalm, E.L. et al., Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA. Science (2016)

Release Date

2016-04-13

Peptides

Dual-specificity RNA methyltransferase RlmN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Dual-specificity RNA methyltransferase RlmN

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