SMTL ID : 5hr6.1 (1 other biounit)

X-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

monomer

Ligands

1 x MET: METHIONINE(Non-covalent)

MET.1: 13 residues within 4Å: Chain A: C.132, M.175, M.176, G.177, G.179, E.180, P.181, S.211, T.212, S.213, S.233 Ligands: SF4.2, 5AD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.180, A:E.180, A:S.233

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

SF4.2: 9 residues within 4Å: Chain A: C.125, L.127, C.129, C.132, A.135, E.180, S.213 Ligands: MET.1, 5AD.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.180 Metal complexes: A:C.125, A:C.129, A:C.132, MET.1

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

5AD.3: 16 residues within 4Å: Chain A: F.131, C.132, M.176, S.233, H.235, E.278, V.280, I.309, P.310, W.311, N.312, R.344, C.355, G.356 Ligands: MET.1, SF4.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.176 Hydrogen bonds: A:S.233, A:N.312, A:N.312, A:N.312 Water bridges: A:S.233 pi-Stacking: A:F.131

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 4 residues within 4Å: Chain A: L.196, L.203 Chain B: A.25, C.26 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.196, A:L.203 MG.5: 2 residues within 4Å: Chain B: C.37, G.38 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: U.6, C.7 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: U.6, A.12, G.13 No protein-ligand interaction detected (PLIP)

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

RlmN methylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RlmN methylase

Related Entries With Identical Sequence