SMTL ID : 1p91.1

Crystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltransferase (NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER19)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.5, C.8, C.21, H.25 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.5, A:C.8, A:C.21, A:H.25 ZN.4: 6 residues within 4Å: Chain B: C.5, L.7, C.8, C.21, Q.23, H.25 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.5, B:C.8, B:C.21, B:H.25

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

SO4.2: 2 residues within 4Å: Chain A: R.71, H.101 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.71, A:H.101 SO4.5: 2 residues within 4Å: Chain B: R.71, H.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.129 Water bridges: B:D.105 Salt bridges: B:R.71, B:H.101 SO4.6: 3 residues within 4Å: Chain B: S.213, N.261, H.263 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.213, B:S.213, B:N.261 Salt bridges: B:H.263 SO4.7: 2 residues within 4Å: Chain B: R.59, R.128 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.59, B:R.128 SO4.8: 2 residues within 4Å: Chain B: H.66, R.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.221, B:R.221 Salt bridges: B:H.66

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 16 residues within 4Å: Chain A: L.62, Y.67, G.93, C.94, G.95, E.96, G.97, Y.98, Y.99, I.155, Y.156, T.178, P.179, H.183, L.184, F.260 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.67 Hydrogen bonds: A:Y.67, A:Y.67, A:C.94, A:E.96, A:G.97, A:Y.98, A:Y.99 Water bridges: A:Y.99, A:T.100 SAM.9: 17 residues within 4Å: Chain B: R.58, Y.67, L.70, G.93, C.94, G.95, E.96, G.97, Y.98, Y.99, I.155, Y.156, H.183, L.184, M.233, T.234, P.235 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.67 Hydrogen bonds: B:R.58, B:R.58, B:Y.67, B:E.96, B:E.96, B:G.97, B:Y.98, B:Y.99, B:Y.156 Salt bridges: B:H.183 pi-Cation interactions: B:Y.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, K. et al., Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-03-30

Peptides

Ribosomal RNA large subunit methyltransferase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribosomal RNA large subunit methyltransferase A