SMTL ID : 4auk.1 (1 other biounit)

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.34, V.35, K.36, Y.41, V.42, I.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.34, A:K.36, A:K.36, A:I.43 GOL.2: 7 residues within 4Å: Chain A: D.22, Q.26, Y.313, E.314, S.317, H.318 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.22, A:Q.26, A:E.314, A:S.317 GOL.3: 3 residues within 4Å: Chain A: M.309, E.346 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.346

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

SO4.4: 4 residues within 4Å: Chain A: K.99, A.138, N.139, Y.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.139, A:Y.140 Water bridges: A:K.99, A:N.139 Salt bridges: A:K.99

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 7 residues within 4Å: Chain A: K.14, E.15, A.18, K.311, R.312, Y.313, E.314 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.14, A:E.15, A:E.15, A:R.312, A:Y.313, A:E.314 Water bridges: A:K.311, A:K.311

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.6: 5 residues within 4Å: Chain A: I.332, N.333, R.354, I.355, W.356 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.333, A:N.333, A:N.333 Water bridges: A:N.333, A:I.355 Salt bridges: A:R.354

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: I.56, R.57, Y.164, N.166, N.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.57, A:N.166 PEG.8: 5 residues within 4Å: Chain A: N.241, R.258, E.259, D.260, K.263 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.241, A:N.241, A:E.259, A:D.260 Water bridges: A:E.259, A:E.259

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 9 residues within 4Å: Chain A: K.23, S.62, S.63, L.64, I.65, Q.337, A.338 Ligands: EDO.10, EDO.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.23, A:S.63, A:L.64, A:A.338 Water bridges: A:R.27, A:R.27, A:S.63

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 6 residues within 4Å: Chain A: K.23, Q.26, Y.313, S.317 Ligands: GOL.2, PGE.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.26, A:Q.26, A:Y.313, A:S.317 EDO.11: 8 residues within 4Å: Chain A: S.62, L.64, V.198, F.199, Q.337, A.338, R.339 Ligands: PGE.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.62, A:V.198, A:A.338 Water bridges: A:Q.337 EDO.12: 8 residues within 4Å: Chain A: G.11, F.12, E.13, K.14, E.15, E.37, N.38, R.312 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.13, A:E.13, A:E.15, A:E.37, A:N.38, A:R.312 Water bridges: A:E.37, A:E.37 EDO.13: 5 residues within 4Å: Chain A: Y.227, V.230, S.247, L.248, T.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.247 EDO.14: 3 residues within 4Å: Chain A: D.109, R.177, Y.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.177, A:R.177, A:Y.342 Water bridges: A:D.109 EDO.15: 5 residues within 4Å: Chain A: P.170, F.171, Y.172, I.175, R.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.172, A:I.175, A:R.177 Water bridges: A:R.104 EDO.16: 3 residues within 4Å: Chain A: G.219, C.221, D.240 No protein-ligand interaction detected (PLIP) EDO.17: 5 residues within 4Å: Chain A: G.11, F.12, R.312, E.346 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.11, A:R.312, A:R.312, A:E.346 EDO.18: 5 residues within 4Å: Chain A: K.281, P.282, A.283, E.315, N.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.283, A:N.319 EDO.19: 5 residues within 4Å: Chain A: Y.237, F.264, P.266, T.267, R.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.267 EDO.20: 5 residues within 4Å: Chain A: L.103, R.104, V.105, T.124, Y.172 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.103, A:V.105, A:V.105 Water bridges: A:E.102, A:E.102, A:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punekar, A.S. et al., Crystal Structure of Rlmm, the 2'O-Ribose Methyltransferase for C2498 of Escherichia Coli 23S Rrna. Nucleic Acids Res. (2012)

Release Date

2012-08-15

Peptides

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M

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