SMTL ID : 4atn.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

5 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.34, A:K.36, A:K.36, A:I.43 Water bridges: A:R.34 GOL.2: 4 residues within 4Å: Chain A: N.211, N.233, W.235, Q.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.211, A:N.233, A:Q.253 Water bridges: A:W.235 GOL.3: 7 residues within 4Å: Chain A: V.96, V.97, E.98, R.145, P.146, Y.162, Y.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.98, A:R.145, A:R.145, A:Y.164 GOL.4: 8 residues within 4Å: Chain A: S.62, S.63, I.65, L.320, I.336, Q.337, A.338 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.338, A:A.338 Water bridges: A:K.23, A:S.63 GOL.5: 5 residues within 4Å: Chain A: F.171, P.176, R.177, L.178, H.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.177, A:R.177 Water bridges: A:I.175

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

EDO.6: 4 residues within 4Å: Chain A: F.264, P.266, T.267, R.268 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: P.60, F.61, S.62, N.166, N.167 Ligands: EDO.16 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: N.38, T.110, N.111, E.112 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: D.109, T.110, N.111, K.114 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: A.17, A.18, T.21, F.32, A.33 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.308, M.309, K.310 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: E.15, A.18, R.312, Y.313, E.314 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.34, V.35 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: E.259, D.260, K.263 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: Q.48, P.49, D.50, D.51 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: R.57, E.58, P.60, N.166, N.167 Ligands: EDO.7, EDO.19 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: D.22, Y.313, E.314 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: S.62, S.63, I.336 Ligands: GOL.4 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: R.57, Y.164, N.166, N.167 Ligands: EDO.16 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: G.91, M.92 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: K.99, R.132, D.133, G.135 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: V.230, N.233, T.251, Q.253 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: S.269, I.271, G.296, W.297, C.298, R.299, W.356 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: G.331, I.332, N.333, R.354, I.355 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: R.187, L.190, H.343 Ligands: SO4.30 Ligand excluded by PLIP EDO.26: 1 residues within 4Å: Chain A: D.206 Ligand excluded by PLIP

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

SO4.27: 4 residues within 4Å: Chain A: K.99, A.138, N.139, Y.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.139, A:Y.140 Water bridges: A:K.99 Salt bridges: A:K.99 SO4.28: 4 residues within 4Å: Chain A: K.118, R.121, K.122 Ligands: SO4.29 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.118, A:R.121, A:K.122 SO4.29: 3 residues within 4Å: Chain A: R.121, K.122 Ligands: SO4.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.121 Salt bridges: A:K.122 SO4.30: 4 residues within 4Å: Chain A: R.187, S.188, K.191 Ligands: EDO.25 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.191

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

Related Entries With Identical Sequence