SMTL ID : 4b17.1

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli in complex with S-adenosylmethionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: S.186, S.188, G.219, A.220, C.221, P.222, G.223, G.224, W.225, D.240, E.259, D.260, G.261, F.262, D.277, M.278, V.279 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.186, A:S.188, A:C.221, A:G.223, A:G.224, A:W.225, A:W.225, A:D.260, A:G.261 Salt bridges: A:D.277 SAM.19: 17 residues within 4Å: Chain B: S.186, S.188, G.219, A.220, C.221, P.222, G.223, G.224, W.225, D.240, E.259, D.260, G.261, F.262, D.277, M.278, V.279 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.186, B:S.188, B:C.221, B:G.223, B:G.224, B:W.225, B:W.225, B:D.260, B:G.261, B:D.277 Salt bridges: B:D.277

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.14, E.15, A.18, K.311, R.312, Y.313, E.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.311, A:R.312, A:Y.313 GOL.3: 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:K.36, A:K.36, A:I.43 Water bridges: A:R.34, A:I.43 GOL.20: 7 residues within 4Å: Chain B: K.14, E.15, A.18, K.311, R.312, Y.313, E.314 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.15, B:K.311, B:R.312, B:Y.313 GOL.21: 6 residues within 4Å: Chain B: R.34, V.35, K.36, Y.41, V.42, I.43 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.36, B:K.36, B:I.43 Water bridges: B:R.34, B:E.45

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

EDO.4: 6 residues within 4Å: Chain A: E.112, S.113, K.114, E.115, L.116, P.155 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: F.171, P.176, R.177, H.197 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: P.308, M.309, K.310 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: E.259, D.260, K.263 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.114, Y.172, M.173, I.175 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: F.171, F.196, H.197, I.200, P.201, A.202, W.205 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: K.23, S.63, I.336 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: R.85, F.119 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: R.57, Y.164, N.166, N.167 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: F.264, P.266, T.267, R.268 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: D.22, Y.313, E.314 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: E.112, S.113, K.114, E.115, L.116, P.155 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: F.171, P.176, R.177, H.197 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: P.308, M.309, K.310 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: E.259, D.260, K.263 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: K.114, Y.172, M.173, I.175 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: F.171, F.196, H.197, I.200, P.201, A.202, W.205 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: K.23, S.63, I.336 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: R.85, F.119 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: R.57, Y.164, N.166, N.167 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: F.264, P.266, T.267, R.268 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain B: D.22, Y.313, E.314 Ligand excluded by PLIP

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

SO4.15: 8 residues within 4Å: Chain A: K.99, A.138, N.139, Y.140 Chain B: K.99, A.138, N.139 Ligands: SO4.33 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.139, A:N.139, A:Y.140, B:N.139, B:N.139 Salt bridges: A:K.99, B:K.99 SO4.16: 2 residues within 4Å: Chain A: K.118, K.122 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.118, A:K.122 SO4.17: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.122 SO4.18: 5 residues within 4Å: Chain A: V.96, R.145, P.146, Y.162, Y.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.145 SO4.33: 8 residues within 4Å: Chain A: K.99, A.138, N.139 Chain B: K.99, A.138, N.139, Y.140 Ligands: SO4.15 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.139, A:N.139, B:N.139, B:N.139, B:Y.140 Salt bridges: A:K.99, B:K.99 SO4.34: 2 residues within 4Å: Chain B: K.118, K.122 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.118, B:K.122 SO4.35: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.122 SO4.36: 5 residues within 4Å: Chain B: V.96, R.145, P.146, Y.162, Y.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.145, B:Y.164

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M

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