SMTL ID : 3tka.1

crystal structure and solution saxs of methyltransferase rsmh from E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 21 residues within 4Å: Chain A: T.65, F.66, G.67, R.68, G.69, G.70, H.71, D.89, R.90, D.91, G.111, P.112, F.113, D.135, L.136, G.137, V.138, S.139, Q.142, M.162, E.252 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.65, A:F.66, A:G.67, A:R.68, A:G.69, A:G.70, A:H.71, A:H.71, A:R.90, A:R.90, A:F.113, A:Q.142, A:E.252 Water bridges: A:T.65, A:S.72, A:D.91, A:S.139 Salt bridges: A:H.71, A:D.135 SAM.9: 21 residues within 4Å: Chain B: T.65, F.66, G.67, R.68, G.69, G.70, H.71, D.89, R.90, D.91, G.111, P.112, F.113, D.135, L.136, G.137, V.138, S.139, Q.142, M.162, E.252 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.65, B:F.66, B:G.67, B:R.68, B:G.69, B:G.70, B:H.71, B:H.71, B:R.90, B:R.90, B:F.113, B:Q.142, B:E.252 Water bridges: B:T.65, B:S.72, B:D.91, B:S.139 Salt bridges: B:H.71, B:D.135

2 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.2: 4 residues within 4Å: Chain A: W.173, A.177, D.181, W.245 No protein-ligand interaction detected (PLIP) CTN.10: 4 residues within 4Å: Chain B: W.173, A.177, D.181, W.245 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: K.284, K.320, R.340 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.340, A:R.340 Salt bridges: A:K.284, A:K.320, A:R.340 SO4.4: 3 residues within 4Å: Chain A: R.84, S.107, R.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.107 Salt bridges: A:R.84, A:R.123 SO4.5: 1 residues within 4Å: Chain A: R.161 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.161, A:R.161, A:R.161, A:R.161, A:R.161, A:P.164 Salt bridges: A:R.161 SO4.6: 4 residues within 4Å: Chain A: R.193, F.194, K.196, R.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.196, A:R.197 Salt bridges: A:R.197 SO4.7: 4 residues within 4Å: Chain A: R.316, T.345, N.346, A.347 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.345, A:T.345, A:N.346, A:N.346, A:A.347 Salt bridges: A:R.316 SO4.11: 3 residues within 4Å: Chain B: K.284, K.320, R.340 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.340, B:R.340 Salt bridges: B:K.284, B:K.320, B:R.340 SO4.12: 3 residues within 4Å: Chain B: R.84, S.107, R.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.107 Salt bridges: B:R.84, B:R.123 SO4.13: 1 residues within 4Å: Chain B: R.161 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.161, B:R.161, B:R.161, B:R.161, B:R.161, B:P.164 Salt bridges: B:R.161 SO4.14: 4 residues within 4Å: Chain B: R.193, F.194, K.196, R.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.196, B:R.197 Salt bridges: B:R.197 SO4.15: 4 residues within 4Å: Chain B: R.316, T.345, N.346, A.347 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.345, B:T.345, B:N.346, B:N.346, B:A.347 Salt bridges: B:R.316

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 4 residues within 4Å: Chain A: R.166, G.167, Q.168, E.172 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.168 Hydrogen bonds: A:G.167 PG4.16: 4 residues within 4Å: Chain B: R.166, G.167, Q.168, E.172 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.168 Hydrogen bonds: B:G.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, Y. et al., Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA. J.Struct.Biol. (2012)

Release Date

2012-05-30

Peptides

Ribosomal RNA small subunit methyltransferase H: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribosomal RNA small subunit methyltransferase H