SMTL ID : 3l0o.1

Structure of RNA-free Rho transcription termination factor from Thermotoga maritima

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

7 x IUM: URANYL (VI) ION(Non-covalent)

IUM.1: 5 residues within 4Å: Chain A: R.74, E.76, D.77, S.82, D.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.82, A:D.84 IUM.2: 2 residues within 4Å: Chain A: R.37, D.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.37 IUM.3: 3 residues within 4Å: Chain A: E.14, K.38, R.39 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.39 IUM.9: 5 residues within 4Å: Chain B: E.326, S.350, R.351, Q.352, E.396 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.350, B:R.351, B:R.351, B:Q.352, B:Q.352 IUM.10: 7 residues within 4Å: Chain A: Y.147, R.371 Chain B: T.189, T.190, K.193, E.219, D.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.190, A:R.371 IUM.11: 2 residues within 4Å: Chain B: R.371, E.373 No protein-ligand interaction detected (PLIP) IUM.12: 6 residues within 4Å: Chain B: R.74, E.76, D.77, S.82, N.83, D.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.82, B:N.83, B:D.84, B:D.84

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

SO4.4: 5 residues within 4Å: Chain A: K.185, A.186, G.187, K.188, T.189 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.185, A:G.187, A:K.188, A:T.189, A:T.189, A:T.189 Salt bridges: A:K.188 SO4.5: 3 residues within 4Å: Chain A: R.73, K.242, K.245 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.73, A:K.242, A:K.245 SO4.6: 5 residues within 4Å: Chain A: K.174, H.203, P.204, D.205, T.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.203, A:D.205 Water bridges: A:D.263 Salt bridges: A:K.174, A:H.203 SO4.7: 4 residues within 4Å: Chain A: S.350, R.351, Q.352, E.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.351, A:R.351, A:Q.352 SO4.8: 2 residues within 4Å: Chain A: R.276, S.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.329 Salt bridges: A:R.276 SO4.13: 5 residues within 4Å: Chain B: G.187, K.188, T.189, E.219 Ligands: NA.17 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.185, B:G.187, B:K.188, B:T.189, B:T.189 Water bridges: B:A.186, B:A.186, B:T.190 Salt bridges: B:K.188 SO4.14: 4 residues within 4Å: Chain B: R.177, N.344, R.370, R.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.344 Salt bridges: B:R.177, B:R.370, B:R.371 SO4.15: 7 residues within 4Å: Chain A: G.343, N.344, M.345, E.346, G.368, R.370 Chain B: K.185 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.185, A:R.370 Hydrogen bonds: A:G.343 SO4.16: 6 residues within 4Å: Chain B: K.174, N.202, H.203, P.204, D.205, T.206 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.202, B:D.205, B:T.206, B:T.206, B:D.263 Salt bridges: B:K.174, B:H.203

2 x NA: SODIUM ION(Non-functional Binders)

NA.17: 3 residues within 4Å: Chain B: P.184, K.185 Ligands: SO4.13 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.185, A:R.370 Water bridges: B:P.183, B:A.186 NA.18: 2 residues within 4Å: Chain B: G.328, E.333 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canals, A. et al., The Structure of RNA-Free Rho Termination Factor Indicates a Dynamic Mechanism of Transcript Capture. J.Mol.Biol. (2010)

Release Date

2010-05-26

Peptides

Transcription termination factor rho: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transcription termination factor rho