SMTL ID : 3d9j.1 (1 other biounit)

Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

6 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 5 residues within 4Å: Chain A: E.48, F.88, N.91, I.92, T.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.48, A:T.95, A:T.95 Water bridges: A:N.90 NH4.2: 7 residues within 4Å: Chain A: P.56, E.57, K.59, V.60, C.102, P.103, D.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.57, A:K.59, A:V.60 NH4.3: 4 residues within 4Å: Chain A: I.37, F.77, K.81 Ligands: NH4.4 No protein-ligand interaction detected (PLIP) NH4.4: 7 residues within 4Å: Chain A: I.37, S.73, F.77, K.81, D.82, V.83 Ligands: NH4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.81, A:V.83 NH4.5: 5 residues within 4Å: Chain A: D.67, R.71, V.113, L.116, W.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.71, A:W.117, A:W.117 NH4.6: 4 residues within 4Å: Chain A: Y.12, F.50, K.53, C.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.53

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

SO4.7: 2 residues within 4Å: Chain A: N.91, S.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.94, A:S.94 Water bridges: A:N.91 SO4.8: 5 residues within 4Å: Chain A: Y.40, K.41, P.86, R.87, N.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.86, A:N.90 Water bridges: A:R.87, A:R.87 Salt bridges: A:R.87 SO4.9: 2 residues within 4Å: Chain A: K.41, R.87 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.41, A:R.87 SO4.10: 3 residues within 4Å: Chain A: R.71, L.116, N.120 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.120 Water bridges: A:K.119, A:N.120 Salt bridges: A:R.71, A:K.119 SO4.11: 3 residues within 4Å: Chain A: P.20, Y.64, K.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.64 Water bridges: A:I.21 Salt bridges: A:K.109 SO4.12: 3 residues within 4Å: Chain A: E.10, Y.17, K.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.10 Water bridges: A:S.13, A:S.13 Salt bridges: A:K.25

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain A: Q.72, H.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.72, A:Q.72 GOL.14: 1 residues within 4Å: Chain A: K.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.31 Water bridges: A:K.31 GOL.15: 3 residues within 4Å: Chain A: S.89, N.90, I.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.89 Water bridges: A:S.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Becker, R. et al., Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II. J.Biol.Chem. (2008)

Release Date

2008-06-10

Peptides

RNA-binding protein 16: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-binding protein 16

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