SMTL ID : 1uvk.2 (2 other biounits)

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.1: 5 residues within 4Å: Chain A: K.223, R.225, R.268 Ligands: MG.2, G.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.270 Salt bridges: A:R.225, A:R.225, A:R.268

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.324 Ligands: POP.1, G.4 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.1 MG.5: 3 residues within 4Å: Chain A: D.624, Y.630 Ligands: GTP.6 No protein-ligand interaction detected (PLIP)

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: T.323, D.454, E.491, A.495 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.454, A:E.491, A:A.495

1 x G: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

G.4: 7 residues within 4Å: Chain A: R.81, Q.206, R.270, E.529 Ligands: POP.1, MG.2, GTP.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.204, A:R.270 Salt bridges: A:R.81 pi-Cation interactions: A:R.270

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.6: 9 residues within 4Å: Chain A: R.204, S.520, N.523, N.524, E.529, N.626, Y.630 Ligands: G.4, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.523, A:N.524, A:E.529, A:E.529, A:E.529 Water bridges: A:T.208 Salt bridges: A:R.204 pi-Stacking: A:Y.630, A:Y.630

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado, P.S. et al., The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Structure (2004)

Release Date

2004-02-19

Peptides

RNA-directed RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

RNA-directed RNA polymerase

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