SMTL ID : 2im3.1

Crystal structure of poliovirus polymerase complexed with UTP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: Y.234, D.328 Ligands: MN.2, UTP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.234 MN.2: 2 residues within 4Å: Chain A: D.328 Ligands: MN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.328, A:D.328

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

NA.3: 7 residues within 4Å: Chain A: L.268, N.269, S.271, H.273, V.282, G.284, G.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.271, A:G.285

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.4: 15 residues within 4Å: Chain A: K.159, R.163, K.167, R.174, L.175, I.176, Y.234, T.235, G.236, Y.237, D.238, S.288, D.328, K.359 Ligands: MN.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.174 Hydrogen bonds: A:R.174, A:G.236, A:Y.237, A:D.238, A:D.238, A:S.288 Water bridges: A:K.167, A:D.238, A:D.238, A:A.239 Salt bridges: A:R.163, A:K.167, A:K.167, A:K.167, A:R.174, A:K.359 pi-Cation interactions: A:R.174

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 7 residues within 4Å: Chain A: S.28, I.401, W.403, T.404, T.410, H.413, V.414 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.414 Hydrogen bonds: A:T.404 Salt bridges: A:H.413 ACY.6: 4 residues within 4Å: Chain A: D.71, K.311, D.349, Y.350 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.349 Hydrogen bonds: A:Y.350 Salt bridges: A:K.311 ACY.7: 2 residues within 4Å: Chain A: P.440, R.443 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.440 Salt bridges: A:R.443 ACY.8: 1 residues within 4Å: Chain A: R.379 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.424 Salt bridges: A:R.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.A. et al., Stabilization of Poliovirus Polymerase by NTP Binding and Fingers-Thumb Interactions. J.Mol.Biol. (2007)

Release Date

2006-12-12

Peptides

poliovirus polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

poliovirus polymerase

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