SMTL ID : 3bsn.1

Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x U- G- C- C- C- G- G- G: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')(Non-covalent)

U-G-C-C-C-G-G-G.1: 28 residues within 4Å: Chain A: K.115, T.116, R.126, N.128, W.131, S.306, Y.341, G.342, D.343, D.344, L.391, R.392, L.406, S.410, R.413, Q.414, R.419 Ligands: U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, MN.5, N5C.8, GOL.9 Protein-ligand interaction information (PLIP) not available

1 x U- G- C- C- C- G- G- G- N5M: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*GP*(N5M))-3')(Non-covalent)

U-G-C-C-C-G-G-G-N5M.2: 37 residues within 4Å: Chain A: S.23, T.117, S.118, K.127, A.164, K.166, D.167, L.184, W.185, G.186, S.187, M.192, K.207, V.217, G.218, M.219, N.220, S.300, G.301, V.302, P.303, C.304, T.305, Y.341, N.422, I.438, Q.439, S.442 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, N5C.8, GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.439

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.30, L.36, R.52, S.427 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.30, A:R.30 Water bridges: A:E.42, A:E.42, A:Y.176, A:Y.176, A:S.427, A:S.427 GOL.4: 7 residues within 4Å: Chain A: A.256, L.259, E.260, V.263, Q.273, A.276, L.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.260, A:E.260, A:Q.273 GOL.9: 9 residues within 4Å: Chain A: F.28, L.169, R.413, Q.414, W.417, T.418, R.419 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.419, A:R.419 Water bridges: A:R.413 GOL.10: 6 residues within 4Å: Chain A: D.114, T.117, K.166 Ligands: U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2, U-G-C-C-C-G-G-G-N5M.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.114, A:D.114

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

MN.5: 6 residues within 4Å: Chain A: D.242, D.343, D.344 Ligands: U-G-C-C-C-G-G-G.1, MN.6, N5C.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:D.343, A:D.344, H2O.6 MN.6: 5 residues within 4Å: Chain A: D.242, Y.243, D.343 Ligands: MN.5, N5C.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.242, A:Y.243, A:D.343 MN.7: 3 residues within 4Å: Chain A: D.99, E.205, H.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.99, A:D.99, A:E.205, A:H.209

1 x N5C: 5-nitrocytidine 5'-(tetrahydrogen triphosphate)(Non-covalent)

N5C.8: 16 residues within 4Å: Chain A: K.166, R.182, D.242, Y.243, S.244, R.245, W.246, D.247, S.300, T.305, N.309, D.343 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G-N5M.2, MN.5, MN.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.245, A:W.246, A:D.247, A:D.247, A:S.300, A:N.309 Water bridges: A:K.166, A:K.166, A:K.174, A:K.174, A:R.182, A:R.182 Salt bridges: A:R.182, A:R.182, A:K.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zamyatkin, D.F. et al., Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase. J.Biol.Chem. (2008)

Release Date

2008-01-08

Peptides

RNA dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA dependent RNA polymerase

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