SMTL ID : 3flo.4 (3 other biounits)

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UNK- UNK- UNK: DNA polymerase alpha catalytic subunit A(Non-covalent)

UNK-UNK-UNK.1: 3 residues within 4Å: Chain A: Q.236, F.279, Q.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.280, A:Q.280

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

SO4.2: 4 residues within 4Å: Chain A: R.314, E.317, H.318, Q.321 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.317, A:Q.321, A:Q.321 Water bridges: A:S.96, A:T.306 Salt bridges: A:H.318 SO4.3: 2 residues within 4Å: Chain A: R.309, D.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.313, A:D.313 Salt bridges: A:R.309 SO4.4: 3 residues within 4Å: Chain A: R.309, Y.310, R.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.311 Water bridges: A:R.314 SO4.5: 2 residues within 4Å: Chain A: R.260, K.267 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.260, A:R.260 Salt bridges: A:R.260, A:K.267 SO4.6: 2 residues within 4Å: Chain A: K.210, T.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.211, A:T.211 Salt bridges: A:K.222 SO4.7: 2 residues within 4Å: Chain A: R.260, K.261 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.267 Salt bridges: A:R.260, A:K.261 SO4.8: 3 residues within 4Å: Chain A: K.210, T.211, Q.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.212 Water bridges: A:K.210, A:Q.212 SO4.9: 3 residues within 4Å: Chain A: S.45, Q.46, S.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.46, A:S.47, A:S.47 SO4.10: 7 residues within 4Å: Chain A: C.154, G.155, D.292, P.389, S.390, E.391, R.409 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.244, A:R.409 SO4.11: 4 residues within 4Å: Chain A: R.412, A.413, T.414 Ligands: SO4.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.413, A:T.414 SO4.12: 4 residues within 4Å: Chain A: R.412, T.414, N.416 Ligands: SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.414, A:T.414, A:N.416 Salt bridges: A:R.412 SO4.15: 5 residues within 4Å: Chain B: D.135, C.136, E.137, R.173, R.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.136, B:E.137 Salt bridges: B:R.173, B:R.180 SO4.16: 3 residues within 4Å: Chain B: R.44, K.53, E.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.158 Salt bridges: B:R.44, B:K.53 SO4.17: 2 residues within 4Å: Chain B: A.74, H.75 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.75 SO4.18: 3 residues within 4Å: Chain B: W.83, V.94, K.117 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.83 Salt bridges: B:K.117

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain B: C.25, C.28, C.52, C.55 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.25, B:C.28, B:C.52, B:C.55 ZN.14: 4 residues within 4Å: Chain B: C.86, C.91, C.105, C.110 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.86, B:C.91, B:C.105, B:C.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klinge, S. et al., 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. Embo J. (2009)

Release Date

2009-06-09

Peptides

DNA polymerase alpha subunit B: A
DNA polymerase alpha catalytic subunit A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

DNA polymerase alpha subunit B

DNA polymerase alpha catalytic subunit A

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