SMTL ID : 7kc0.1

Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: C.25 Chain D: D.762, D.764 Ligands: D3T.3 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.764, D:D.764 MG.4: 4 residues within 4Å: Chain D: D.608, F.609, D.764 Ligands: D3T.3 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.608, D:F.609, D:D.764

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 12 residues within 4Å: Chain D: Q.490, K.491, E.492, Q.1055, C.1056, C.1059, V.1067, C.1069, N.1071, C.1074, R.1080 Chain E: L.119 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.1056, D:C.1059, D:C.1069, D:C.1074

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.3: 17 residues within 4Å: Chain A: C.25 Chain B: A.13, G.14 Chain D: D.608, F.609, N.610, S.611, L.612, Y.613, R.674, K.701, I.702, N.705, D.764, E.800 Ligands: MG.1, MG.4 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.613, D:Y.613 Hydrogen bonds: D:D.608, D:S.611, D:L.612, D:E.800 Salt bridges: D:R.674, D:R.674, D:K.678, D:K.701, D:K.701

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain D: C.1009, K.1010, C.1012, C.1024, C.1027 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1009, D:C.1012, D:C.1024, D:C.1027

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, F. et al., Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-12-02

Peptides

Proliferating cell nuclear antigen: CGH
DNA polymerase: D
POL31 isoform 1: E
POL32 isoform 1: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
F

G
E

H
G

D
A

E
B

F
C

Proliferating cell nuclear antigen

DNA polymerase

POL31 isoform 1

POL32 isoform 1

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