SMTL ID : 6v93.1

Structure of DNA Polymerase Zeta/DNA/dNTP Ternary Complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-1-mer

Ligands

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

SF4.1: 6 residues within 4Å: Chain A: P.888, C.1480, C.1483, C.1502, C.1507, R.1513 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.1480, A:C.1483, A:C.1502, A:C.1507

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.1009, F.1010, D.1178 Ligands: DCP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.1009, A:F.1010, A:D.1178 CA.3: 5 residues within 4Å: Chain A: D.1009, D.1178, S.1179 Chain F: C.30 Ligands: DCP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.1178, A:S.1179, H2O.1, H2O.2

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.4: 17 residues within 4Å: Chain A: D.1009, F.1010, Q.1011, S.1012, L.1013, Y.1014, P.1015, R.1091, K.1120, N.1124, Y.1127, D.1178 Chain F: C.30 Chain G: G.5, G.6 Ligands: CA.2, CA.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.1014 Hydrogen bonds: A:F.1010, A:S.1012, A:L.1013, A:Y.1014 Salt bridges: A:R.1091, A:K.1120, A:K.1120, A:K.1120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malik, R. et al., Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-08-19

Peptides

DNA polymerase zeta catalytic subunit: A
DNA polymerase zeta processivity subunit: BC
DNA polymerase delta small subunit: D
DNA polymerase delta subunit 3: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
F

E
G

DNA polymerase zeta catalytic subunit

DNA polymerase zeta processivity subunit

DNA polymerase delta small subunit

DNA polymerase delta subunit 3

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