SMTL ID : 8v6j.1

DNA elongation complex (configuration 2) of Xenopus laevis DNA polymerase alpha-primase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.949, C.952, T.954, C.976, C.981, A.983 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.949, A:C.952, A:C.976, A:C.981 ZN.2: 7 residues within 4Å: Chain A: C.1014, C.1019, N.1021, C.1037, A.1039, C.1040, A.1043 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1014, A:C.1019, A:C.1037, A:C.1040 ZN.6: 6 residues within 4Å: Chain D: C.126, C.127, I.132, C.133, K.135, C.136 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.126, D:C.127, D:C.133, D:C.136

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.3: 20 residues within 4Å: Chain A: D.528, F.529, N.530, S.531, L.532, Y.533, P.534, R.587, K.591, Q.611, K.615, L.616, N.619, Y.622, G.623, D.669 Chain E: C.16, G.17 Chain F: C.20 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.533 Hydrogen bonds: A:N.530, A:S.531, A:L.532, A:Y.533, A:N.619, A:N.619 Salt bridges: A:R.587, A:R.587, A:K.591, A:K.615, A:K.615, A:K.615

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 5 residues within 4Å: Chain A: D.528, F.529, S.531, D.669 Ligands: DGT.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.528, A:F.529, A:D.669 MG.7: 1 residues within 4Å: Chain F: G.1 No protein-ligand interaction detected (PLIP)

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

SF4.5: 13 residues within 4Å: Chain C: P.291, L.292, C.293, C.373, V.376, C.390, P.391, F.392, Q.427, C.430, L.447, P.450, Y.453 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.293, C:C.373, C:C.390, C:C.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, E.A. et al., A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-12-20

Peptides

DNA polymerase alpha catalytic subunit: A
DNA polymerase alpha subunit B: B
DNA primase large subunit: C
DNA primase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DNA polymerase alpha catalytic subunit

DNA polymerase alpha subunit B

DNA primase large subunit

DNA primase

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