SMTL ID : 6fwk.2 (1 other biounit)

The crystal structure of Pol2CORE-M644G in complex with DNA and an incoming nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 16 residues within 4Å: Chain A: D.645, V.646, A.647, S.648, G.649, Y.650, P.651, R.786, K.829, N.833, Y.836, D.882 Chain B: C.11 Chain C: T.4, G.5 Ligands: CA.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.650 Hydrogen bonds: A:S.648, A:G.649, A:Y.650, A:N.833 Salt bridges: A:R.786, A:K.829, A:K.829, A:K.829

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.645, V.646, D.882 Ligands: DTP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.645, A:V.646, A:D.882 CA.3: 3 residues within 4Å: Chain A: D.295, E.297, D.482 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.295, A:E.297, A:D.482, H2O.1 CA.4: 4 residues within 4Å: Chain A: D.295, I.296, F.387, D.388 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.388, A:D.388, H2O.1

1 x FE: FE (III) ION(Non-covalent)

FE.5: 2 residues within 4Å: Chain A: C.682, C.768 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.682, A:C.768

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkash, V. et al., Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Nat Commun (2019)

Release Date

2019-01-30

Peptides

DNA polymerase epsilon catalytic subunit A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase epsilon catalytic subunit A

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