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

MsDpo4-DNA complex 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.1: 17 residues within 4Å: Chain A: D.9, L.10, D.11, Q.12, F.13, Y.14, T.46, C.47, Y.50, R.53, A.59, D.107, K.159 Chain B: G.4 Chain C: C.18 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.14, A:A.59 Hydrogen bonds: A:Q.12, A:F.13, A:Y.14, A:R.53 Water bridges: A:D.9, A:T.46, A:R.53, A:R.53 Salt bridges: A:R.53, A:K.159

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.9, D.107, E.108 Chain C: C.18 Ligands: 0KX.1, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.9, A:D.107, A:E.108, H2O.3 MG.3: 6 residues within 4Å: Chain A: D.9, L.10, D.107, K.159 Ligands: 0KX.1, MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.9, A:L.10, A:D.107, A:D.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, M.K. et al., A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res. (2019)

Release Date

2020-02-19

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

DNA polymerase IV

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