SMTL ID : 6jur.1 (1 other biounit)

MsDpo4-DNA complex 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.1: 18 residues within 4Å: Chain A: D.9, L.10, D.11, Q.12, F.13, Y.14, T.46, Y.50, R.53, D.107, E.108, K.152, K.159 Chain B: G.4, G.5 Chain C: C.18 Ligands: MN.2, MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.12, A:F.13, A:T.46, A:Y.50, A:R.53, A:K.152 Water bridges: A:Y.14, A:A.48, A:R.53, A:R.53 Salt bridges: A:R.53, A:K.159

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.9, D.107, E.108 Ligands: 2TM.1, MN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.9, A:D.107, A:D.107, A:E.108 MN.3: 6 residues within 4Å: Chain A: D.9, L.10, D.107, K.159 Ligands: 2TM.1, MN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:L.10, 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
A

DNA polymerase IV

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