SMTL ID : 5oxj.1

Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.318, Y.319, D.493 Ligands: MN.2, NZI.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:Y.319, A:D.493 MN.2: 6 residues within 4Å: Chain A: D.318, D.493, E.494, K.539 Ligands: MN.1, NZI.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.318, H2O.1, H2O.1

1 x NZI: [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate(Non-covalent)

NZI.3: 20 residues within 4Å: Chain A: R.281, R.295, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, R.368, K.371, T.372, F.375, D.493 Chain B: G.12 Chain C: G.4, C.5 Ligands: MN.1, MN.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.323, A:K.371, A:F.375, A:F.375 Hydrogen bonds: A:R.281, A:Q.321, A:I.322 Water bridges: A:D.318, A:K.371 Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: H.151, F.477, E.481 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.151 ACT.5: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.260 Salt bridges: A:R.21 ACT.8: 3 residues within 4Å: Chain C: G.13, G.14, T.15 No protein-ligand interaction detected (PLIP)

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

MG.6: 2 residues within 4Å: Chain A: E.170, R.301 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.170, H2O.1 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase. Chem. Commun. (Camb.) (2017)

Release Date

2017-11-29

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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