SMTL ID : 4c8k.1

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.133, W.136, L.137, F.432, Y.519 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.133 GOL.5: 6 residues within 4Å: Chain B: A.2, C.3, C.4 Chain C: T.12, G.13, G.14 No protein-ligand interaction detected (PLIP)

1 x BMR: ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate(Non-covalent)

BMR.2: 15 residues within 4Å: Chain A: R.295, Q.321, E.323, H.347, R.367, R.368, K.371, T.372, F.375, Y.379 Chain B: C.12 Chain C: X.4, G.5 Ligands: MG.3, TRS.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:K.371, A:K.371, A:F.375 Hydrogen bonds: A:Q.321, A:Y.379 Water bridges: A:R.281, A:R.295, A:R.295, A:R.295, A:R.295 Salt bridges: A:R.295, A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

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

MG.3: 2 residues within 4Å: Chain A: R.295 Ligands: BMR.2 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 7 residues within 4Å: Chain B: C.11, C.12 Chain C: X.4, G.5, G.6, C.7 Ligands: BMR.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betz, K. et al., Structural Insights Into DNA Replication without Hydrogen Bonds. J.Am.Chem.Soc. (2013)

Release Date

2013-12-11

Peptides

DNA POLYMERASE I, THERMOSTABLE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE I, THERMOSTABLE

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