SMTL ID : 4c8l.1

Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the artificial base pair dNaM-d5SICS at the postinsertion site (sequence context 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: V.294, R.295, E.323, F.375, Y.379 Chain B: X.11 Chain C: A.1, G.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.295, A:Y.379 Water bridges: A:D.493 GOL.5: 6 residues within 4Å: Chain A: D.79, F.121, W.125, Y.138, R.139, R.143 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.79, A:R.139, A:R.139, A:R.143, A:R.143 GOL.6: 5 residues within 4Å: Chain A: R.133, W.136, L.431, F.432, Y.519 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.431 GOL.7: 7 residues within 4Å: Chain A: M.25, W.26, A.27, D.28, R.70, H.262, R.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.27, A:H.262, A:R.264 Water bridges: A:R.70 GOL.8: 5 residues within 4Å: Chain A: Y.163, A.166, L.167, E.170, R.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.166, A:E.170, A:R.301, A:R.301

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.101, Y.102, R.127 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.102, A:R.127 Salt bridges: A:R.101, A:R.127 SO4.3: 4 residues within 4Å: Chain A: Q.321, H.347, R.367, K.371 6 PLIP interactions: 6 interactions with chain A Water bridges: A:Q.321, A:H.347, A:H.347 Salt bridges: A:H.347, A:R.367, A:K.371 SO4.4: 4 residues within 4Å: Chain A: S.382, A.383, H.384, Y.394 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.383, A:H.384, A:Y.394, A:Y.394 Salt bridges: A:H.384 SO4.11: 3 residues within 4Å: Chain B: C.5 Chain C: C.7, C.8 No protein-ligand interaction detected (PLIP)

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

MG.9: 4 residues within 4Å: Chain A: E.245, K.248 Chain B: C.8, G.9 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: C.5 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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