SMTL ID : 3lwm.1

Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x DDS: 2',3'-dideoxyadenosine triphosphate(Non-covalent)

DDS.1: 11 residues within 4Å: Chain A: R.295, Q.321, H.347, R.367, K.371, F.375, Y.379, D.493 Chain B: A.12 Ligands: MG.7, GOL.14 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.375 Hydrogen bonds: A:Q.321, A:Q.321 Water bridges: A:R.281, A:R.295, A:R.295, A:D.493 Salt bridges: A:H.347, A:H.347, A:R.367, A:K.371, A:K.371, A:K.371 pi-Stacking: A:F.375

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

ACT.2: 4 residues within 4Å: Chain A: R.21, W.26, D.259, L.260 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.21 ACT.3: 4 residues within 4Å: Chain A: T.155, R.267, E.309, R.486 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.267, A:R.486 ACT.4: 2 residues within 4Å: Chain A: Y.163, A.166 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.163 ACT.15: 3 residues within 4Å: Chain A: R.436 Chain C: G.2, C.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.436

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: V.18, L.19, K.22, E.108, R.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.19, A:R.113, A:R.113 GOL.6: 8 residues within 4Å: Chain A: T.252, Y.253, P.256, P.287, N.288, N.291 Chain C: C.5, C.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.288, A:N.288, A:N.291 Water bridges: A:D.286, A:N.291 GOL.12: 6 residues within 4Å: Chain A: R.244, K.248 Chain B: G.7, G.8, C.9 Chain C: C.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.244, A:K.248, A:K.248 Water bridges: A:N.193, A:R.244 GOL.13: 6 residues within 4Å: Chain B: C.6, G.7, G.8, C.9 Chain C: G.4, C.5 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain A: D.318, E.494, K.539 Chain B: A.12 Ligands: DDS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.318, A:D.318

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: D.318 Ligands: DDS.1 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.8: 5 residues within 4Å: Chain A: E.323, Y.379, N.458, Q.462 Chain C: T.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.458, A:Q.462 Water bridges: A:R.281 NA.9: 2 residues within 4Å: Chain A: R.449, E.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.449 Water bridges: A:R.423, A:R.449 NA.10: 1 residues within 4Å: Chain A: E.482 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.482 NA.11: 3 residues within 4Å: Chain A: L.60, K.62, D.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.62, A:D.63 Water bridges: A:K.62, A:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Obeid, S. et al., Replication through an abasic DNA lesion: structural basis for adenine selectivity. Embo J. (2010)

Release Date

2010-05-05

Peptides

DNA polymerase I, thermostable: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I, thermostable

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