SMTL ID : 3lwl.1

Structure of Klenow fragment of Taq polymerase in complex with an abasic site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

DDS.1: 9 residues within 4Å: Chain A: R.295, Q.321, H.347, R.367, K.371, F.375, Y.379 Chain B: A.12 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.321, A:Q.321 Water bridges: A:R.295, A:R.295 Salt bridges: A:H.347, A:H.347, A:R.367, A:K.371, A:K.371, A:K.371

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.318, E.528 Ligands: DDS.1 No protein-ligand interaction detected (PLIP)

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

ACT.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.4: 3 residues within 4Å: Chain A: R.21, W.26, L.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.260 Salt bridges: A:R.21 ACT.5: 3 residues within 4Å: Chain A: K.250, S.251, D.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.255 Salt bridges: A:K.250 ACT.17: 3 residues within 4Å: Chain A: R.436 Chain C: G.6, C.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.436 ACT.18: 7 residues within 4Å: Chain A: N.193, S.194, R.195 Chain B: G.7 Chain C: G.11, T.12 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195 Water bridges: A:D.196

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: T.252, Y.253, P.287, N.288, N.291 Chain C: C.9, C.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.288, A:N.288, A:N.291 Water bridges: A:D.286 GOL.7: 4 residues within 4Å: Chain A: R.133, W.136, F.432, Y.519 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:Y.519 GOL.8: 6 residues within 4Å: Chain A: K.62, D.63, R.271, F.272, N.273, Q.274 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.62, A:D.63, A:Q.274 Water bridges: A:T.93, A:R.271, A:N.273, A:Q.274, A:T.275, A:T.275, A:T.275 GOL.9: 9 residues within 4Å: Chain A: E.23, P.24, M.25, W.26, E.153, H.269, T.270, R.271, D.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.23, A:M.25, A:E.153, A:D.286 GOL.10: 3 residues within 4Å: Chain A: V.445, S.447, V.448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.447 GOL.15: 5 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: C.9, C.10 No protein-ligand interaction detected (PLIP) GOL.16: 7 residues within 4Å: Chain A: R.244, K.248 Chain B: G.7, G.8, C.9 Chain C: C.10 Ligands: ACT.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.248, A:K.248

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

NA.11: 5 residues within 4Å: Chain A: P.24, K.62, D.63, E.153, R.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62, A:R.271 Water bridges: A:K.62 NA.12: 3 residues within 4Å: Chain A: K.22, D.286 Chain C: C.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.22, A:D.286 NA.13: 2 residues within 4Å: Chain A: D.89, S.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:S.91 NA.14: 3 residues within 4Å: Chain A: T.93, A.276 Chain C: C.7 No protein-ligand interaction detected (PLIP)

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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