SMTL ID : 4e0d.1

Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x DC- DC- DT- DG- DA- DC- DT- DC- DOC: DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')(Non-covalent)

DC-DC-DT-DG-DA-DC-DT-DC-DOC.1: 36 residues within 4Å: Chain A: P.247, T.266, K.267, T.268, S.271, T.272, S.273, A.274, R.294, Q.295, K.298, Y.303, R.331, Q.340, N.341, I.342, P.343, I.344, R.345, L.346, R.353, F.426, Y.430, V.544, H.545, D.546, E.547 Chain B: G.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.331, A:R.331, A:R.345, A:Y.430 Water bridges: A:R.345, A:R.353 Salt bridges: A:R.345

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

SO4.2: 4 residues within 4Å: Chain A: H.398, R.418, K.422 Ligands: MES.10 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.398 Salt bridges: A:R.418, A:K.422 SO4.3: 4 residues within 4Å: Chain A: Y.370, S.371, Q.372 Ligands: MES.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.371, A:Q.372, A:Q.372 Water bridges: A:S.371, A:D.581 SO4.4: 4 residues within 4Å: Chain A: K.14, M.15, A.16, R.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.16 Water bridges: A:R.59, A:R.59 Salt bridges: A:R.59 SO4.5: 1 residues within 4Å: Chain A: R.495 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.495 SO4.6: 5 residues within 4Å: Chain A: V.39, E.40, R.151, A.152, V.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.40, A:E.40, A:R.151 Water bridges: A:V.153

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 8 residues within 4Å: Chain A: R.188, L.189, E.192, L.193, L.483, K.522, V.572 Ligands: DCP.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.483 MPD.8: 11 residues within 4Å: Chain A: M.219, E.222, L.223, Q.226, L.296, L.299, I.304, E.348, G.349, K.351, I.352 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.222, A:L.223, A:L.223, A:I.352 Hydrogen bonds: A:E.348 MPD.9: 10 residues within 4Å: Chain A: E.37, V.38, V.39, E.40, E.41, R.91, D.141, Y.145, R.151, K.166 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.41, A:Y.145 Hydrogen bonds: A:R.151 Water bridges: A:R.91, A:K.166

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 10 residues within 4Å: Chain A: S.371, Q.372, L.395, D.396, I.397, H.398, R.418, K.579 Ligands: SO4.2, SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.397 Water bridges: A:D.581 Salt bridges: A:D.396

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.11: 10 residues within 4Å: Chain A: R.182, E.185, Q.186, D.187, R.188, L.189, L.482, L.483, H.484 Ligands: MPD.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.185 Hydrogen bonds: A:D.187, A:R.188, A:L.189 Water bridges: A:R.188, A:R.188, A:H.484, A:H.484 Salt bridges: A:H.484, A:H.484, A:H.484 pi-Cation interactions: A:R.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem. (2012)

Release Date

2012-06-06

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

Related Entries With Identical Sequence