SMTL ID : 5u2r.1

PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER(Non-covalent)

DG-DT-DC-DG-DG.1: 19 residues within 4Å: Chain A: H.36, K.37, A.40, Y.41, L.64, P.65, G.66, V.67, G.68, T.69, K.70, I.71, E.290 Chain B: C.1, C.2, G.3, A.4, C.5 Ligands: NA.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.285, A:R.285, A:R.285 Water bridges: A:N.39 pi-Stacking: A:H.36

1 x 1S0: 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

1S0.2: 17 residues within 4Å: Chain A: R.151, G.181, S.182, R.185, S.190, G.191, D.192, D.194, Y.273, F.274, G.276, D.278, N.281 Chain B: G.6 Chain C: C.10 Ligands: CA.3, CA.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.273, A:D.278 Hydrogen bonds: A:S.182, A:S.182, A:S.182, A:G.191, A:D.192, A:D.192, A:D.194, A:D.194, A:N.281 Water bridges: A:F.183, A:D.278 Salt bridges: A:R.151, A:R.185

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.192, D.194, D.258 Chain C: C.10 Ligands: 1S0.2, CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.192, A:D.194, A:D.258, H2O.4 CA.4: 4 residues within 4Å: Chain A: D.192, D.194 Ligands: 1S0.2, CA.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.192, A:D.194, H2O.2

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

NA.5: 4 residues within 4Å: Chain A: T.103, V.105, I.108 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.105, A:G.107, A:I.108 NA.6: 4 residues within 4Å: Chain A: K.62, L.64, V.67 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.62, A:V.67

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

ACT.7: 4 residues within 4Å: Chain A: F.202, T.207, E.234, T.235 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.207 Hydrogen bonds: A:E.234 Water bridges: A:L.212 ACT.8: 8 residues within 4Å: Chain A: E.23, F.78, G.82, K.83, L.84, L.87, E.88, R.91 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.87 Hydrogen bonds: A:L.84, A:E.88 Salt bridges: A:R.91 ACT.9: 4 residues within 4Å: Chain A: I.176, T.198, K.264, Y.267 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.176, A:Y.267 Hydrogen bonds: A:T.198 Water bridges: A:I.176, A:T.178 Salt bridges: A:K.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vyas, R. et al., Structural basis for the D-stereoselectivity of human DNA polymerase beta. Nucleic Acids Res. (2017)

Release Date

2017-05-24

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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