SMTL ID : 8f69.1

Crystal structure of murine PolG2 dimer bound to DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: R.50, E.176, K.177, T.178, D.286 Chain B: D.72 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:D.72, A:R.50, A:R.50, A:E.176, A:T.178 Water bridges: A:R.41, A:R.41 EDO.3: 6 residues within 4Å: Chain A: W.58, V.71, Q.153, I.154 Ligands: EDO.7, MPD.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.71, A:I.154 EDO.4: 1 residues within 4Å: Chain A: W.194 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain B: F.69 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: K.51 Chain B: S.55 Ligands: MPD.2 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: A.54, S.55, W.58 Chain B: K.51 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.55 EDO.8: 10 residues within 4Å: Chain A: H.75, R.125, G.155, V.156 Chain B: H.75, R.125, G.155, V.156 Ligands: MPD.2, MPD.12 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.125, A:V.156, B:R.125, B:V.156 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: M.211, S.212, N.215, Y.294, D.295, Q.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.215, B:Q.298 EDO.13: 3 residues within 4Å: Chain B: G.344, L.345, E.348 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain B: T.245, S.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.179 EDO.15: 2 residues within 4Å: Chain A: F.69 Chain B: V.356 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.356 EDO.16: 3 residues within 4Å: Chain B: F.417, Y.421, S.424 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.417, B:S.424 EDO.17: 4 residues within 4Å: Chain B: S.60, R.65, H.201, K.208 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.65, B:K.208, B:K.208 Water bridges: B:S.60

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

MPD.2: 5 residues within 4Å: Chain A: R.50, A.54, I.154 Ligands: EDO.6, EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.54, A:I.154 Hydrogen bonds: A:R.50, A:R.50 MPD.12: 6 residues within 4Å: Chain B: R.50, A.54, V.156, T.178 Ligands: EDO.3, EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.54, B:V.156

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

MES.11: 6 residues within 4Å: Chain B: V.341, T.390, L.391, N.393, G.394, H.410 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.410

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wojtaszek, J.L. et al., Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA. Nucleic Acids Res. (2023)

Release Date

2023-08-09

Peptides

DNA polymerase subunit gamma-2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

DNA polymerase subunit gamma-2, mitochondrial