SMTL ID : 8f6b.1

Crystal structure of murine PolG2 hexamer bound to DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-hexamer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: N.443 Chain F: L.448 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.443 GOL.13: 3 residues within 4Å: Chain A: E.367 Chain B: A.446 Ligands: MPD.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.367, A:E.367

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

EDO.2: 1 residues within 4Å: Chain A: M.424 Ligand excluded by PLIP EDO.3: 1 residues within 4Å: Chain A: R.66 Ligand excluded by PLIP EDO.4: 1 residues within 4Å: Chain A: I.340 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: L.220, A.446, A.447, L.448 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: F.80 Chain B: E.367 Ligands: MPD.12 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain B: P.339, I.340 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain B: R.66 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain B: A.447, L.448 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: N.368, G.369, V.435, L.438 Ligand excluded by PLIP EDO.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: A.70, I.170 Chain D: K.67 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain C: W.74, Q.169, I.170 Chain D: K.67 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain D: Q.209, W.210 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain D: S.251, K.256 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain D: E.26, A.27 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain D: R.81, A.446 Ligands: MPD.7, EDO.22 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: K.67 Chain D: W.74, Q.169, I.170 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain D: S.76, R.81, H.217, K.224 Ligands: EDO.20 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain D: R.66 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain D: T.261, S.298, G.299, D.300 Ligand excluded by PLIP EDO.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Ligands: EDO.29, EDO.35 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain E: I.259, E.260, T.261, S.298 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain E: K.67 Chain F: A.70, S.71, W.74 Ligands: EDO.35 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain E: A.70, S.71 Chain F: K.67 Ligands: EDO.26 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain F: R.81, A.446, E.449 Ligands: EDO.34 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain F: E.195, P.258, T.261, S.298, G.299, D.300 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain F: R.66 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain F: Q.209, W.210 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain F: S.76, R.81, H.217, K.224, E.449 Ligands: EDO.30 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain F: W.74, V.87, Q.169, I.170 Ligands: EDO.26, EDO.28 Ligand excluded by PLIP EDO.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

MPD.7: 4 residues within 4Å: Chain A: E.367 Chain D: A.447 Ligands: GOL.13, EDO.20 No protein-ligand interaction detected (PLIP) MPD.12: 2 residues within 4Å: Chain B: E.367 Ligands: EDO.6 No protein-ligand interaction detected (PLIP)

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

NA.37: 2 residues within 4Å: Chain G: T.13, A.14 No protein-ligand interaction detected (PLIP) NA.38: 2 residues within 4Å: Chain J: T.13, A.14 No protein-ligand interaction detected (PLIP)

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

PolG2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

PolG2