- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.8: 5 residues within 4Å:- Chain A: D.318, D.493
- Chain B: C.12
- Ligands: MG.9, N5P.11
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.318, A:D.318, A:D.493, A:D.493, H2O.7
MG.9: 5 residues within 4Å:- Chain A: D.318, Y.319, D.493
- Ligands: MG.8, N5P.11
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.318, A:Y.319, A:D.493
MG.17: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.23: 1 residues within 4Å:- Chain C: G.14
No protein-ligand interaction detected (PLIP)- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x N5P: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE(Non-covalent)
N5P.11: 18 residues within 4Å:- Chain A: R.281, D.318, Y.319, S.320, Q.321, I.322, E.323, H.347, R.367, K.371, F.375, G.376, D.493
- Chain B: C.12
- Chain C: N.4, G.5
- Ligands: MG.8, MG.9
15 PLIP interactions:15 interactions with chain A- Hydrophobic interactions: A:E.323, A:F.375, A:F.375
- Hydrogen bonds: A:R.281, A:Q.321, A:I.322
- Water bridges: A:E.323, A:E.323, A:K.371, A:K.371
- Salt bridges: A:H.347, A:R.367, A:K.371, A:K.371, A:K.371
- 4 x FMT: FORMIC ACID(Non-functional Binders)
FMT.12: 1 residues within 4Å:- Chain A: K.475
2 PLIP interactions:2 interactions with chain A- Water bridges: A:K.475, A:K.475
FMT.13: 4 residues within 4Å:- Chain A: E.45, P.46, Y.47, K.48
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.47, A:K.48
FMT.14: 2 residues within 4Å:- Chain A: H.151, T.155
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.151
FMT.15: 5 residues within 4Å:- Chain A: R.57, D.79, F.121, W.125, R.143
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.57, A:R.143
- Water bridges: A:R.143
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Obeid, S. et al., Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem. (2012)
- Release Date
- 2012-02-15
- Peptides
- DNA polymerase I, thermostable: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- monomer
- Ligands
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x N5P: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE(Non-covalent)
- 4 x FMT: FORMIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Obeid, S. et al., Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. J.Biol.Chem. (2012)
- Release Date
- 2012-02-15
- Peptides
- DNA polymerase I, thermostable: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A