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Ligand · 8DG

8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate

8DG, 8-oxo-2'-deoxyguanosine-5'-triphosphate (C10 H16 N5 O14 P3, 523.2 g/mol), in the MolNFT structures on GenesisL1: bound in 38 records (31 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and…

Component
8DG
Formula
C10 H16 N5 O14 P3
Class
ligand
Structures
38
PDB entries
31

Binding sites

8DG in 38 structures; the first of them:

  • 5FSI · MTH1 substrate recognition: Complex with 8-oxo-dGTP. · 8DG A1157 · binds TYR7, THR8, LEU9, PHE27, ASN33, GLY36, GLY37, LYS38 and 7 more
  • 5GG6 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP · 8DG A401 · binds ALA26, ARG55, ARG57, TYR58, ASP60, SER62, LYS65, GLY66 and 9 more
  • 5GHI · Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP · 8DG A201 · binds TYR7, THR8, LEU9, LYS23, PHE27, ASN33, GLY36, GLY37 and 10 more
  • 5GHO · Crystal structure of human MTH1(G2K/D120A mutant) in complex with 8-oxo-dGTP · 8DG B201 · binds TYR7, LYS23, ASN33, LYS38, PHE72, PHE74, MET81, TRP117 and 2 more
  • 5MZE · Crystal structure of mouse MTH1 with 8-oxo-dGTP · 8DG A204 · binds TYR7, THR8, LEU9, LYS23, PHE27, ASN33, GLY36, GLY37 and 10 more
  • 6AK8 · Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and… · 8DG A504 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 8 more
  • 6AK9 · Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Cytosine and… · 8DG A503 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 10 more
  • 6IJY · Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dGTP… · 8DG A201 · binds TYR7, THR8, LEU9, LYS23, ARG25, PHE27, ASN33, GLY36 and 11 more
  • 6IPK · Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP · 8DG A502 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 8 more
  • 7KTB · DNA Polymerase Mu, 8-oxodGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (40min) · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 13 more
  • 7KTK · DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Ground State Ternary Complex, 50 mM Mg2+ (90min) · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 13 more
  • 8I18 · Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 7.7 · 8DG A201 · binds TYR7, THR8, LEU9, LYS23, ARG25, PHE27, ASN33, PHE35 and 14 more
  • 5MZE · Crystal structure of mouse MTH1 with 8-oxo-dgtp · 8DG A204 · binds TYR7, THR8, LEU9, LYS23, PHE27, ASN33, GLY36, GLY37 and 10 more
  • 6AK8 · Pre-catalytic ternary complex of human DNA polymerase mu with templating adenine and… · 8DG A504 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 8 more
  • 6AK9 · Pre-catalytic ternary complex of human DNA polymerase mu with templating cytosine and… · 8DG A503 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 10 more
  • 6FL4 · A. thaliana NUDT1 in complex with 8-oxo-dgtp · 8DG A203 · binds ALA11, VAL13, ARG27, ILE31, ALA37, LEU38, GLY40, GLY41 and 11 more
  • 6IJY · Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dgtp… · 8DG A201 · binds TYR7, THR8, LEU9, LYS23, ARG25, PHE27, ASN33, GLY36 and 11 more
  • 6ILI · Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8- oxo-dgtp at pH 6.5 · 8DG A201 · binds TYR7, LEU9, ASN33, GLY37, LYS38, GLU52, PHE72, MET81 and 4 more
  • 6IPK · Binary complex of human DNA polymerase mu with MN8OXODGTP · 8DG A502 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 8 more
  • 6M6Y · Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgtp · 8DG A401 · binds ARG55, ARG57, TYR58, SER62, LYS65, GLY66, LYS67, TYR101 and 6 more
  • 6VF7 · DNA polymerase mu, 8-OXODGTP:AT ground state ternary complex, 50 mm MN2+ (15 min) · 8DG A508 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 7 more
  • 7KT3 · DNA polymerase mu, 8-OXODGTP:AT pre-catalytic ground state ternary complex, 20 mm CA2+… · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 7 more
  • 7KT4 · DNA polymerase mu, 8-OXODGTP:AT reaction state ternary complex, 10 mm MN2+ (30MIN) · 8DG A512 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 9 more
  • 7KT7 · DNA polymerase mu, 8-OXODGTP:AT reaction state ternary complex, 50 mm MG2+ (60MIN) · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 8 more
  • 7KTA · DNA polymerase mu, 8-OXODGTP:CT pre-catalytic ground state ternary complex, 20 mm CA2+… · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLN327, GLY328, HIS329, ASP330 and 10 more
  • 7KTB · DNA polymerase mu, 8-OXODGTP:CT reaction state ternary complex, 10 mm MN2+ (40MIN) · 8DG A501 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 11 more
  • 7KTE · DNA polymerase mu, 8-OXODGTP:CT reaction state ternary complex, 50 mm MG2+ (90MIN) · 8DG A506 · binds GLY319, GLY320, ARG323, LYS325, GLY328, HIS329, ASP330, ASP332 and 10 more

Residues it binds most

GLY 50, LYS 52, ASP 41, GLU 32, PHE 31, TRP 38, ARG 35, ASN 31, TYR 25, THR 30 (residue and the binding sites it lines).

Found with

  • NA · Sodium ion
  • EDO · 1,2-ethanediol
  • EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid
  • MN · Manganese (II) ion
  • SO4 · Sulfate ion
  • CL · Chloride ion
  • MG · Magnesium ion
  • CA · Calcium ion
  • DTT · 2,3-dihydroxy-1,4-dithiobutane
  • PPV · Pyrophosphate
  • FRU · beta-D-fructofuranose
  • GLC · alpha-D-glucopyranose

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