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Ligand · XG4

XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine

XG4, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine (C10 H17 N6 O12 P3, 506.2 g/mol), in the MolNFT structures on GenesisL1: bound in 45 records (40 PDB entries). Every binding site with its…

Component
XG4
Formula
C10 H17 N6 O12 P3
Class
ligand
Structures
45
PDB entries
40

Binding sites

XG4 in 45 structures; the first of them:

  • 5DLG · Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Methylhymidine · XG4 A504 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 9 more
  • 6FBD · KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A903 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 9 more
  • 6US5 · DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template… · XG4 A901 · binds ARG615, ASP653, TYR654, SER655, GLN656, GLU658, HIS682, ARG702 and 10 more
  • 7U7U · Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 0.1 mM Mg2+ for 600s · XG4 A505 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 11 more
  • 7U7W · Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 1.0 mM Mg2+ for 600s · XG4 A505 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 12 more
  • 7U83 · Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 3.0 mM Mn2+ for 600s · XG4 A505 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 12 more
  • 8E88 · Human DNA polymerase eta-DNA-rU-ended primer-dGMPNPP ternary mismatch complex with Mg2+ · XG4 A503 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 12 more
  • 8E8J · Human DNA polymerase eta-DNA-rG-ended primer-dGMPNPP ternary mismatch complex with Mg2+ · XG4 A503 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 12 more
  • 9EMI · KOD-H4 DNA polymerase mutant in a ternary complex containing six HNA nucleotides and a… · XG4 A803 · binds PHE405, ARG406, SER407, LEU408, TYR409, PRO410, ARG460, LYS464 and 10 more
  • 6CRH · Structure of human DNA polymerase beta complexed with 8-clg in the template base paired… · XG4 A405 · binds GLY179, SER180, ARG183, SER188, GLY189, ASP190, ASP192, TYR271 and 8 more
  • 6CUA · Structure of human DNA polymerase beta complexed with 8-clg in the template base paired… · XG4 A405 · binds GLY179, SER180, ARG183, SER188, GLY189, ASP190, ASP192, TYR271 and 8 more
  • 6E3W · Structure of human DNA polymerase beta complexed with 8OA in the template base paired… · XG4 A405 · binds GLY179, SER180, ARG183, SER188, GLY189, ASP190, ASP192, TYR271 and 9 more
  • 6FBC · Klentaq DNA polymerase processing a modified primer - bearing the modification at the… · XG4 A901 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 9 more
  • 6FBD · Klentaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A903 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 9 more
  • 6FBE · Klentaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A904 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 8 more
  • 6FBF · Klentaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A903 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 9 more
  • 6FBG · Klentaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A907 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 8 more
  • 6FBH · Klentaq DNA polymerase processing a modified primer - bearing the modification upstream… · XG4 A904 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 10 more
  • 6FBI · Klentaq DNA polymerase in a closed, ternary complex with dgpnhpp bound in the active site · XG4 A901 · binds ARG573, ASP610, TYR611, SER612, GLN613, ILE614, GLU615, HIS639 and 9 more
  • 6PKZ · Structure of human DNA polymerase beta N279A complexed with 8OA in the template base… · XG4 A404 · binds GLY179, SER180, ARG183, SER188, GLY189, ASP190, ASP192, TYR271 and 7 more
  • 6PLC · Structure of human DNA polymerase eta complexed with 8OA in the template base paired with… · XG4 A501 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 10 more
  • 6PZ3 · Polymerase eta-catalyzed insertion of correct G opposite template cytarabine (arac)… · XG4 A501 · binds ASP13, MET14, ASP15, CYS16, PHE17, PHE18, GLN38, ILE48 and 11 more
  • 6TXA · Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with xtp, dgmpnpp… · XG4 A705 · binds GLN149, LEU150, ARG164, HIS167, ASP207, HIS210, HIS215, HIS233 and 8 more

Residues it binds most

ASP 78, ARG 78, HIS 49, LYS 74, TYR 57, ILE 49, PHE 53, GLN 53, GLY 26, DT 30 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • GOL · Glycerol
  • MN · Manganese (II) ion
  • EDO · 1,2-ethanediol
  • K · Potassium ion
  • NA · Sodium ion
  • SO4 · Sulfate ion
  • CZF · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • CA · Calcium ion
  • FE · Fe (III) ion

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