Ligand clusters for UniProt code E1C9K5

Ligand clusters for E1C9K5: DNA polymerase I from Geobacillus stearothermophilus

		Top 6 (of 17) ligand clusters Cluster 1. 14 ligand types 70 ligands Cluster 2. 5 ligand types 19 ligands Cluster 3. 2 ligand types 4 ligands Cluster 4. 2 ligand types 2 ligands Cluster 5. 2 ligand types 15 ligands Cluster 6. 1 ligand type 10 ligands
Representative protein: 2xy5A

Structures

PDB		Schematic diagram
2xy5A
2xo7A
4b9tA
2xy7A
2y1iA
		more ...

Cluster 1 contains 14 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 10 PDB codes: 4b9m(A), 4b9t(A), 4b9u(A), 4b9v(A), 6dsu(A), 6dsv(A), 6dsw(A), 6dsx(A), 6dsy(A), 6mu4(A).
		2. Ligand: GOL × 2 glycerin Glycerol PDB codes: 4dsi(A), 4dwi(A).
		3. Ligand: SO4 × 45 Sulfate ion PDB codes: 2xo7(A), 2xy5(A), 2xy6(A), 2y1i(A), 2y1j(A), 4b9l(A), 4b9m(A), 4b9n(A), 4b9s(A), 4b9t(A), 4b9u(A), 4b9v(A), 4dsi(A), 4dsl(A), 4dwi(A), 4uqg(A), 6dsv(A), 6dsw(A), 6dsx(A), 6dsy(A), 6mu4(A), 6mu5(A), 7k5o(A), 7k5p(A), 7k5q(A), 7k5r(A), 7k5s(A), 7k5t(A), 7k5u(A),
_Ca		4. Metal: _CA × 3 PDB codes: 4dsi(A), 4dsj(A), 4dsk(A).
		5. Ligand: 2DT × 1 3'-Deoxythymidine-5'-Monophosphate PDB code: 4yfu(A).
		6. Ligand: DCP × 1 2'-Deoxycytidine-5'-Triphosphate PDB code: 7k5t(A).
		7. Ligand: DGT × 1 2'-Deoxyguanosine-5'-Triphosphate PDB code: 4dsj(A).
		8. Ligand: DTP × 1 2'-Deoxyadenosine 5'-Triphosphate PDB code: 7k5q(A).
		9. Ligand: DZ4 × 1 2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine PDB code: 6dsu(A).
		10. Ligand: GFL-UF2-A5L-CFL-GFL-UF2-GFL-A5L-UF2-CFL-GFL-CFL-A5L × 1 GFL=2-Amino-9-(2-Deoxy-2-Fluoro-5-O-Phosphono-Beta-D- Arabinofuranosyl)-1,9-Dihydro-6h-Purin-6-One, UF2=1-(2-Deoxy-2-Fluoro-5-O-Phosphono-Beta-D- Arabinofuranosyl)pyrimidine-2,4(1h,3h)-Dione, A5L=9-(2-Deoxy-2-Fluoro-5-O-Phosphono-Beta-D- Arabinofuranosyl)-9h-Purin-6-Amine, CFL=4-Amino-1-(2-Deoxy-2-Fluoro-5-O-Phosphono-Beta-D- Arabinofuranosyl)pyrimidin-2(1h)-One. PDB code: 6mu4(A).
		11. Ligand: MPD × 1 (4s)-2-Methyl-2,4-Pentanediol PDB code: 6mu4(A).
		12. Ligand: POP × 1 Pyrophosphate 2- PDB code: 4dsk(A).
		13. Ligand: TTP × 1 Thymidine-5'-Triphosphate PDB code: 4yfu(A).
		14. Ligand: _TG-TFT-FA2-_TC-_TG-TFT-_TG-FA2-TFT-_TC-_TG-_TC-FA2 × 1 TG=2-Azanyl-9-[(2~{r},3~{r},4~{s})-3-Oxidanyl-4-[Oxidanyl- Bis(oxidanylidene)-L^{6}-Phosphanyl]oxy- Oxolan-2-Yl]- 1~{h}-Purin-6-One, TFT=(L)-Alpha-Threofuranosyl-Thymine-3'-Monophosphate, FA2=5-(6-Amino-9h-Purin-9-Yl)-4-Hydroxytetrahydrofuran-3-Yl dihydrogen phosphate, TC=4-Azanyl-1-[(2~{r},3~{r},4~{s})-3-Oxidanyl-4-[Oxidanyl- Bis(oxidanylidene)-L^{6}-Phosphanyl]oxy- Oxolan-2- Yl]pyrimidin-2-One. PDB code: 6mu5(A).

Cluster 2 contains 5 ligand types

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Ligand		Description
		1. Ligand: GOL × 4 glycerin Glycerol PDB codes: 4dsi(A), 4dwi(A),
		2. Ligand: SO4 × 7 Sulfate ion PDB codes: 2xy5(A), 4b9m(A), 4b9n(A), 4b9s(A), 4b9u(A), 4b9v(A), 4uqg(A).
		3. Ligand: GLC-FRU × 6 GLC=Alpha-D-Glucopyranose, FRU=Beta-D-Fructofuranose. PDB codes: 2xy7(A), 4b9l(A), 4b9n(A), 4b9s(A), 4uqg(A), 4yfu(A).
		4. Ligand: GLC-Z9N × 1 GLC=Alpha-D-Glucopyranose, Z9N=Alpha-D-Fructofuranose. PDB code: 2xy5(A).
		5. Ligand: MES × 1 2-(N-Morpholino)-Ethanesulfonic acid PDB code: 2xy6(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 2 glycerin Glycerol PDB codes: 4dsi(A), 4dwi(A).
		2. Ligand: MRD × 2 (4r)-2-Methylpentane-2,4-Diol PDB codes: 2xy5(A), 2xy6(A).

Cluster 4 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4dsi(A).
		2. Ligand: MPD × 1 (4s)-2-Methyl-2,4-Pentanediol PDB code: 6mu4(A).

Cluster 5 contains 2 ligand types

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Ligand		Description
		1. Ligand: SO4 × 13 Sulfate ion PDB codes: 2xy7(A), 2y1i(A), 2y1j(A), 4b9l(A), 4b9m(A), 4dsi(A), 4dsl(A), 4dwi(A), 6dsu(A), 6dsx(A), 6mu4(A), 6mu5(A), 7k5o(A).
		2. Ligand: MPD × 2 (4s)-2-Methyl-2,4-Pentanediol PDB codes: 6dsw(A), 6mu4(A).

Cluster 6 contains 1 ligand type

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Ligand		Description
		1. Ligand: SO4 × 10 Sulfate ion PDB codes: 2xo7(A), 2xy5(A), 2xy6(A), 4b9n(A), 4b9s(A), 4b9t(A), 4b9u(A), 4b9v(A), 4uqg(A), 7k5q(A).