Fluorine in PDB 8g9e: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7:
2.7.4.21; 2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7, PDB code: 8g9e was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.52 / 1.75
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	88.082, 109.899, 41.09, 90, 90, 90
*R / R_free (%)*	12.4 / 17.5

Other elements in 8g9e:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 (pdb code 8g9e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7, PDB code: 8g9e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8g9e

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Fluorine Binding Sites List in 8g9e

Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F402 b:32.6 occ:1.00	F51	A:YUT402	0.0	32.6	1.0
	C45	A:YUT402	1.3	28.4	1.0
	F52	A:YUT402	2.2	31.6	1.0
	PA5	A:YUT402	2.5	24.9	1.0
	O26	A:YUT402	2.6	31.6	1.0
	PB5	A:YUT402	2.8	32.4	1.0
	O65	A:YUT402	2.9	38.0	1.0
	NZ	A:LYS214	2.9	25.5	1.0
	O25	A:YUT402	2.9	22.1	1.0
	O15	A:YUT402	3.0	23.6	1.0
	O36	A:YUT402	3.1	30.2	1.0
	O55	A:YUT402	3.2	33.5	1.0
	PA6	A:YUT402	3.2	27.6	1.0
	O	A:HOH611	3.2	36.5	1.0
	O16	A:YUT402	3.4	24.0	1.0
	CE	A:LYS214	3.4	28.0	1.0
	NZ	A:LYS278	3.6	78.7	1.0
	O	A:HOH507	3.7	44.2	1.0
	O35	A:YUT402	3.8	28.2	1.0
	O75	A:YUT402	3.9	37.7	1.0
	C5	A:YUT402	4.0	20.0	1.0
	C6	A:YUT402	4.2	22.1	1.0
	O	A:HOH619	4.3	35.5	1.0
	O46	A:YUT402	4.7	30.1	1.0
	CD	A:LYS214	4.7	28.6	1.0
	NH1	A:ARG273	4.8	30.7	1.0
	O	A:HOH533	5.0	28.5	1.0

Fluorine binding site 2 out of 2 in 8g9e

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Fluorine Binding Sites List in 8g9e

Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F402 b:31.6 occ:1.00	F52	A:YUT402	0.0	31.6	1.0
	C45	A:YUT402	1.4	28.4	1.0
	F51	A:YUT402	2.2	32.6	1.0
	PA5	A:YUT402	2.7	24.9	1.0
	PB5	A:YUT402	2.8	32.4	1.0
	O15	A:YUT402	2.9	23.6	1.0
	O75	A:YUT402	3.0	37.7	1.0
	O	A:HOH533	3.1	28.5	1.0
	O	A:HOH619	3.1	35.5	1.0
	O65	A:YUT402	3.1	38.0	1.0
	O35	A:YUT402	3.1	28.2	1.0
	O	A:HOH774	3.4	43.8	1.0
	NZ	A:LYS278	3.4	78.7	1.0
	O36	A:YUT402	3.6	30.2	1.0
	O	A:HOH507	3.6	44.2	1.0
	O	A:HOH502	3.8	22.9	1.0
	O25	A:YUT402	4.0	22.1	1.0
	O55	A:YUT402	4.0	33.5	1.0
	C5	A:YUT402	4.3	20.0	1.0
	PA6	A:YUT402	4.4	27.6	1.0
	O26	A:YUT402	4.5	31.6	1.0
	O16	A:YUT402	4.5	24.0	1.0
	C6	A:YUT402	4.7	22.1	1.0
	O	A:HOH611	4.7	36.5	1.0
	CE	A:LYS278	4.8	76.0	1.0
	O	A:HOH618	4.9	34.4	1.0

Reference:

S.Hostachy, H.Wang, G.Zong, K.Franke, A.M.Riley, P.Schmieder, B.V.L.Potter, S.B.Shears, D.Fiedler. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry V. 29 02426 2023.
ISSN: ISSN 0947-6539
PubMed: 37773020
DOI: 10.1002/CHEM.202302426

Page generated: Wed Jul 16 04:57:14 2025

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