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Fluorine in PDB 3t9e: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic):
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 Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic), PDB code: 3t9e was solved by H.Wang, J.Falck, T.M.T.Hall, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.070, 109.987, 41.338, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.3

Other elements in 3t9e:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic) also contains other interesting chemical elements:

Magnesium (Mg) 6 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 Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic) (pdb code 3t9e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic), PDB code: 3t9e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3t9e

Go back to Fluorine Binding Sites List in 3t9e
Fluorine binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic)


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 Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:39.9
occ:1.00
 F1 A:MGF701 0.0 39.9 1.0
MG A:MGF701 1.8 20.7 1.0
NH1 A:ARG213 2.4 24.5 1.0
O21 A:I7P501 2.6 19.1 1.0
O3B A:ADP401 2.8 8.0 1.0
F3 A:MGF701 3.0 11.4 1.0
NH2 A:ARG213 3.2 21.7 1.0
CZ A:ARG213 3.2 24.2 1.0
O A:HOH687 3.3 27.1 1.0
F2 A:MGF701 3.4 12.9 1.0
ND1 A:HIS194 3.5 11.8 1.0
O1B A:ADP401 3.6 11.5 1.0
O A:HOH730 3.7 33.2 1.0
PB A:ADP401 3.7 10.6 1.0
CE1 A:HIS194 3.8 14.0 1.0
O A:HOH597 3.9 23.3 1.0
O A:HOH610 4.2 15.1 1.0
CG A:HIS194 4.2 11.7 1.0
PA1 A:I7P501 4.2 20.1 1.0
MG A:MG602 4.3 10.0 1.0
O2B A:ADP401 4.4 11.1 1.0
O A:HOH18 4.5 9.2 1.0
NE A:ARG213 4.5 24.8 1.0
MG A:MG601 4.5 2.0 1.0
NE2 A:HIS194 4.6 12.0 1.0
O A:HOH460 4.6 20.5 1.0
C1 A:I7P501 4.6 18.0 1.0
O A:HOH27 4.8 13.1 1.0
CD2 A:HIS194 4.8 13.1 1.0
CB A:HIS194 4.9 9.3 1.0
O11 A:I7P501 4.9 19.1 1.0
O31 A:I7P501 5.0 19.3 1.0
O16 A:I7P501 5.0 17.6 1.0
O A:HOH590 5.0 15.8 1.0

Fluorine binding site 2 out of 3 in 3t9e

Go back to Fluorine Binding Sites List in 3t9e
Fluorine binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic)


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 Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:12.9
occ:1.00
 F2 A:MGF701 0.0 12.9 1.0
MG A:MGF701 1.9 20.7 1.0
MG A:MG602 2.0 10.0 1.0
NZ A:LYS248 2.7 18.1 1.0
O3B A:ADP401 2.7 8.0 1.0
O21 A:I7P501 2.8 19.1 1.0
OD2 A:ASP321 2.8 8.4 1.0
O A:HOH18 2.8 9.2 1.0
OD2 A:ASP309 3.0 10.1 1.0
F3 A:MGF701 3.0 11.4 1.0
ND2 A:ASN323 3.0 10.1 1.0
O A:HOH730 3.3 33.2 1.0
F1 A:MGF701 3.4 39.9 1.0
O41 A:I7P501 3.5 20.1 1.0
PA1 A:I7P501 3.6 20.1 1.0
MG A:MG601 3.7 2.0 1.0
OD1 A:ASP309 3.8 15.3 1.0
CG A:ASP309 3.8 10.3 1.0
CG A:ASN323 4.0 9.1 1.0
CG A:ASP321 4.0 8.0 1.0
O2A A:ADP401 4.0 10.2 1.0
PB A:ADP401 4.1 10.6 1.0
O A:HOH687 4.1 27.1 1.0
OD1 A:ASN323 4.1 10.0 1.0
CE A:LYS248 4.1 17.6 1.0
O31 A:I7P501 4.5 19.3 1.0
O2B A:ADP401 4.5 11.1 1.0
NH2 A:ARG262 4.7 16.8 1.0
CB A:ASP321 4.8 6.5 1.0
O A:HOH515 4.8 12.5 1.0
OD1 A:ASP321 4.8 8.6 1.0
O A:HOH610 4.9 15.1 1.0
CD A:LYS248 5.0 15.8 1.0
O11 A:I7P501 5.0 19.1 1.0

Fluorine binding site 3 out of 3 in 3t9e

Go back to Fluorine Binding Sites List in 3t9e
Fluorine binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp, 5-(Pp)-IP5 (5-IP7) and MGF3 (Transition State Mimic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:11.4
occ:1.00
 F3 A:MGF701 0.0 11.4 1.0
MG A:MG601 1.8 2.0 1.0
MG A:MGF701 1.8 20.7 1.0
O A:HOH610 2.6 15.1 1.0
OD1 A:ASN323 2.8 10.0 1.0
O3B A:ADP401 2.9 8.0 1.0
O2B A:ADP401 2.9 11.1 1.0
F1 A:MGF701 3.0 39.9 1.0
O21 A:I7P501 3.0 19.1 1.0
F2 A:MGF701 3.0 12.9 1.0
O A:HOH764 3.0 13.0 1.0
OD2 A:ASP321 3.2 8.4 1.0
PB A:ADP401 3.3 10.6 1.0
CE1 A:HIS194 3.3 14.0 1.0
CG A:ASN323 3.4 9.1 1.0
ND2 A:ASN323 3.5 10.1 1.0
ND1 A:HIS194 3.8 11.8 1.0
MG A:MG602 3.8 10.0 1.0
O31 A:I7P501 3.9 19.3 1.0
PA1 A:I7P501 4.0 20.1 1.0
CG A:ASP321 4.0 8.0 1.0
OD1 A:ASP321 4.1 8.6 1.0
O1B A:ADP401 4.1 11.5 1.0
NH2 A:ARG213 4.1 21.7 1.0
NE2 A:HIS194 4.5 12.0 1.0
O A:HOH638 4.6 17.8 1.0
CB A:ASN323 4.6 7.5 1.0
O41 A:I7P501 4.8 20.1 1.0
O3A A:ADP401 4.8 10.3 1.0
NH1 A:ARG213 4.9 24.5 1.0
O A:ALA191 4.9 11.2 1.0
CZ A:ARG213 5.0 24.2 1.0

Reference:

H.Wang, J.R.Falck, T.M.Hall, S.B.Shears. Structural Basis For An Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nat.Chem.Biol. V. 8 111 2011.
ISSN: ISSN 1552-4450
PubMed: 22119861
DOI: 10.1038/NCHEMBIO.733
Page generated: Mon Jul 14 19:26:14 2025

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