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Fluorine in PDB 2q9p: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex

Enzymatic activity of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex

All present enzymatic activity of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex:
3.6.1.52;

Protein crystallography data

The structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex, PDB code: 2q9p was solved by A.G.Thorsell, R.Busam, C.H.Arrowsmith, H.Berglund, R.Collins, L.G.Dahlgren, A.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, L.Holmberg-Schiavone, I.Johansson, A.Kallas, T.Karlberg, T.Kotenyova, L.Lehtio, M.Moche, P.Nordlund, T.Nyman, D.Ogg, J.Sagemark, M.Sundstrom, S.Van Den Berg, J.Weigelt, M.Welin, C.Persson, B.M.Hallberg, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.21 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.193, 59.444, 62.547, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23

Other elements in 2q9p:

The structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex (pdb code 2q9p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex, PDB code: 2q9p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 2q9p

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Fluorine binding site 1 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:17.6
occ:1.00
 MG A:MG302 2.2 15.8 1.0
OE1 A:GLU70 2.5 12.6 1.0
O A:GLY50 2.8 10.8 1.0
O45 A:IHP201 2.8 18.9 0.6
O44 A:IHP201 2.8 7.8 0.3
O A:HOH566 2.8 18.9 1.0
O24 A:IHP201 2.9 8.5 0.3
OE2 A:GLU70 3.0 11.9 1.0
O35 A:IHP201 3.1 13.4 0.6
CD A:GLU70 3.1 13.8 1.0
O24 A:IHP201 3.2 12.7 0.6
P4 A:IHP201 3.2 13.5 0.3
P5 A:IHP201 3.2 14.9 0.6
CD1 A:ILE47 3.3 16.1 1.0
O15 A:IHP201 3.5 20.5 0.6
O35 A:IHP201 3.5 10.4 0.3
O14 A:IHP201 3.5 16.6 0.3
N A:GLY50 3.8 11.3 1.0
C A:GLY50 3.9 12.4 1.0
F A:F403 4.1 13.1 1.0
O A:HOH602 4.1 24.4 1.0
NH2 A:ARG20 4.2 14.9 1.0
O33 A:IHP201 4.3 22.1 0.3
NH2 A:ARG115 4.4 19.1 1.0
NH1 A:ARG115 4.5 15.7 1.0
CA A:GLY50 4.5 11.2 1.0
O A:VAL48 4.5 11.5 1.0
CG1 A:ILE47 4.6 13.1 1.0
CA A:PRO49 4.6 10.8 1.0
CG A:GLU70 4.6 12.9 1.0
O46 A:IHP201 4.6 18.8 0.6
C A:PRO49 4.7 10.8 1.0
CZ A:ARG115 4.7 15.7 1.0
P4 A:IHP201 4.7 14.0 0.6
O34 A:IHP201 4.7 12.8 0.3
O25 A:IHP201 4.8 19.0 0.6
P5 A:IHP201 4.9 9.8 0.3
O15 A:IHP201 4.9 14.9 0.3
C5 A:IHP201 4.9 20.0 0.6
MG A:MG301 4.9 16.2 1.0
C4 A:IHP201 4.9 17.7 0.3
F A:F410 5.0 21.9 1.0

Fluorine binding site 2 out of 10 in 2q9p

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Fluorine binding site 2 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:13.1
occ:1.00
 MG A:MG303 1.9 18.1 1.0
MG A:MG302 2.0 15.8 1.0
MG A:MG301 2.0 16.2 1.0
O44 A:IHP201 2.5 9.6 0.6
O35 A:IHP201 2.6 13.4 0.6
O A:HOH837 2.7 24.9 1.0
OE2 A:GLU70 2.7 11.9 1.0
F A:F409 2.7 19.6 1.0
O24 A:IHP201 2.8 12.7 0.6
O35 A:IHP201 2.9 10.4 0.3
F A:F404 2.9 16.4 1.0
OE1 A:GLU66 2.9 13.0 1.0
F A:F410 2.9 21.9 1.0
O24 A:IHP201 3.1 8.5 0.3
O A:GLY50 3.1 10.8 1.0
P4 A:IHP201 3.2 14.0 0.6
CA A:GLY51 3.2 12.3 1.0
O45 A:IHP201 3.3 9.3 0.3
P5 A:IHP201 3.4 9.8 0.3
CD A:GLU66 3.6 16.4 1.0
O15 A:IHP201 3.7 14.9 0.3
MG A:MG304 3.8 16.3 1.0
OE2 A:GLU66 3.9 13.6 1.0
CD A:GLU70 3.9 13.8 1.0
C A:GLY50 3.9 12.4 1.0
O A:HOH836 4.0 23.3 1.0
N A:GLY51 4.0 13.1 1.0
F A:F402 4.1 17.6 1.0
O14 A:IHP201 4.1 17.1 0.6
F A:F405 4.2 21.4 1.0
P5 A:IHP201 4.2 14.9 0.6
C A:GLY51 4.3 13.2 1.0
N A:GLY52 4.3 12.7 1.0
O34 A:IHP201 4.4 9.4 0.6
P4 A:IHP201 4.6 13.5 0.3
OE1 A:GLU70 4.7 12.6 1.0
O14 A:IHP201 4.7 16.6 0.3
O15 A:IHP201 4.8 20.5 0.6
CG A:GLU66 4.8 14.2 1.0
CG A:GLU70 4.8 12.9 1.0
O45 A:IHP201 4.9 18.9 0.6
F A:F406 4.9 19.8 1.0
O25 A:IHP201 5.0 17.7 0.3
O25 A:IHP201 5.0 19.0 0.6

Fluorine binding site 3 out of 10 in 2q9p

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Fluorine binding site 3 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:16.4
occ:1.00
 MG A:MG303 2.0 18.1 1.0
MG A:MG304 2.0 16.3 1.0
F A:F409 2.6 19.6 1.0
N A:GLY52 2.7 12.7 1.0
O A:HOH836 2.8 23.3 1.0
O44 A:IHP201 2.8 9.6 0.6
F A:F406 2.9 19.8 1.0
OE2 A:GLU66 2.9 13.6 1.0
F A:F407 2.9 20.7 1.0
F A:F403 2.9 13.1 1.0
O A:HOH821 3.0 27.4 1.0
O45 A:IHP201 3.1 9.3 0.3
C A:GLY51 3.6 13.2 1.0
CA A:GLY51 3.6 12.3 1.0
O A:HOH837 3.6 24.9 1.0
CA A:GLY52 3.6 13.2 1.0
CD A:GLU66 3.7 16.4 1.0
MG A:MG301 3.8 16.2 1.0
OE1 A:GLU66 3.9 13.0 1.0
F A:F408 4.0 20.5 1.0
O A:GLY52 4.1 16.0 1.0
P4 A:IHP201 4.2 14.0 0.6
P5 A:IHP201 4.3 9.8 0.3
C A:GLY52 4.4 14.2 1.0
O35 A:IHP201 4.6 10.4 0.3
O A:HOH803 4.7 49.0 1.0
O A:GLY51 4.8 11.0 1.0
MG A:MG302 4.8 15.8 1.0
CG A:GLU66 4.8 14.2 1.0
O46 A:IHP201 4.8 17.0 0.3
O24 A:IHP201 4.8 12.7 0.6
F A:F410 4.9 21.9 1.0
O34 A:IHP201 4.9 9.4 0.6
O15 A:IHP201 4.9 14.9 0.3
O A:HOH611 4.9 42.5 1.0
N A:GLY51 5.0 13.1 1.0

Fluorine binding site 4 out of 10 in 2q9p

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Fluorine binding site 4 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:21.4
occ:1.00
 MG A:MG301 2.2 16.2 1.0
OE2 A:GLU69 2.6 17.4 1.0
O A:HOH725 2.7 18.1 1.0
OE1 A:GLU66 2.8 13.0 1.0
F A:F410 3.0 21.9 1.0
F A:F409 3.1 19.6 1.0
CG A:GLU70 3.2 12.9 1.0
CB A:GLU69 3.2 15.4 1.0
OE2 A:GLU70 3.4 11.9 1.0
CD A:GLU69 3.6 16.0 1.0
CD A:GLU66 3.6 16.4 1.0
F A:F408 3.8 20.5 1.0
O A:HOH612 3.8 28.8 1.0
CD A:GLU70 3.8 13.8 1.0
OE2 A:GLU66 4.0 13.6 1.0
CG A:GLU69 4.0 15.7 1.0
F A:F403 4.2 13.1 1.0
OD2 A:ASP109 4.2 14.8 1.0
N A:GLU70 4.2 14.9 1.0
MG A:MG304 4.3 16.3 1.0
O A:GLU66 4.3 12.2 1.0
O A:HOH589 4.3 24.7 1.0
C A:GLU69 4.4 15.3 1.0
CA A:GLU69 4.4 15.2 1.0
CB A:GLU70 4.5 14.1 1.0
OD1 A:ASP109 4.6 17.7 1.0
CA A:GLU70 4.7 14.4 1.0
OE1 A:GLU69 4.7 15.9 1.0
OE2 A:GLU108 4.7 26.8 1.0
CA A:GLU66 4.7 12.8 1.0
CG A:ASP109 4.8 18.8 1.0
CG A:GLU66 4.8 14.2 1.0
O A:GLU69 4.9 14.9 1.0
CB A:GLU66 4.9 12.7 1.0

Fluorine binding site 5 out of 10 in 2q9p

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Fluorine binding site 5 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:19.8
occ:1.00
 MG A:MG304 2.1 16.3 1.0
O A:HOH836 2.7 23.3 1.0
F A:F409 2.8 19.6 1.0
F A:F404 2.9 16.4 1.0
F A:F408 3.0 20.5 1.0
F A:F407 3.0 20.7 1.0
O A:HOH824 3.5 31.5 1.0
MG A:MG303 3.5 18.1 1.0
O A:HOH612 3.7 28.8 1.0
O A:HOH637 4.0 43.3 1.0
OE2 A:GLU66 4.1 13.6 1.0
O A:HOH803 4.2 49.0 1.0
O A:HOH821 4.2 27.4 1.0
O A:HOH837 4.4 24.9 1.0
MG A:MG301 4.8 16.2 1.0
F A:F403 4.9 13.1 1.0
O44 A:IHP201 5.0 9.6 0.6

Fluorine binding site 6 out of 10 in 2q9p

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Fluorine binding site 6 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:20.7
occ:1.00
 MG A:MG304 2.1 16.3 1.0
OE2 A:GLU66 2.8 13.6 1.0
O A:GLY52 2.8 16.0 1.0
O A:HOH637 2.8 43.3 1.0
F A:F404 2.9 16.4 1.0
F A:F406 3.0 19.8 1.0
F A:F408 3.0 20.5 1.0
NH2 A:ARG65 3.6 15.4 1.0
O A:HOH611 3.6 42.5 1.0
NH1 A:ARG65 3.6 15.3 1.0
C A:GLY52 3.7 14.2 1.0
N A:GLY52 3.9 12.7 1.0
F A:F409 3.9 19.6 1.0
CD A:GLU66 4.0 16.4 1.0
CZ A:ARG65 4.0 13.3 1.0
CA A:GLY52 4.0 13.2 1.0
CG A:GLU54 4.5 20.7 1.0
O A:HOH821 4.6 27.4 1.0
OE2 A:GLU54 4.6 32.3 1.0
CG A:GLU66 4.7 14.2 1.0
MG A:MG303 4.7 18.1 1.0
C A:GLY51 4.8 13.2 1.0
O A:HOH836 4.8 23.3 1.0
OE1 A:GLU66 4.9 13.0 1.0
N A:MET53 4.9 13.9 1.0

Fluorine binding site 7 out of 10 in 2q9p

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Fluorine binding site 7 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:20.5
occ:1.00
 MG A:MG304 2.0 16.3 1.0
OE2 A:GLU69 2.5 17.4 1.0
F A:F409 2.8 19.6 1.0
OE2 A:GLU66 2.8 13.6 1.0
O A:HOH824 2.9 31.5 1.0
F A:F406 3.0 19.8 1.0
F A:F407 3.0 20.7 1.0
NH1 A:ARG65 3.2 15.3 1.0
CD A:GLU69 3.3 16.0 1.0
O A:HOH637 3.4 43.3 1.0
OE1 A:GLU69 3.4 15.9 1.0
CD A:GLU66 3.6 16.4 1.0
F A:F405 3.8 21.4 1.0
O A:HOH612 3.9 28.8 1.0
F A:F404 4.0 16.4 1.0
OE1 A:GLU66 4.0 13.0 1.0
MG A:MG301 4.2 16.2 1.0
O A:HOH818 4.2 50.1 1.0
CZ A:ARG65 4.4 13.3 1.0
CG A:GLU66 4.8 14.2 1.0
CG A:GLU69 4.8 15.7 1.0
O A:HOH725 4.8 18.1 1.0
NH2 A:ARG65 4.8 15.4 1.0
MG A:MG303 4.9 18.1 1.0

Fluorine binding site 8 out of 10 in 2q9p

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Fluorine binding site 8 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F409

b:19.6
occ:1.00
 MG A:MG304 1.9 16.3 1.0
MG A:MG301 2.1 16.2 1.0
MG A:MG303 2.4 18.1 1.0
F A:F404 2.6 16.4 1.0
F A:F403 2.7 13.1 1.0
F A:F408 2.8 20.5 1.0
F A:F406 2.8 19.8 1.0
OE2 A:GLU66 2.9 13.6 1.0
F A:F410 2.9 21.9 1.0
O A:HOH612 3.0 28.8 1.0
F A:F405 3.1 21.4 1.0
OE1 A:GLU66 3.1 13.0 1.0
O A:HOH837 3.2 24.9 1.0
O A:HOH836 3.3 23.3 1.0
CD A:GLU66 3.4 16.4 1.0
OE2 A:GLU69 3.8 17.4 1.0
F A:F407 3.9 20.7 1.0
O44 A:IHP201 4.1 9.6 0.6
OE2 A:GLU70 4.2 11.9 1.0
O A:HOH824 4.2 31.5 1.0
O A:HOH725 4.5 18.1 1.0
O35 A:IHP201 4.6 13.4 0.6
MG A:MG302 4.6 15.8 1.0
CG A:GLU66 4.8 14.2 1.0
O45 A:IHP201 4.9 9.3 0.3
CA A:GLY51 4.9 12.3 1.0
O24 A:IHP201 5.0 8.5 0.3

Fluorine binding site 9 out of 10 in 2q9p

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Fluorine binding site 9 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F410

b:21.9
occ:1.00
 MG A:MG301 2.1 16.2 1.0
O A:HOH589 2.7 24.7 1.0
OE2 A:GLU70 2.8 11.9 1.0
O24 A:IHP201 2.9 8.5 0.3
O35 A:IHP201 2.9 13.4 0.6
O A:HOH837 2.9 24.9 1.0
F A:F409 2.9 19.6 1.0
F A:F403 2.9 13.1 1.0
F A:F405 3.0 21.4 1.0
O A:HOH612 3.4 28.8 1.0
MG A:MG303 3.5 18.1 1.0
NH2 A:ARG115 3.6 19.1 1.0
MG A:MG302 3.6 15.8 1.0
CD A:GLU70 3.7 13.8 1.0
O A:HOH725 3.8 18.1 1.0
P5 A:IHP201 4.0 14.9 0.6
CG A:GLU70 4.0 12.9 1.0
O A:HOH738 4.0 33.8 1.0
OD2 A:ASP109 4.1 14.8 1.0
OE1 A:GLU66 4.1 13.0 1.0
O25 A:IHP201 4.1 19.0 0.6
O45 A:IHP201 4.3 18.9 0.6
P4 A:IHP201 4.4 13.5 0.3
O34 A:IHP201 4.6 12.8 0.3
O A:HOH836 4.6 23.3 1.0
O44 A:IHP201 4.7 9.6 0.6
OE1 A:GLU70 4.8 12.6 1.0
MG A:MG304 4.8 16.3 1.0
F A:F404 4.9 16.4 1.0
OD1 A:ASP109 4.9 17.7 1.0
CZ A:ARG115 4.9 15.7 1.0
CG A:ASP109 4.9 18.8 1.0
F A:F402 5.0 17.6 1.0

Fluorine binding site 10 out of 10 in 2q9p

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Fluorine binding site 10 out of 10 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:9.5
occ:1.00
 O A:HOH647 3.1 17.5 1.0
O A:HOH559 3.2 11.5 1.0
ND2 A:ASN86 3.3 22.9 1.0
NE2 A:GLN136 3.7 18.0 1.0
CE1 A:HIS91 3.7 15.8 1.0
CG A:GLN136 3.8 12.2 1.0
CB A:VAL135 4.1 14.4 1.0
CD A:LYS133 4.2 19.8 1.0
CD A:GLN136 4.2 15.6 1.0
CB A:ASN86 4.2 17.1 1.0
CG A:ASN86 4.3 19.6 1.0
NE2 A:HIS91 4.4 19.2 1.0
N A:GLN136 4.5 10.8 1.0
O A:HOH838 4.7 24.6 1.0
CG2 A:VAL135 4.7 13.3 1.0
CG1 A:VAL135 4.7 14.0 1.0
CE A:LYS133 4.8 21.9 1.0
OH A:TYR139 4.8 12.5 1.0
ND1 A:HIS91 4.8 15.0 1.0
O A:HOH556 4.8 13.5 1.0
CB A:GLN136 4.9 13.7 1.0
CA A:VAL135 4.9 13.0 1.0
C A:VAL135 5.0 13.0 1.0

Reference:

A.G.Thorsell, C.Persson, S.Graslund, M.Hammarstrom, R.D.Busam, B.M.Hallberg. Crystal Structure of Human Diphosphoinositol Phosphatase 1. Proteins V. 77 242 2009.
ISSN: ISSN 0887-3585
PubMed: 19585659
DOI: 10.1002/PROT.22489
Page generated: Wed Jul 31 15:47:20 2024

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