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Magnesium 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:

Fluorine (F) 10 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex, PDB code: 2q9p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2q9p

Go back to Magnesium Binding Sites List in 2q9p
Magnesium binding site 1 out of 4 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg301

b:16.2
occ:1.00
 F A:F403 2.0 13.1 1.0
F A:F410 2.1 21.9 1.0
OE1 A:GLU66 2.1 13.0 1.0
F A:F409 2.1 19.6 1.0
OE2 A:GLU70 2.2 11.9 1.0
F A:F405 2.2 21.4 1.0
CD A:GLU66 3.1 16.4 1.0
MG A:MG303 3.2 18.1 1.0
MG A:MG302 3.2 15.8 1.0
CD A:GLU70 3.2 13.8 1.0
OE2 A:GLU66 3.4 13.6 1.0
CG A:GLU70 3.5 12.9 1.0
MG A:MG304 3.5 16.3 1.0
O35 A:IHP201 3.6 13.4 0.6
O A:HOH837 3.6 24.9 1.0
F A:F404 3.8 16.4 1.0
O24 A:IHP201 3.8 8.5 0.3
OE2 A:GLU69 4.0 17.4 1.0
O A:GLY50 4.0 10.8 1.0
O A:HOH612 4.1 28.8 1.0
F A:F408 4.2 20.5 1.0
O A:HOH725 4.3 18.1 1.0
OE1 A:GLU70 4.3 12.6 1.0
O44 A:IHP201 4.4 9.6 0.6
CG A:GLU66 4.4 14.2 1.0
CA A:GLY51 4.5 12.3 1.0
O A:HOH589 4.5 24.7 1.0
C A:GLY50 4.7 12.4 1.0
O24 A:IHP201 4.7 12.7 0.6
O35 A:IHP201 4.8 10.4 0.3
O A:HOH836 4.8 23.3 1.0
CB A:GLU66 4.8 12.7 1.0
F A:F406 4.8 19.8 1.0
F A:F402 4.9 17.6 1.0
NH2 A:ARG115 4.9 19.1 1.0
N A:GLY51 4.9 13.1 1.0
CB A:GLU70 5.0 14.1 1.0

Magnesium binding site 2 out of 4 in 2q9p

Go back to Magnesium Binding Sites List in 2q9p
Magnesium binding site 2 out of 4 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg302

b:15.8
occ:1.00
 F A:F403 2.0 13.1 1.0
O24 A:IHP201 2.0 12.7 0.6
O35 A:IHP201 2.0 13.4 0.6
O A:GLY50 2.1 10.8 1.0
O35 A:IHP201 2.2 10.4 0.3
OE2 A:GLU70 2.2 11.9 1.0
F A:F402 2.2 17.6 1.0
O24 A:IHP201 2.3 8.5 0.3
CD A:GLU70 3.1 13.8 1.0
MG A:MG301 3.2 16.2 1.0
P5 A:IHP201 3.2 14.9 0.6
P4 A:IHP201 3.2 14.0 0.6
C A:GLY50 3.3 12.4 1.0
OE1 A:GLU70 3.4 12.6 1.0
P5 A:IHP201 3.4 9.8 0.3
P4 A:IHP201 3.4 13.5 0.3
O44 A:IHP201 3.4 9.6 0.6
O14 A:IHP201 3.6 16.6 0.3
O45 A:IHP201 3.6 18.9 0.6
O15 A:IHP201 3.6 20.5 0.6
O15 A:IHP201 3.6 14.9 0.3
CA A:GLY51 3.6 12.3 1.0
MG A:MG303 3.6 18.1 1.0
F A:F410 3.6 21.9 1.0
O A:HOH837 3.8 24.9 1.0
N A:GLY51 3.9 13.1 1.0
OE1 A:GLU66 3.9 13.0 1.0
O44 A:IHP201 4.0 7.8 0.3
NH2 A:ARG20 4.0 14.9 1.0
O45 A:IHP201 4.0 9.3 0.3
O14 A:IHP201 4.0 17.1 0.6
O A:HOH566 4.2 18.9 1.0
N A:GLY50 4.3 11.3 1.0
O34 A:IHP201 4.4 9.4 0.6
CA A:GLY50 4.4 11.2 1.0
CG A:GLU70 4.5 12.9 1.0
O25 A:IHP201 4.5 19.0 0.6
F A:F409 4.6 19.6 1.0
C4 A:IHP201 4.7 17.7 0.3
C5 A:IHP201 4.7 16.0 0.3
O25 A:IHP201 4.7 17.7 0.3
C5 A:IHP201 4.7 20.0 0.6
O34 A:IHP201 4.8 12.8 0.3
C4 A:IHP201 4.8 19.2 0.6
F A:F404 4.8 16.4 1.0
NH2 A:ARG115 4.8 19.1 1.0
CD A:GLU66 4.9 16.4 1.0

Magnesium binding site 3 out of 4 in 2q9p

Go back to Magnesium Binding Sites List in 2q9p
Magnesium binding site 3 out of 4 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg303

b:18.1
occ:1.00
 O A:HOH837 1.7 24.9 1.0
O44 A:IHP201 1.7 9.6 0.6
F A:F403 1.9 13.1 1.0
F A:F404 2.0 16.4 1.0
O A:HOH836 2.0 23.3 1.0
F A:F409 2.4 19.6 1.0
O45 A:IHP201 2.6 9.3 0.3
P4 A:IHP201 3.1 14.0 0.6
MG A:MG301 3.2 16.2 1.0
MG A:MG304 3.2 16.3 1.0
P5 A:IHP201 3.3 9.8 0.3
O35 A:IHP201 3.4 13.4 0.6
O15 A:IHP201 3.4 14.9 0.3
F A:F410 3.5 21.9 1.0
F A:F406 3.5 19.8 1.0
O46 A:IHP201 3.6 17.0 0.3
O A:HOH821 3.6 27.4 1.0
MG A:MG302 3.6 15.8 1.0
O24 A:IHP201 3.7 12.7 0.6
O35 A:IHP201 3.7 10.4 0.3
O14 A:IHP201 3.8 17.1 0.6
O24 A:IHP201 4.0 8.5 0.3
CA A:GLY51 4.1 12.3 1.0
N A:GLY52 4.2 12.7 1.0
OE2 A:GLU66 4.2 13.6 1.0
OE1 A:GLU66 4.2 13.0 1.0
O34 A:IHP201 4.3 9.4 0.6
O A:HOH803 4.4 49.0 1.0
OE2 A:GLU70 4.5 11.9 1.0
CD A:GLU66 4.5 16.4 1.0
O A:HOH612 4.6 28.8 1.0
C A:GLY51 4.7 13.2 1.0
F A:F407 4.7 20.7 1.0
C5 A:IHP201 4.8 16.0 0.3
P5 A:IHP201 4.8 14.9 0.6
P6 A:IHP201 4.8 20.7 0.3
O25 A:IHP201 4.9 17.7 0.3
F A:F408 4.9 20.5 1.0
O A:GLY50 4.9 10.8 1.0

Magnesium binding site 4 out of 4 in 2q9p

Go back to Magnesium Binding Sites List in 2q9p
Magnesium binding site 4 out of 4 in the Human Diphosphoinositol Polyphosphate Phosphohydrolase 1, Mg-F Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg304

b:16.3
occ:1.00
 F A:F409 1.9 19.6 1.0
F A:F404 2.0 16.4 1.0
OE2 A:GLU66 2.0 13.6 1.0
F A:F408 2.0 20.5 1.0
F A:F407 2.1 20.7 1.0
F A:F406 2.1 19.8 1.0
CD A:GLU66 3.1 16.4 1.0
MG A:MG303 3.2 18.1 1.0
OE1 A:GLU66 3.5 13.0 1.0
MG A:MG301 3.5 16.2 1.0
O A:HOH836 3.7 23.3 1.0
F A:F403 3.8 13.1 1.0
OE2 A:GLU69 3.9 17.4 1.0
O A:HOH637 4.0 43.3 1.0
NH1 A:ARG65 4.0 15.3 1.0
N A:GLY52 4.1 12.7 1.0
O A:HOH824 4.2 31.5 1.0
F A:F405 4.3 21.4 1.0
O A:GLY52 4.3 16.0 1.0
O A:HOH612 4.3 28.8 1.0
CG A:GLU66 4.3 14.2 1.0
O A:HOH837 4.5 24.9 1.0
O44 A:IHP201 4.6 9.6 0.6
O A:HOH821 4.6 27.4 1.0
F A:F410 4.8 21.9 1.0
CA A:GLY51 4.8 12.3 1.0
C A:GLY51 4.8 13.2 1.0
CA A:GLY52 4.8 13.2 1.0
NH2 A:ARG65 4.8 15.4 1.0
CZ A:ARG65 4.9 13.3 1.0
CD A:GLU69 5.0 16.0 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 Aug 14 02:39:22 2024

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