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Magnesium 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:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg601

b:2.0
occ:1.00
 F3 A:MGF701 1.8 11.4 1.0
O A:HOH764 2.0 13.0 1.0
O2B A:ADP401 2.1 11.1 1.0
OD1 A:ASN323 2.2 10.0 1.0
OD2 A:ASP321 2.4 8.4 1.0
OD1 A:ASP321 2.4 8.6 1.0
CG A:ASP321 2.7 8.0 1.0
CG A:ASN323 3.2 9.1 1.0
PB A:ADP401 3.2 10.6 1.0
MG A:MGF701 3.3 20.7 1.0
O3B A:ADP401 3.3 8.0 1.0
ND2 A:ASN323 3.6 10.1 1.0
O A:HOH610 3.7 15.1 1.0
F2 A:MGF701 3.7 12.9 1.0
MG A:MG602 3.9 10.0 1.0
CE1 A:HIS194 4.1 14.0 1.0
NH1 A:ARG134 4.2 8.5 0.7
CB A:ASP321 4.2 6.5 1.0
O1B A:ADP401 4.3 11.5 1.0
O3A A:ADP401 4.3 10.3 1.0
O A:ALA191 4.3 11.2 1.0
O A:HOH544 4.4 21.3 1.0
ND1 A:HIS194 4.5 11.8 1.0
F1 A:MGF701 4.5 39.9 1.0
CB A:ASN323 4.5 7.5 1.0
O21 A:I7P501 4.6 19.1 1.0
O A:HOH637 4.7 16.4 1.0
O A:HOH21 4.7 12.6 1.0
O2A A:ADP401 4.7 10.2 1.0
NH2 A:ARG134 4.8 7.4 0.3
NH2 A:ARG134 4.8 6.9 0.7
O A:HOH638 4.9 17.8 1.0
CA A:ASN323 4.9 7.5 1.0
CZ A:ARG134 5.0 7.7 0.7
PA A:ADP401 5.0 8.9 1.0

Magnesium binding site 2 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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:Mg602

b:10.0
occ:1.00
 F2 A:MGF701 2.0 12.9 1.0
OD2 A:ASP309 2.0 10.1 1.0
O2A A:ADP401 2.1 10.2 1.0
O A:HOH18 2.1 9.2 1.0
OD2 A:ASP321 2.1 8.4 1.0
O3B A:ADP401 2.2 8.0 1.0
MG A:MGF701 3.1 20.7 1.0
CG A:ASP321 3.1 8.0 1.0
PB A:ADP401 3.2 10.6 1.0
CG A:ASP309 3.3 10.3 1.0
PA A:ADP401 3.3 8.9 1.0
CB A:ASP321 3.6 6.5 1.0
O3A A:ADP401 3.6 10.3 1.0
F3 A:MGF701 3.8 11.4 1.0
NZ A:LYS248 3.8 18.1 1.0
MG A:MG601 3.9 2.0 1.0
O2B A:ADP401 3.9 11.1 1.0
OD1 A:ASP309 3.9 15.3 1.0
O A:HOH687 4.0 27.1 1.0
ND2 A:ASN323 4.2 10.1 1.0
O3' A:ADP401 4.2 10.3 1.0
OD1 A:ASP321 4.2 8.6 1.0
F1 A:MGF701 4.3 39.9 1.0
O5' A:ADP401 4.3 7.8 1.0
CB A:ASP309 4.4 7.5 1.0
O1A A:ADP401 4.4 9.9 1.0
C5' A:ADP401 4.4 8.6 1.0
O21 A:I7P501 4.6 19.1 1.0
O1B A:ADP401 4.6 11.5 1.0
O A:HOH730 4.7 33.2 1.0
C3' A:ADP401 4.7 9.6 1.0
OD1 A:ASN323 4.8 10.0 1.0
CG A:ASN323 5.0 9.1 1.0
NH2 A:ARG262 5.0 16.8 1.0

Magnesium binding site 3 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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:Mg603

b:16.8
occ:1.00
 O A:ILE73 2.2 13.9 1.0
O A:HOH430 2.2 42.7 1.0
O A:HOH645 2.3 23.6 1.0
O A:SER68 2.3 16.1 1.0
O A:PHE70 2.4 15.9 1.0
O A:HOH419 3.0 26.1 1.0
C A:SER68 3.3 15.5 1.0
C A:ILE73 3.4 14.0 1.0
C A:PHE70 3.5 16.6 1.0
CA A:SER68 3.8 15.1 1.0
N A:ILE73 3.9 14.9 1.0
CA A:ILE73 4.1 14.3 1.0
N A:PHE70 4.1 16.0 1.0
O A:LYS71 4.2 16.8 1.0
NE2 A:GLN43 4.2 25.9 1.0
C A:LYS71 4.3 17.2 1.0
N A:LEU69 4.3 15.9 1.0
CA A:PHE70 4.4 16.3 1.0
C A:LEU69 4.4 16.6 1.0
N A:THR74 4.4 14.2 1.0
N A:LYS71 4.5 17.4 1.0
O A:HOH495 4.5 17.1 1.0
CB A:ILE73 4.5 14.2 1.0
CB A:SER68 4.5 15.0 1.0
CA A:LYS71 4.6 18.1 1.0
O A:ILE67 4.6 14.2 1.0
CA A:THR74 4.6 14.2 1.0
CA A:LEU69 4.7 16.6 1.0
N A:TYR72 4.8 16.6 1.0
O A:LEU69 4.9 16.6 1.0
CB A:PHE70 5.0 15.9 1.0
C A:TYR72 5.0 15.6 1.0
N A:SER68 5.0 13.7 1.0

Magnesium binding site 4 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg604

b:22.8
occ:1.00
 O44 A:I7P501 2.0 18.9 1.0
O35 A:I7P501 2.1 17.6 1.0
O A:HOH545 2.2 20.5 1.0
O A:HOH699 2.2 23.7 1.0
O A:HOH646 2.2 16.6 1.0
O A:HOH648 2.3 21.7 1.0
PA5 A:I7P501 3.2 18.0 1.0
PA4 A:I7P501 3.3 19.7 1.0
O25 A:I7P501 3.5 16.0 1.0
O14 A:I7P501 3.8 18.0 1.0
O34 A:I7P501 3.9 17.9 1.0
O A:HOH671 4.0 21.8 1.0
O A:HOH468 4.0 30.4 1.0
O A:HOH714 4.1 27.9 1.0
O A:HOH748 4.1 30.9 1.0
O55 A:I7P501 4.1 20.1 1.0
O15 A:I7P501 4.3 17.2 1.0
O A:HOH722 4.3 31.3 1.0
O A:LYS214 4.4 15.8 1.0
O45 A:I7P501 4.4 18.7 1.0
O A:HOH379 4.4 40.0 1.0
O24 A:I7P501 4.6 18.9 1.0
O A:HOH668 4.7 27.5 1.0
PB5 A:I7P501 4.7 20.4 1.0
C4 A:I7P501 4.8 17.2 1.0
C5 A:I7P501 4.9 16.1 1.0
O75 A:I7P501 5.0 21.1 1.0
CD A:ARG213 5.0 22.9 1.0

Magnesium binding site 5 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg605

b:19.2
occ:1.00
 O A:HOH638 2.1 17.8 1.0
O A:HOH675 2.2 15.6 1.0
O A:HOH595 2.2 15.5 1.0
O A:HOH26 2.2 10.9 1.0
O A:HOH680 2.2 21.0 1.0
O A:HOH518 2.2 15.4 1.0
O A:ASN323 3.9 8.5 1.0
O A:HOH532 4.0 13.0 1.0
O A:HOH610 4.1 15.1 1.0
O A:HOH28 4.1 18.8 1.0
O32 A:I7P501 4.1 18.9 1.0
O A:HIS101 4.2 11.5 1.0
O22 A:I7P501 4.3 16.0 1.0
O A:HOH548 4.3 16.6 1.0
O A:HOH544 4.4 21.3 1.0
O33 A:I7P501 4.4 17.5 1.0
O A:PHE325 4.5 8.9 1.0
OE1 A:GLU192 4.5 19.2 1.0
O31 A:I7P501 4.6 19.3 1.0
O A:HOH659 4.8 20.4 1.0
C A:ASN323 4.9 8.0 1.0
O A:HOH563 5.0 20.4 1.0
PA2 A:I7P501 5.0 17.0 1.0
CB A:ASN323 5.0 7.5 1.0

Magnesium binding site 6 out of 6 in 3t9e

Go back to Magnesium Binding Sites List in 3t9e
Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg701

b:20.7
occ:1.00
 MG A:MGF701 0.0 20.7 1.0
F1 A:MGF701 1.8 39.9 1.0
F3 A:MGF701 1.8 11.4 1.0
F2 A:MGF701 1.9 12.9 1.0
O21 A:I7P501 1.9 19.1 1.0
O3B A:ADP401 2.3 8.0 1.0
MG A:MG602 3.1 10.0 1.0
MG A:MG601 3.3 2.0 1.0
PA1 A:I7P501 3.4 20.1 1.0
PB A:ADP401 3.4 10.6 1.0
OD2 A:ASP321 3.5 8.4 1.0
O A:HOH730 3.5 33.2 1.0
O A:HOH610 3.6 15.1 1.0
ND2 A:ASN323 3.8 10.1 1.0
O2B A:ADP401 3.8 11.1 1.0
O A:HOH18 3.9 9.2 1.0
O A:HOH687 3.9 27.1 1.0
O31 A:I7P501 4.0 19.3 1.0
O41 A:I7P501 4.0 20.1 1.0
NH2 A:ARG213 4.1 21.7 1.0
NH1 A:ARG213 4.1 24.5 1.0
O1B A:ADP401 4.1 11.5 1.0
OD1 A:ASN323 4.1 10.0 1.0
NZ A:LYS248 4.1 18.1 1.0
CG A:ASN323 4.3 9.1 1.0
CE1 A:HIS194 4.3 14.0 1.0
ND1 A:HIS194 4.3 11.8 1.0
O11 A:I7P501 4.5 19.1 1.0
CZ A:ARG213 4.5 24.2 1.0
OD2 A:ASP309 4.7 10.1 1.0
CG A:ASP321 4.7 8.0 1.0
C1 A:I7P501 4.8 18.0 1.0
O2A A:ADP401 4.8 10.2 1.0
O A:HOH764 4.8 13.0 1.0
O3A A:ADP401 4.8 10.3 1.0
O A:HOH597 4.9 23.3 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: Thu Aug 15 11:59:51 2024

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