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Magnesium 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 / Rfree (%) 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:

Fluorine (F) 2 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 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 Magnesium atom.
In total 5 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8g9e

Go back to Magnesium Binding Sites List in 8g9e
Magnesium binding site 1 out of 5 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 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 Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:16.1
occ:1.00
 O A:HOH538 2.0 16.9 1.0
O2B A:ANP401 2.0 14.7 1.0
O3G A:ANP401 2.0 16.4 1.0
ND2 A:ASN323 2.1 12.2 1.0
OD1 A:ASP321 2.2 15.2 1.0
OD2 A:ASP321 2.2 14.3 1.0
CG A:ASP321 2.5 15.8 1.0
PG A:ANP401 3.2 18.0 1.0
CG A:ASN323 3.2 15.9 1.0
PB A:ANP401 3.3 16.3 1.0
OD1 A:ASN323 3.6 21.8 1.0
N3B A:ANP401 3.6 18.1 1.0
O1G A:ANP401 3.6 16.3 1.0
MG A:MG404 3.9 17.3 1.0
CB A:ASP321 4.0 15.8 1.0
O A:HOH642 4.1 25.9 1.0
O A:HOH741 4.2 28.8 1.0
NH1 A:ARG134 4.3 18.9 1.0
O1B A:ANP401 4.3 17.7 1.0
O A:ALA191 4.4 16.7 1.0
O3A A:ANP401 4.4 16.0 1.0
O2A A:ANP401 4.4 16.1 1.0
CE1 A:HIS194 4.4 18.9 1.0
CB A:ASN323 4.5 16.0 1.0
O A:HOH517 4.5 26.3 1.0
O2G A:ANP401 4.5 17.2 1.0
O A:HOH676 4.6 16.8 1.0
ND1 A:HIS194 4.8 16.9 1.0
CA A:ASN323 4.8 15.4 1.0
PA A:ANP401 4.8 15.8 1.0
CA A:ASP321 4.9 12.8 1.0
OD2 A:ASP309 5.0 21.2 1.0
O A:VAL322 5.0 16.3 1.0

Magnesium binding site 2 out of 5 in 8g9e

Go back to Magnesium Binding Sites List in 8g9e
Magnesium binding site 2 out of 5 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 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 Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:17.3
occ:1.00
 OD2 A:ASP309 1.9 21.2 1.0
O2A A:ANP401 1.9 16.1 1.0
O1G A:ANP401 2.0 16.3 1.0
O A:HOH555 2.1 23.1 1.0
OD2 A:ASP321 2.1 14.3 1.0
CG A:ASP309 3.1 18.9 1.0
PG A:ANP401 3.1 18.0 1.0
CG A:ASP321 3.1 15.8 1.0
N3B A:ANP401 3.2 18.1 1.0
PA A:ANP401 3.4 15.8 1.0
CB A:ASP321 3.5 15.8 1.0
O3G A:ANP401 3.8 16.4 1.0
O3A A:ANP401 3.9 16.0 1.0
OD1 A:ASP309 3.9 23.5 1.0
PB A:ANP401 3.9 16.3 1.0
MG A:MG403 3.9 16.1 1.0
O2B A:ANP401 3.9 14.7 1.0
CB A:ASP309 4.0 13.8 1.0
OD1 A:ASN323 4.0 21.8 1.0
O3' A:ANP401 4.2 20.6 1.0
OD1 A:ASP321 4.3 15.2 1.0
O1A A:ANP401 4.3 17.6 1.0
O2G A:ANP401 4.3 17.2 1.0
O5' A:ANP401 4.4 15.8 1.0
C5' A:ANP401 4.5 18.1 1.0
C3' A:ANP401 4.7 18.5 1.0
NZ A:LYS248 4.7 65.1 1.0
ND2 A:ASN323 4.8 12.2 1.0
CG A:ASN323 4.8 15.9 1.0
CA A:ASP321 5.0 12.8 1.0

Magnesium binding site 3 out of 5 in 8g9e

Go back to Magnesium Binding Sites List in 8g9e
Magnesium binding site 3 out of 5 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 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 Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:26.0
occ:1.00
 O A:SER68 2.3 21.0 1.0
O A:ILE73 2.3 20.9 1.0
O A:PHE70 2.3 21.9 1.0
O A:HOH503 2.4 37.1 1.0
O A:HOH783 2.4 34.3 1.0
O A:HOH795 2.6 25.1 1.0
C A:SER68 3.3 20.5 1.0
C A:PHE70 3.5 21.8 1.0
C A:ILE73 3.5 21.5 1.0
O A:HOH606 3.5 41.3 1.0
CA A:SER68 3.9 19.5 1.0
N A:ILE73 4.0 20.9 1.0
O A:HOH634 4.1 53.4 1.0
NE2 A:GLN43 4.1 39.6 1.0
O A:LYS71 4.1 27.5 1.0
N A:PHE70 4.2 21.4 1.0
C A:LYS71 4.2 25.1 1.0
CA A:ILE73 4.2 20.3 1.0
C A:LEU69 4.3 22.9 1.0
N A:LEU69 4.3 20.9 1.0
N A:LYS71 4.4 25.1 1.0
CA A:PHE70 4.4 21.8 1.0
CA A:LYS71 4.4 27.9 1.0
N A:THR74 4.5 19.7 1.0
CB A:SER68 4.6 19.6 1.0
CA A:LEU69 4.7 21.4 1.0
O A:ILE67 4.7 18.8 1.0
O A:LEU69 4.7 22.7 1.0
CB A:ILE73 4.7 20.1 1.0
O A:HOH633 4.7 24.8 1.0
N A:TYR72 4.7 26.9 1.0
CA A:THR74 4.8 20.9 1.0
CB A:PHE70 5.0 19.1 1.0

Magnesium binding site 4 out of 5 in 8g9e

Go back to Magnesium Binding Sites List in 8g9e
Magnesium binding site 4 out of 5 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 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 Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:30.4
occ:1.00
 O44 A:YUT402 2.0 28.7 1.0
O A:HOH586 2.0 30.6 1.0
O A:HOH762 2.1 29.3 1.0
O35 A:YUT402 2.1 28.2 1.0
O A:HOH618 2.1 34.4 1.0
O A:HOH594 2.2 26.1 1.0
PA4 A:YUT402 3.3 25.1 1.0
PA5 A:YUT402 3.3 24.9 1.0
O A:HOH502 3.4 22.9 1.0
O25 A:YUT402 3.7 22.1 1.0
O A:HOH668 3.9 35.4 1.0
O34 A:YUT402 3.9 29.1 1.0
O14 A:YUT402 3.9 22.3 1.0
O75 A:YUT402 4.1 37.7 1.0
O A:HOH644 4.1 45.4 1.0
O A:HOH533 4.2 28.5 1.0
O A:HOH692 4.3 36.8 1.0
O15 A:YUT402 4.4 23.6 1.0
O A:LYS214 4.5 23.3 1.0
O A:HOH720 4.5 39.2 1.0
O24 A:YUT402 4.5 26.4 1.0
O55 A:YUT402 4.5 33.5 1.0
C45 A:YUT402 4.6 28.4 1.0
PB5 A:YUT402 4.7 32.4 1.0
CG A:ARG213 4.9 20.5 1.0
O A:HOH781 4.9 43.1 1.0
CD A:ARG213 4.9 22.1 1.0

Magnesium binding site 5 out of 5 in 8g9e

Go back to Magnesium Binding Sites List in 8g9e
Magnesium binding site 5 out of 5 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 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 Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:27.9
occ:1.00
 O A:HOH514 2.0 28.1 1.0
O A:HOH823 2.1 29.3 1.0
O A:HOH614 2.1 27.5 1.0
O A:HOH588 2.1 26.9 1.0
O A:HOH550 2.2 32.6 1.0
O A:HOH575 2.2 26.8 1.0
O A:ASN323 3.9 18.6 1.0
O A:HOH527 4.0 25.0 1.0
O33 A:YUT402 4.1 23.4 1.0
O A:HOH642 4.1 25.9 1.0
O A:HOH521 4.1 30.2 1.0
O A:HIS101 4.3 18.4 1.0
O22 A:YUT402 4.3 33.3 1.0
O A:HOH617 4.4 30.1 1.0
O A:HOH565 4.4 24.2 1.0
O A:HOH649 4.4 24.4 1.0
OE1 A:GLU192 4.4 42.5 1.0
O A:PHE325 4.5 13.2 1.0
O A:HOH741 4.5 28.8 1.0
O43 A:YUT402 4.7 26.3 1.0
C A:ASN323 4.9 15.8 1.0
CB A:ASN323 4.9 16.0 1.0
PA3 A:YUT402 5.0 23.4 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: Fri Oct 4 03:03:10 2024

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