Atomistry » Magnesium » PDB 8g6y-8gj2 » 8g9e
Atomistry »
  Magnesium »
    PDB 8g6y-8gj2 »
      8g9e »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy