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Magnesium in PDB 4q4d: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8):
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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8), PDB code: 4q4d 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) 47.01 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.790, 110.681, 41.379, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.6

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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8) (pdb code 4q4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8), PDB code: 4q4d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4q4d

Go back to Magnesium Binding Sites List in 4q4d
Magnesium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8)


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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:18.9
occ:1.00
 O A:HOH819 1.7 28.1 1.0
O3G A:ANP401 2.0 19.4 1.0
OD1 A:ASN323 2.1 17.0 1.0
O1B A:ANP401 2.1 18.3 1.0
OD2 A:ASP321 2.2 16.7 1.0
OD1 A:ASP321 2.4 15.2 1.0
CG A:ASP321 2.6 14.3 1.0
PG A:ANP401 3.1 23.5 1.0
CG A:ASN323 3.2 15.0 1.0
PB A:ANP401 3.4 17.4 1.0
O1G A:ANP401 3.6 22.5 1.0
ND2 A:ASN323 3.6 16.0 1.0
N3B A:ANP401 3.6 19.7 1.0
O A:HOH709 3.9 30.2 1.0
MG A:MG404 4.0 19.8 1.0
CB A:ASP321 4.1 12.2 1.0
O2B A:ANP401 4.3 17.5 1.0
O A:ALA191 4.3 13.5 1.0
CE1 A:HIS194 4.4 16.2 1.0
NH1 A:ARG134 4.4 10.1 0.6
CB A:ASN323 4.5 13.3 1.0
O2G A:ANP401 4.5 21.8 1.0
O3A A:ANP401 4.5 16.9 1.0
O A:HOH609 4.6 32.2 1.0
ND1 A:HIS194 4.7 16.1 1.0
O2A A:ANP401 4.7 16.2 1.0
NH2 A:ARG134 4.8 13.1 0.4
O A:HOH505 4.8 19.5 1.0
CA A:ASN323 4.8 12.1 1.0
O A:HOH714 4.8 46.2 1.0
O A:VAL322 4.9 11.3 1.0

Magnesium binding site 2 out of 3 in 4q4d

Go back to Magnesium Binding Sites List in 4q4d
Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8)


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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:19.8
occ:1.00
 OD2 A:ASP309 1.9 18.6 1.0
O1G A:ANP401 2.0 22.5 1.0
O2A A:ANP401 2.1 16.2 1.0
O A:HOH522 2.1 24.3 1.0
OD2 A:ASP321 2.3 16.7 1.0
N3B A:ANP401 2.9 19.7 1.0
PG A:ANP401 3.0 23.5 1.0
CG A:ASP309 3.2 15.9 1.0
CG A:ASP321 3.2 14.3 1.0
PA A:ANP401 3.5 16.0 1.0
CB A:ASP321 3.5 12.2 1.0
PB A:ANP401 3.8 17.4 1.0
O1B A:ANP401 3.8 18.3 1.0
O3G A:ANP401 3.8 19.4 1.0
O A:HOH580 3.9 40.2 1.0
OD1 A:ASP309 3.9 18.0 1.0
MG A:MG403 4.0 18.9 1.0
O3A A:ANP401 4.0 16.9 1.0
ND2 A:ASN323 4.0 16.0 1.0
CB A:ASP309 4.1 13.7 1.0
O2G A:ANP401 4.2 21.8 1.0
O3' A:ANP401 4.2 15.7 1.0
NZ A:LYS248 4.3 24.7 1.0
OD1 A:ASP321 4.3 15.2 1.0
O1A A:ANP401 4.4 15.5 1.0
O5' A:ANP401 4.5 15.5 1.0
C5' A:ANP401 4.5 15.7 1.0
OD1 A:ASN323 4.7 17.0 1.0
C3' A:ANP401 4.8 15.0 1.0
CG A:ASN323 4.8 15.0 1.0

Magnesium binding site 3 out of 3 in 4q4d

Go back to Magnesium Binding Sites List in 4q4d
Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and Synthetic 3,5-(Pp)2-IP4 (3,5-IP8)


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 Synthetic 3,5-(Pp)2-IP4 (3,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:17.5
occ:1.00
 O A:ILE73 2.3 15.6 1.0
O A:HOH678 2.3 19.2 1.0
O A:SER68 2.3 17.4 1.0
O A:HOH766 2.4 41.6 1.0
O A:PHE70 2.4 16.9 1.0
O A:HOH637 2.5 35.0 1.0
C A:SER68 3.4 16.8 1.0
C A:ILE73 3.5 15.2 1.0
C A:PHE70 3.6 18.0 1.0
CA A:SER68 3.9 15.8 1.0
N A:ILE73 4.0 15.9 1.0
O A:LYS71 4.1 19.2 1.0
N A:PHE70 4.2 17.2 1.0
CA A:ILE73 4.2 15.1 1.0
C A:LYS71 4.3 19.3 1.0
NE2 A:GLN43 4.3 29.0 1.0
C A:LEU69 4.4 18.3 1.0
N A:LEU69 4.4 17.5 1.0
N A:LYS71 4.5 18.3 1.0
CA A:PHE70 4.5 17.0 1.0
CA A:LYS71 4.5 20.2 1.0
N A:THR74 4.5 14.9 1.0
CB A:SER68 4.6 16.3 1.0
O A:HOH867 4.7 37.4 1.0
CB A:ILE73 4.7 14.8 1.0
CA A:LEU69 4.7 18.7 1.0
O A:ILE67 4.7 15.1 1.0
O A:HOH767 4.7 46.8 1.0
CA A:THR74 4.8 15.0 1.0
N A:TYR72 4.8 18.3 1.0
O A:LEU69 4.8 18.2 1.0

Reference:

S.Capolicchio, H.Wang, D.T.Thakor, S.B.Shears, H.J.Jessen. Synthesis of Densely Phosphorylated Bis-1,5-Diphospho-Myo-Inositol Tetrakisphosphate and Its Enantiomer By Bidirectional P-Anhydride Formation. Angew.Chem.Int.Ed.Engl. V. 53 9508 2014.
ISSN: ISSN 1433-7851
PubMed: 25044992
DOI: 10.1002/ANIE.201404398
Page generated: Mon Dec 14 19:21:39 2020

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