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Magnesium in PDB 5byb: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4:
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 Adp and 1,5- (Pa)2-IP4, PDB code: 5byb 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) 35.57 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.807, 110.411, 41.423, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.6

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 Adp and 1,5- (Pa)2-IP4 (pdb code 5byb). 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 Adp and 1,5- (Pa)2-IP4, PDB code: 5byb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5byb

Go back to Magnesium Binding Sites List in 5byb
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 Adp and 1,5- (Pa)2-IP4


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 and 1,5- (Pa)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:10.7
occ:1.00
O A:HOH583 2.0 6.3 1.0
O1B A:ADP401 2.1 11.2 1.0
OD1 A:ASN323 2.2 10.8 1.0
OD2 A:ASP321 2.2 10.9 1.0
OD1 A:ASP321 2.2 10.8 1.0
CG A:ASP321 2.5 10.6 1.0
CG A:ASN323 3.1 11.0 1.0
PB A:ADP401 3.2 11.6 1.0
O3B A:ADP401 3.4 11.2 1.0
O A:HOH645 3.4 10.6 1.0
ND2 A:ASN323 3.5 10.4 1.0
MG A:MG404 3.7 11.0 1.0
CB A:ASP321 4.1 10.6 1.0
NH1 A:ARG134 4.1 13.8 1.0
O A:HOH593 4.2 28.6 1.0
O3A A:ADP401 4.2 11.7 1.0
O2B A:ADP401 4.3 11.9 1.0
CE1 A:HIS194 4.3 13.1 1.0
O A:ALA191 4.4 16.2 1.0
CB A:ASN323 4.4 11.3 1.0
O2A A:ADP401 4.5 11.3 1.0
ND1 A:HIS194 4.6 12.0 1.0
O A:HOH634 4.8 14.2 1.0
PA A:ADP401 4.9 12.1 1.0
CA A:ASN323 4.9 11.6 1.0
NH2 A:ARG134 5.0 12.2 1.0

Magnesium binding site 2 out of 3 in 5byb

Go back to Magnesium Binding Sites List in 5byb
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 Adp and 1,5- (Pa)2-IP4


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 and 1,5- (Pa)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:11.0
occ:1.00
O A:HOH525 2.1 8.5 1.0
O3B A:ADP401 2.1 11.2 1.0
OD2 A:ASP309 2.1 11.0 1.0
OD2 A:ASP321 2.2 10.9 1.0
O2A A:ADP401 2.2 11.3 1.0
O A:HOH645 2.2 10.6 1.0
CG A:ASP309 3.3 11.7 1.0
CG A:ASP321 3.3 10.6 1.0
PB A:ADP401 3.4 11.6 1.0
PA A:ADP401 3.6 12.1 1.0
MG A:MG403 3.7 10.7 1.0
CB A:ASP321 3.7 10.6 1.0
OD1 A:ASP309 3.8 12.3 1.0
NZ A:LYS248 3.8 19.6 1.0
O3A A:ADP401 3.9 11.7 1.0
O1B A:ADP401 3.9 11.2 1.0
ND2 A:ASN323 4.0 10.4 1.0
OD1 A:ASP321 4.3 10.8 1.0
O3' A:ADP401 4.3 12.1 1.0
C5' A:ADP401 4.4 12.0 1.0
CB A:ASP309 4.5 11.4 1.0
O5' A:ADP401 4.5 12.0 1.0
O2B A:ADP401 4.6 11.9 1.0
O1A A:ADP401 4.7 11.2 1.0
OD1 A:ASN323 4.7 10.8 1.0
CG A:ASN323 4.8 11.0 1.0
CE A:LYS248 4.8 18.7 1.0
C3' A:ADP401 4.9 12.2 1.0
O A:HOH640 5.0 46.9 1.0

Magnesium binding site 3 out of 3 in 5byb

Go back to Magnesium Binding Sites List in 5byb
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 Adp and 1,5- (Pa)2-IP4


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 and 1,5- (Pa)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:21.8
occ:1.00
O A:SER68 2.2 21.8 1.0
O A:PHE70 2.2 21.5 1.0
O A:ILE73 2.2 20.0 1.0
O A:HOH664 2.4 16.0 1.0
O A:HOH684 2.7 35.5 1.0
C A:SER68 3.2 19.7 1.0
C A:PHE70 3.4 23.4 1.0
C A:ILE73 3.4 18.9 1.0
CA A:SER68 3.8 18.7 1.0
N A:ILE73 4.0 20.4 1.0
N A:PHE70 4.1 22.3 1.0
CA A:ILE73 4.1 18.4 1.0
N A:LYS71 4.3 24.4 1.0
CA A:PHE70 4.3 21.5 1.0
OE1 A:GLN43 4.3 30.5 1.0
N A:LEU69 4.3 20.1 1.0
O A:LYS71 4.3 25.9 1.0
C A:LYS71 4.3 25.7 1.0
C A:LEU69 4.3 21.4 1.0
CA A:LYS71 4.4 26.4 1.0
N A:THR74 4.5 18.2 1.0
CB A:ILE73 4.5 17.8 1.0
CB A:SER68 4.5 18.9 1.0
CA A:LEU69 4.6 20.8 1.0
O A:ILE67 4.7 16.8 1.0
CA A:THR74 4.8 18.1 1.0
N A:TYR72 4.9 25.0 1.0
CB A:PHE70 4.9 21.1 1.0
O A:LEU69 4.9 21.7 1.0

Reference:

A.M.Riley, H.Wang, S.B.Shears, B.V.L Potter. Synthetic Tools For Studying the Chemical Biology of INSP8. Chem.Commun.(Camb.) V. 51 12605 2015.
ISSN: ESSN 1364-548X
PubMed: 26153667
DOI: 10.1039/C5CC05017K
Page generated: Mon Dec 14 20:04:32 2020

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