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Magnesium in PDB 5bya: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pcp)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- (Pcp)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- (Pcp)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- (Pcp)2-IP4, PDB code: 5bya 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.567, 110.400, 41.455, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 19.9

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- (Pcp)2-IP4 (pdb code 5bya). 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 Adp and 1,5- (Pcp)2-IP4, PDB code: 5bya:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5bya

Go back to Magnesium Binding Sites List in 5bya
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 Adp and 1,5- (Pcp)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- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:9.4
occ:1.00
 O1B A:ADP401 2.0 10.6 1.0
O A:HOH599 2.0 12.0 1.0
OD1 A:ASN323 2.1 8.2 1.0
O A:HOH596 2.1 9.4 1.0
OD2 A:ASP321 2.1 9.7 1.0
OD1 A:ASP321 2.3 9.3 1.0
CG A:ASP321 2.6 8.9 1.0
PB A:ADP401 3.1 10.9 1.0
CG A:ASN323 3.1 8.0 1.0
O3B A:ADP401 3.3 9.5 1.0
ND2 A:ASN323 3.6 7.5 1.0
MG A:MG404 3.8 12.9 1.0
O51 A:4WZ402 3.9 13.2 1.0
NH1 A:ARG134 4.0 15.2 1.0
CB A:ASP321 4.1 8.9 1.0
O3A A:ADP401 4.2 10.5 1.0
O2B A:ADP401 4.2 10.4 1.0
O A:ALA191 4.3 10.8 1.0
CE1 A:HIS194 4.4 14.4 1.0
O A:HOH876 4.4 21.5 1.0
CB A:ASN323 4.5 8.9 1.0
O31 A:4WZ402 4.5 19.4 1.0
O A:HOH511 4.5 17.4 1.0
O A:HOH631 4.6 11.6 1.0
ND1 A:HIS194 4.6 12.2 1.0
O2A A:ADP401 4.6 9.7 1.0
NH2 A:ARG134 4.7 10.9 1.0
CZ A:ARG134 4.8 13.3 1.0
PA A:ADP401 4.9 10.4 1.0
CA A:ASN323 4.9 9.5 1.0
O A:HOH885 5.0 19.9 1.0
CA A:ASP321 5.0 8.7 1.0

Magnesium binding site 2 out of 5 in 5bya

Go back to Magnesium Binding Sites List in 5bya
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 Adp and 1,5- (Pcp)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- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.9
occ:1.00
 O3B A:ADP401 2.0 9.5 1.0
OD2 A:ASP309 2.1 11.2 1.0
O2A A:ADP401 2.1 9.7 1.0
O A:HOH568 2.1 11.4 1.0
O51 A:4WZ402 2.2 13.2 1.0
OD2 A:ASP321 2.2 9.7 1.0
PB1 A:4WZ402 3.2 16.7 1.0
CG A:ASP321 3.2 8.9 1.0
PB A:ADP401 3.2 10.9 1.0
CG A:ASP309 3.3 11.2 1.0
PA A:ADP401 3.3 10.4 1.0
O3A A:ADP401 3.6 10.5 1.0
CB A:ASP321 3.6 8.9 1.0
O61 A:4WZ402 3.7 17.2 1.0
O71 A:4WZ402 3.7 16.5 1.0
O A:HOH596 3.8 9.4 1.0
O1B A:ADP401 3.8 10.6 1.0
MG A:MG403 3.8 9.4 1.0
OD1 A:ASP309 3.9 14.1 1.0
O A:HOH657 3.9 17.4 1.0
ND2 A:ASN323 4.2 7.5 1.0
O3' A:ADP401 4.2 12.7 1.0
OD1 A:ASP321 4.3 9.3 1.0
C5' A:ADP401 4.3 10.7 1.0
O5' A:ADP401 4.3 10.3 1.0
CB A:ASP309 4.4 10.1 1.0
O1A A:ADP401 4.5 10.3 1.0
O2B A:ADP401 4.5 10.4 1.0
CB1 A:4WZ402 4.7 18.3 1.0
C3' A:ADP401 4.7 11.1 1.0
MG A:MG406 4.8 22.6 1.0
OD1 A:ASN323 4.8 8.2 1.0
O A:HOH742 4.9 49.3 1.0
CG A:ASN323 4.9 8.0 1.0
O21 A:4WZ402 5.0 23.4 1.0

Magnesium binding site 3 out of 5 in 5bya

Go back to Magnesium Binding Sites List in 5bya
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 Adp and 1,5- (Pcp)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- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:25.5
occ:1.00
 O A:HOH590 2.3 37.9 1.0
O A:PHE70 2.3 18.3 1.0
O A:HOH804 2.3 27.5 1.0
O A:ILE73 2.4 18.5 1.0
O A:SER68 2.4 16.5 1.0
O A:HOH816 2.4 33.5 1.0
C A:SER68 3.4 16.5 1.0
C A:PHE70 3.4 18.2 1.0
C A:ILE73 3.5 16.1 1.0
N A:ILE73 4.0 18.1 1.0
CA A:SER68 4.0 16.0 1.0
O A:LYS71 4.0 21.2 1.0
N A:PHE70 4.1 17.6 1.0
C A:LYS71 4.2 20.2 1.0
CA A:ILE73 4.3 16.7 1.0
OE1 A:GLN43 4.3 36.9 1.0
N A:LYS71 4.3 20.0 1.0
CA A:LYS71 4.3 21.5 1.0
C A:LEU69 4.4 18.5 1.0
CA A:PHE70 4.4 17.4 1.0
O A:HOH822 4.4 63.0 1.0
N A:LEU69 4.4 17.0 1.0
O A:HOH764 4.5 45.7 1.0
N A:THR74 4.6 16.2 1.0
CB A:SER68 4.7 17.2 1.0
CB A:ILE73 4.7 16.4 1.0
CA A:LEU69 4.7 18.1 1.0
N A:TYR72 4.8 19.0 1.0
O A:ILE67 4.8 15.9 1.0
O A:LEU69 4.8 18.8 1.0
CA A:THR74 4.9 17.2 1.0
CB A:PHE70 5.0 14.8 1.0

Magnesium binding site 4 out of 5 in 5bya

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


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 and 1,5- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:22.6
occ:1.00
 O61 A:4WZ402 1.9 17.2 1.0
O21 A:4WZ402 2.0 23.4 1.0
O A:HOH740 2.1 30.5 1.0
O A:HOH719 2.1 26.6 1.0
O A:HOH657 2.1 17.4 1.0
O46 A:4WZ402 2.4 34.9 1.0
PB1 A:4WZ402 3.1 16.7 1.0
PA1 A:4WZ402 3.2 20.0 1.0
CB1 A:4WZ402 3.6 18.3 1.0
O51 A:4WZ402 3.7 13.2 1.0
PA6 A:4WZ402 3.7 33.9 1.0
O16 A:4WZ402 3.8 31.6 1.0
NZ A:LYS248 3.9 37.8 1.0
O A:HOH568 4.0 11.4 1.0
O A:HOH669 4.1 50.5 1.0
O11 A:4WZ402 4.1 21.4 1.0
O A:HOH742 4.1 49.3 1.0
O A:HOH893 4.1 47.5 1.0
O A:HOH776 4.3 40.3 1.0
O71 A:4WZ402 4.3 16.5 1.0
O A:HOH539 4.4 45.9 1.0
O3B A:ADP401 4.4 9.5 1.0
O31 A:4WZ402 4.5 19.4 1.0
O A:HOH918 4.5 25.7 1.0
C1 A:4WZ402 4.6 24.9 1.0
O26 A:4WZ402 4.6 33.7 1.0
O36 A:4WZ402 4.7 29.9 1.0
MG A:MG404 4.8 12.9 1.0
O A:HOH596 4.8 9.4 1.0
C6 A:4WZ402 4.8 27.8 1.0
O A:HOH613 5.0 39.2 1.0

Magnesium binding site 5 out of 5 in 5bya

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


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 and 1,5- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:28.8
occ:1.00
 O A:HOH597 2.1 22.8 1.0
O A:HOH664 2.1 23.8 1.0
O A:HOH713 2.2 18.4 1.0
O A:HOH519 2.2 23.3 1.0
O A:HOH885 2.2 19.9 1.0
O A:HOH563 2.3 24.5 1.0
O A:ASN323 3.9 13.4 1.0
O A:HOH674 4.0 20.7 1.0
O A:HOH554 4.1 21.3 1.0
O42 A:4WZ402 4.1 22.3 1.0
O A:HOH543 4.2 25.4 1.0
OXT A:ACT415 4.3 23.7 1.0
O A:HOH876 4.4 21.5 1.0
O A:HIS101 4.4 13.1 1.0
OE2 A:GLU192 4.4 26.8 1.0
O33 A:4WZ402 4.5 27.5 1.0
O A:PHE325 4.5 11.2 1.0
O A:HOH569 4.6 22.2 1.0
CB A:ASN323 4.8 8.9 1.0
C A:ASN323 4.8 10.6 1.0
O43 A:4WZ402 4.9 25.9 1.0
O A:ACT415 4.9 26.7 1.0
C A:ACT415 5.0 27.3 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: Sun Sep 29 01:46:44 2024

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