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Magnesium in PDB 4q4c: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8)

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8)

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-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 Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8), PDB code: 4q4c 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) 46.98 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.519, 110.224, 41.381, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) (pdb code 4q4c). 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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8), PDB code: 4q4c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4q4c

Go back to Magnesium Binding Sites List in 4q4c
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 Synthetic 1,5-(Pp)2-IP4 (1,5-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 Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:7.5
occ:1.00
 O A:HOH830 2.0 18.2 1.0
O61 A:I8P402 2.0 21.8 1.0
OD1 A:ASN323 2.1 13.9 1.0
O1B A:ADP401 2.1 13.9 1.0
OD2 A:ASP321 2.2 11.6 1.0
OD1 A:ASP321 2.3 12.4 1.0
CG A:ASP321 2.6 12.1 1.0
CG A:ASN323 3.1 12.9 1.0
PB A:ADP401 3.2 13.9 1.0
O3B A:ADP401 3.4 13.4 1.0
PB1 A:I8P402 3.5 37.0 1.0
ND2 A:ASN323 3.5 13.5 1.0
O51 A:I8P402 3.8 27.0 1.0
MG A:MG404 3.9 10.3 1.0
O A:HOH710 4.0 29.2 1.0
CB A:ASP321 4.1 11.3 1.0
CE1 A:HIS194 4.2 14.1 1.0
NH1 A:ARG134 4.2 10.9 0.6
O2B A:ADP401 4.3 15.0 1.0
O3A A:ADP401 4.3 14.2 1.0
O A:ALA191 4.4 13.2 1.0
O A:HOH716 4.4 22.3 1.0
CB A:ASN323 4.5 12.0 1.0
O71 A:I8P402 4.5 32.1 1.0
O41 A:I8P402 4.5 28.7 1.0
ND1 A:HIS194 4.5 13.5 1.0
O A:HOH610 4.6 23.6 1.0
NH2 A:ARG134 4.6 11.6 0.4
O2A A:ADP401 4.7 13.4 1.0
O A:HOH505 4.7 15.0 1.0
CA A:ASN323 4.9 11.5 1.0
PA A:ADP401 5.0 13.6 1.0

Magnesium binding site 2 out of 5 in 4q4c

Go back to Magnesium Binding Sites List in 4q4c
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 Synthetic 1,5-(Pp)2-IP4 (1,5-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 Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:10.3
occ:1.00
 OD2 A:ASP309 2.1 15.8 1.0
O2A A:ADP401 2.1 13.4 1.0
O A:HOH522 2.1 14.8 1.0
O51 A:I8P402 2.2 27.0 1.0
O3B A:ADP401 2.2 13.4 1.0
OD2 A:ASP321 2.2 11.6 1.0
CG A:ASP321 3.2 12.1 1.0
CG A:ASP309 3.3 14.6 1.0
PB1 A:I8P402 3.3 37.0 1.0
PB A:ADP401 3.3 13.9 1.0
PA A:ADP401 3.3 13.6 1.0
CB A:ASP321 3.6 11.3 1.0
O61 A:I8P402 3.7 21.8 1.0
O3A A:ADP401 3.7 14.2 1.0
O71 A:I8P402 3.7 32.1 1.0
O1B A:ADP401 3.8 13.9 1.0
O A:HOH581 3.9 28.8 1.0
MG A:MG403 3.9 7.5 1.0
NZ A:LYS248 3.9 14.9 1.0
OD1 A:ASP309 4.0 18.1 1.0
O3' A:ADP401 4.1 14.5 1.0
O A:HOH794 4.2 29.4 1.0
ND2 A:ASN323 4.2 13.5 1.0
OD1 A:ASP321 4.3 12.4 1.0
C5' A:ADP401 4.3 13.3 1.0
O5' A:ADP401 4.3 13.7 1.0
CB A:ASP309 4.3 13.1 1.0
O1A A:ADP401 4.5 13.6 1.0
O2B A:ADP401 4.6 15.0 1.0
C3' A:ADP401 4.6 13.3 1.0
O41 A:I8P402 4.8 28.7 1.0
NH2 A:ARG262 4.8 16.7 1.0
OD1 A:ASN323 4.9 13.9 1.0

Magnesium binding site 3 out of 5 in 4q4c

Go back to Magnesium Binding Sites List in 4q4c
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 Synthetic 1,5-(Pp)2-IP4 (1,5-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 Adp and Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:20.1
occ:1.00
 O A:HOH770 2.2 37.4 1.0
O A:ILE73 2.3 17.5 1.0
O A:PHE70 2.4 18.5 1.0
O A:HOH680 2.4 22.3 1.0
O A:SER68 2.4 19.5 1.0
O A:HOH637 2.8 36.2 1.0
C A:SER68 3.4 18.3 1.0
C A:ILE73 3.4 17.0 1.0
C A:PHE70 3.5 18.5 1.0
CA A:SER68 3.9 17.1 1.0
N A:ILE73 4.0 17.6 1.0
O A:LYS71 4.1 20.9 1.0
N A:PHE70 4.2 17.6 1.0
CA A:ILE73 4.2 16.8 1.0
C A:LYS71 4.2 20.9 1.0
NE2 A:GLN43 4.3 30.1 1.0
C A:LEU69 4.3 18.9 1.0
N A:LYS71 4.4 20.0 1.0
CA A:PHE70 4.4 17.7 1.0
N A:LEU69 4.4 19.0 1.0
CA A:LYS71 4.4 21.9 1.0
N A:THR74 4.5 16.7 1.0
O A:HOH557 4.5 18.3 1.0
CB A:ILE73 4.6 16.3 1.0
O A:ILE67 4.6 15.0 1.0
CB A:SER68 4.6 17.6 1.0
O A:LEU69 4.7 19.1 1.0
CA A:LEU69 4.7 19.7 1.0
CA A:THR74 4.8 16.8 1.0
N A:TYR72 4.8 19.8 1.0
CB A:PHE70 5.0 16.9 1.0

Magnesium binding site 4 out of 5 in 4q4c

Go back to Magnesium Binding Sites List in 4q4c
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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8)


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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:20.2
occ:1.00
 O44 A:I8P402 2.1 18.6 1.0
O25 A:I8P402 2.1 17.1 1.0
O A:HOH832 2.1 16.0 1.0
O A:HOH674 2.1 16.6 1.0
O A:HOH660 2.2 22.2 1.0
O A:HOH718 2.2 19.4 1.0
PA5 A:I8P402 3.2 17.0 1.0
PA4 A:I8P402 3.3 19.0 1.0
O35 A:I8P402 3.5 16.3 1.0
O14 A:I8P402 3.8 17.3 1.0
O A:HOH776 3.9 32.1 1.0
O34 A:I8P402 4.0 18.4 1.0
O A:HOH738 4.1 31.8 1.0
O65 A:I8P402 4.1 20.4 1.0
O A:HOH781 4.1 29.0 1.0
O A:LYS214 4.2 15.3 1.0
O15 A:I8P402 4.3 16.5 1.0
O45 A:I8P402 4.4 17.4 1.0
O A:HOH788 4.4 28.8 1.0
O A:HOH757 4.5 24.7 1.0
O24 A:I8P402 4.5 20.3 1.0
O A:HOH759 4.6 32.7 1.0
PB5 A:I8P402 4.7 20.1 1.0
O75 A:I8P402 4.9 21.0 1.0
C4 A:I8P402 4.9 16.9 1.0

Magnesium binding site 5 out of 5 in 4q4c

Go back to Magnesium Binding Sites List in 4q4c
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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8)


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 Synthetic 1,5-(Pp)2-IP4 (1,5-IP8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:21.7
occ:1.00
 O A:HOH645 2.1 21.5 1.0
O A:HOH615 2.1 16.1 1.0
O A:HOH714 2.1 23.5 1.0
O A:HOH651 2.1 17.1 1.0
O A:HOH796 2.2 20.4 1.0
O A:HOH612 2.2 21.4 1.0
O A:ASN323 3.8 12.6 1.0
O A:HOH679 4.0 17.8 1.0
O A:HOH710 4.1 29.2 1.0
O A:HIS101 4.1 12.9 1.0
O A:HOH670 4.2 22.8 1.0
O43 A:I8P402 4.4 15.9 1.0
O A:HOH551 4.4 16.8 1.0
O A:HOH716 4.4 22.3 1.0
O22 A:I8P402 4.6 25.9 1.0
OE1 A:GLU192 4.6 22.6 1.0
O42 A:I8P402 4.6 21.9 1.0
O A:PHE325 4.6 11.5 1.0
O A:HOH729 4.8 19.5 1.0
O31 A:I8P402 4.8 27.0 1.0
O A:HOH545 4.9 21.0 1.0
C A:ASN323 4.9 11.6 1.0
CB A:SER102 5.0 13.4 1.0
CA A:SER102 5.0 13.7 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: Tue Aug 20 01:46:14 2024

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