Atomistry » Magnesium » PDB 4pyl-4q8b » 4q4c
Atomistry »
  Magnesium »
    PDB 4pyl-4q8b »
      4q4c »

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: Mon Aug 11 22:14:34 2025

Last articles

Mg in 5ESS
Mg in 5ESU
Mg in 5ESO
Mg in 5ESR
Mg in 5ERM
Mg in 5ES4
Mg in 5ERV
Mg in 5ERR
Mg in 5ERS
Mg in 5ERU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy