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Magnesium in PDB 3t9b: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 5.2

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 5.2

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp at pH 5.2:
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 Amppnp at pH 5.2, PDB code: 3t9b was solved by H.Wang, J.Falck, T.M.T.Hall, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.44 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.788, 110.557, 41.249, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.1

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 Amppnp at pH 5.2 (pdb code 3t9b). 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 Amppnp at pH 5.2, PDB code: 3t9b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3t9b

Go back to Magnesium Binding Sites List in 3t9b
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 Amppnp at pH 5.2


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 Amppnp at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:9.9
occ:1.00
 O3G A:ANP401 1.9 11.0 1.0
O A:HOH3 2.0 13.6 1.0
O2B A:ANP401 2.0 9.4 1.0
OD1 A:ASN323 2.1 11.1 1.0
OD2 A:ASP321 2.2 10.5 1.0
OD1 A:ASP321 2.3 9.8 1.0
CG A:ASP321 2.6 8.1 1.0
PG A:ANP401 3.1 13.4 1.0
CG A:ASN323 3.2 10.6 1.0
PB A:ANP401 3.2 10.4 1.0
N3B A:ANP401 3.5 10.8 1.0
O1G A:ANP401 3.6 11.7 1.0
ND2 A:ASN323 3.6 10.0 1.0
MG A:MG602 3.8 10.4 1.0
O A:HOH563 3.9 23.3 1.0
CB A:ASP321 4.1 7.7 1.0
O1B A:ANP401 4.3 12.1 1.0
NH1 A:ARG134 4.3 14.8 1.0
O A:HOH656 4.3 59.0 1.0
O3A A:ANP401 4.3 9.7 1.0
O2G A:ANP401 4.4 12.3 1.0
O A:ALA191 4.4 12.0 1.0
O A:HOH579 4.4 27.1 1.0
CE1 A:HIS194 4.4 14.1 1.0
O2A A:ANP401 4.5 7.3 1.0
CB A:ASN323 4.5 9.7 1.0
O A:HOH405 4.7 11.8 1.0
ND1 A:HIS194 4.7 13.4 1.0
CA A:ASN323 4.8 8.9 1.0
PA A:ANP401 4.8 10.0 1.0
O A:VAL322 4.9 8.9 1.0
CA A:ASP321 5.0 7.8 1.0

Magnesium binding site 2 out of 3 in 3t9b

Go back to Magnesium Binding Sites List in 3t9b
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 Amppnp at pH 5.2


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 Amppnp at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:10.4
occ:1.00
 OD2 A:ASP309 1.9 13.2 1.0
O1G A:ANP401 1.9 11.7 1.0
O2A A:ANP401 2.0 7.3 1.0
O A:HOH16 2.1 11.9 1.0
OD2 A:ASP321 2.1 10.5 1.0
N3B A:ANP401 2.9 10.8 1.0
PG A:ANP401 3.0 13.4 1.0
CG A:ASP321 3.1 8.1 1.0
CG A:ASP309 3.2 10.9 1.0
PA A:ANP401 3.4 10.0 1.0
CB A:ASP321 3.5 7.7 1.0
PB A:ANP401 3.7 10.4 1.0
O3G A:ANP401 3.8 11.0 1.0
O2B A:ANP401 3.8 9.4 1.0
O A:HOH369 3.8 27.9 1.0
MG A:MG601 3.8 9.9 1.0
O3A A:ANP401 3.9 9.7 1.0
OD1 A:ASP309 3.9 13.1 1.0
O A:HOH394 4.0 30.0 1.0
ND2 A:ASN323 4.0 10.0 1.0
O3' A:ANP401 4.1 9.2 1.0
CB A:ASP309 4.2 8.3 1.0
O2G A:ANP401 4.2 12.3 1.0
OD1 A:ASP321 4.2 9.8 1.0
NZ A:LYS248 4.3 18.0 1.0
O1A A:ANP401 4.3 10.3 1.0
O5' A:ANP401 4.4 9.2 1.0
C5' A:ANP401 4.4 10.2 1.0
O A:HOH443 4.6 25.7 1.0
OD1 A:ASN323 4.7 11.1 1.0
C3' A:ANP401 4.7 9.9 1.0
CG A:ASN323 4.8 10.6 1.0

Magnesium binding site 3 out of 3 in 3t9b

Go back to Magnesium Binding Sites List in 3t9b
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 Amppnp at pH 5.2


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 Amppnp at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:14.7
occ:1.00
 O A:HOH565 2.2 46.9 1.0
O A:ILE73 2.3 12.1 1.0
O A:SER68 2.3 13.2 1.0
O A:PHE70 2.3 12.9 1.0
O A:HOH710 2.4 19.3 1.0
C A:SER68 3.4 12.8 1.0
C A:ILE73 3.4 12.0 1.0
C A:PHE70 3.5 14.2 1.0
O A:HOH379 3.6 42.7 1.0
N A:ILE73 4.0 12.9 1.0
CA A:SER68 4.0 12.6 1.0
O A:LYS71 4.1 15.6 1.0
N A:PHE70 4.2 14.0 1.0
CA A:ILE73 4.2 12.3 1.0
C A:LYS71 4.2 15.2 1.0
OE1 A:GLN43 4.3 26.8 1.0
C A:LEU69 4.3 14.1 1.0
N A:LYS71 4.4 14.6 1.0
N A:LEU69 4.4 13.6 1.0
CA A:PHE70 4.4 13.9 1.0
CA A:LYS71 4.4 15.8 1.0
N A:THR74 4.5 12.0 1.0
CB A:ILE73 4.6 12.0 1.0
CA A:LEU69 4.7 14.1 1.0
O A:ILE67 4.7 11.5 1.0
O A:HOH657 4.7 34.6 1.0
CB A:SER68 4.7 12.9 1.0
CA A:THR74 4.8 12.4 1.0
N A:TYR72 4.8 14.7 1.0
O A:LEU69 4.8 13.9 1.0
CB A:PHE70 5.0 13.9 1.0

Reference:

H.Wang, J.R.Falck, T.M.Hall, S.B.Shears. Structural Basis For An Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nat.Chem.Biol. V. 8 111 2011.
ISSN: ISSN 1552-4450
PubMed: 22119861
DOI: 10.1038/NCHEMBIO.733
Page generated: Mon Aug 11 03:49:30 2025

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