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Magnesium in PDB 4hn2: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5:
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 Amppnp and A Substrate Analog 5PA-IP5, PDB code: 4hn2 was solved by H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.23 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.666, 110.768, 41.536, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.2

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 Amppnp and A Substrate Analog 5PA-IP5 (pdb code 4hn2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 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 and A Substrate Analog 5PA-IP5, PDB code: 4hn2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4hn2

Go back to Magnesium Binding Sites List in 4hn2
Magnesium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5


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 and A Substrate Analog 5PA-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:36.4
occ:1.00
 O A:HOH738 1.8 43.2 1.0
O3G A:ANP401 1.9 38.4 1.0
OD2 A:ASP321 2.1 31.6 1.0
O2B A:ANP401 2.1 34.6 1.0
ND2 A:ASN323 2.1 26.7 1.0
OD1 A:ASP321 2.6 31.1 1.0
CG A:ASP321 2.7 27.7 1.0
PG A:ANP401 3.2 40.5 1.0
CG A:ASN323 3.3 27.5 1.0
PB A:ANP401 3.4 34.4 1.0
N3B A:ANP401 3.7 37.1 1.0
OD1 A:ASN323 3.8 32.0 1.0
O1G A:ANP401 3.9 39.9 1.0
O A:HOH737 4.0 40.1 1.0
MG A:MG404 4.0 43.3 1.0
CB A:ASP321 4.2 25.2 1.0
O A:HOH642 4.3 46.9 1.0
O A:ALA191 4.3 28.2 1.0
O1B A:ANP401 4.4 34.3 1.0
CE1 A:HIS194 4.4 28.8 1.0
O2G A:ANP401 4.4 39.0 1.0
NH2 A:ARG134 4.5 19.1 0.3
O3A A:ANP401 4.5 32.5 1.0
NH1 A:ARG134 4.5 26.0 0.7
CB A:ASN323 4.5 24.8 1.0
ND1 A:HIS194 4.6 29.1 1.0
O2A A:ANP401 4.7 31.8 1.0
O A:HOH581 4.8 32.1 1.0
O A:HOH567 4.8 30.1 1.0
O A:HOH776 4.9 53.4 1.0
CA A:ASN323 4.9 24.4 1.0
O A:VAL322 5.0 22.7 1.0
PA A:ANP401 5.0 29.7 1.0

Magnesium binding site 2 out of 4 in 4hn2

Go back to Magnesium Binding Sites List in 4hn2
Magnesium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5


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 and A Substrate Analog 5PA-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:43.3
occ:1.00
 OD2 A:ASP309 1.8 33.4 1.0
O2A A:ANP401 2.0 31.8 1.0
O1G A:ANP401 2.1 39.9 1.0
OD2 A:ASP321 2.4 31.6 1.0
N3B A:ANP401 2.7 37.1 1.0
PG A:ANP401 2.9 40.5 1.0
CG A:ASP309 3.0 28.2 1.0
CG A:ASP321 3.3 27.7 1.0
PA A:ANP401 3.4 29.7 1.0
O3G A:ANP401 3.6 38.4 1.0
CB A:ASP321 3.6 25.2 1.0
PB A:ANP401 3.7 34.4 1.0
OD1 A:ASP309 3.7 34.6 1.0
O2B A:ANP401 3.8 34.6 1.0
O3A A:ANP401 3.9 32.5 1.0
MG A:MG403 4.0 36.4 1.0
CB A:ASP309 4.1 23.8 1.0
OD1 A:ASN323 4.2 32.0 1.0
O2G A:ANP401 4.2 39.0 1.0
O3' A:ANP401 4.2 32.4 1.0
O A:HOH778 4.3 56.1 1.0
O1A A:ANP401 4.3 30.8 1.0
NZ A:LYS248 4.4 36.8 1.0
O5' A:ANP401 4.4 26.7 1.0
OD1 A:ASP321 4.5 31.1 1.0
C5' A:ANP401 4.5 28.8 1.0
C3' A:ANP401 4.6 31.3 1.0
ND2 A:ASN323 4.7 26.7 1.0
CG A:ASN323 4.9 27.5 1.0
NH2 A:ARG262 4.9 47.5 1.0

Magnesium binding site 3 out of 4 in 4hn2

Go back to Magnesium Binding Sites List in 4hn2
Magnesium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5


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 and A Substrate Analog 5PA-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:30.6
occ:1.00
 O A:ILE73 2.3 23.4 1.0
O A:SER68 2.3 26.6 1.0
O A:HOH695 2.3 53.7 1.0
O A:PHE70 2.3 26.6 1.0
O A:HOH657 2.4 35.7 1.0
O A:HOH777 2.6 49.7 1.0
C A:SER68 3.3 26.5 1.0
C A:ILE73 3.4 23.9 1.0
C A:PHE70 3.5 26.8 1.0
CA A:SER68 3.9 26.0 1.0
N A:ILE73 4.0 24.9 1.0
O A:HOH795 4.0 57.0 1.0
N A:PHE70 4.1 27.2 1.0
O A:LYS71 4.1 26.8 1.0
CA A:ILE73 4.2 24.1 1.0
C A:LYS71 4.2 27.3 1.0
NE2 A:GLN43 4.3 36.7 1.0
C A:LEU69 4.3 27.8 1.0
N A:LEU69 4.4 26.9 1.0
CA A:PHE70 4.4 26.6 1.0
N A:LYS71 4.4 27.5 1.0
CA A:LYS71 4.4 28.0 1.0
N A:THR74 4.5 23.9 1.0
O A:ILE67 4.6 24.2 1.0
O A:HOH741 4.6 31.2 1.0
CB A:ILE73 4.6 24.1 1.0
CB A:SER68 4.7 25.7 1.0
CA A:LEU69 4.7 28.1 1.0
O A:LEU69 4.7 28.2 1.0
O A:HOH732 4.7 66.0 1.0
N A:TYR72 4.7 26.6 1.0
CA A:THR74 4.8 25.1 1.0
CB A:PHE70 4.9 26.2 1.0

Magnesium binding site 4 out of 4 in 4hn2

Go back to Magnesium Binding Sites List in 4hn2
Magnesium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amppnp and A Substrate Analog 5PA-IP5


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 Amppnp and A Substrate Analog 5PA-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:47.0
occ:1.00
 O A:HOH686 2.1 48.0 1.0
O A:HOH628 2.1 38.9 1.0
O A:HOH573 2.2 39.8 1.0
O A:HOH653 2.2 46.3 1.0
O A:HOH776 2.3 53.4 1.0
O A:HOH560 2.4 37.0 1.0
O A:ASN323 3.8 26.4 1.0
O A:HOH593 3.9 39.7 1.0
O A:HOH737 4.2 40.1 1.0
O33 A:0EJ402 4.2 47.1 1.0
O A:HOH618 4.3 40.5 1.0
O22 A:0EJ402 4.3 42.1 1.0
O A:HOH729 4.3 48.5 1.0
O A:HIS101 4.4 24.2 1.0
O32 A:0EJ402 4.4 43.4 1.0
O A:HOH642 4.5 46.9 1.0
O A:HOH557 4.5 29.8 1.0
O A:PHE325 4.6 22.1 1.0
O31 A:0EJ402 4.7 53.6 1.0
C A:ASN323 4.9 24.7 1.0
OE1 A:GLU192 4.9 43.2 1.0
CB A:ASN323 5.0 24.8 1.0

Reference:

A.M.Riley, H.Wang, J.D.Weaver, S.B.Shears, B.V.Potter. First Synthetic Analogues of Diphosphoinositol Polyphosphates: Interaction with Pp-Insp(5) Kinase. Chem.Commun.(Camb.) V. 48 11292 2012.
ISSN: ISSN 1359-7345
PubMed: 23032903
DOI: 10.1039/C2CC36044F
Page generated: Fri Aug 16 16:20:20 2024

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