Atomistry » Magnesium » PDB 4hmy-4hyv » 4hn2
Atomistry »
  Magnesium »
    PDB 4hmy-4hyv »
      4hn2 »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy