Atomistry » Magnesium » PDB 5dar-5djg » 5dgh
Atomistry »
  Magnesium »
    PDB 5dar-5djg »
      5dgh »

Magnesium in PDB 5dgh: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-IP5

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-IP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (Pcp)-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 Amp-Pnp and 5- (Pcp)-IP5, PDB code: 5dgh 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) 29.04 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.900, 110.340, 41.253, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.1

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 Amp-Pnp and 5- (Pcp)-IP5 (pdb code 5dgh). 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 Amp-Pnp and 5- (Pcp)-IP5, PDB code: 5dgh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5dgh

Go back to Magnesium Binding Sites List in 5dgh
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 Amp-Pnp and 5- (Pcp)-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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:16.4
occ:1.00
 O A:HOH563 1.9 21.5 1.0
O1B A:ANP401 2.0 16.7 1.0
O3G A:ANP401 2.1 19.4 1.0
OD1 A:ASN323 2.2 14.6 1.0
OD2 A:ASP321 2.2 15.2 1.0
OD1 A:ASP321 2.2 14.9 1.0
CG A:ASP321 2.5 14.0 1.0
PG A:ANP401 3.2 20.4 1.0
CG A:ASN323 3.2 13.6 1.0
PB A:ANP401 3.3 18.2 1.0
N3B A:ANP401 3.6 18.1 1.0
ND2 A:ASN323 3.7 12.9 1.0
O1G A:ANP401 3.8 18.7 1.0
MG A:MG404 3.9 16.3 1.0
O A:HOH533 3.9 28.5 1.0
CB A:ASP321 4.0 13.2 1.0
NH1 A:ARG134 4.2 17.8 1.0
O A:ALA191 4.3 17.5 1.0
O2B A:ANP401 4.3 17.2 1.0
CE1 A:HIS194 4.3 15.0 1.0
O A:HOH740 4.4 28.9 1.0
O3A A:ANP401 4.4 18.7 1.0
O2A A:ANP401 4.5 18.1 1.0
O2G A:ANP401 4.5 19.2 1.0
O A:HOH613 4.5 13.4 1.0
CB A:ASN323 4.5 12.3 1.0
O A:HOH510 4.6 19.2 1.0
ND1 A:HIS194 4.7 14.1 1.0
PA A:ANP401 4.8 18.5 1.0
CA A:ASN323 4.8 12.2 1.0
NH2 A:ARG134 4.9 15.8 1.0
CA A:ASP321 5.0 12.3 1.0
CZ A:ARG134 5.0 16.6 1.0

Magnesium binding site 2 out of 5 in 5dgh

Go back to Magnesium Binding Sites List in 5dgh
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 Amp-Pnp and 5- (Pcp)-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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:16.3
occ:1.00
 O2A A:ANP401 2.0 18.1 1.0
O1G A:ANP401 2.0 18.7 1.0
O A:HOH574 2.0 22.9 1.0
OD2 A:ASP309 2.1 16.3 1.0
OD2 A:ASP321 2.2 15.2 1.0
N3B A:ANP401 2.8 18.1 1.0
PG A:ANP401 2.9 20.4 1.0
CG A:ASP321 3.2 14.0 1.0
CG A:ASP309 3.3 14.6 1.0
PA A:ANP401 3.3 18.5 1.0
CB A:ASP321 3.5 13.2 1.0
O3G A:ANP401 3.7 19.4 1.0
PB A:ANP401 3.7 18.2 1.0
O1B A:ANP401 3.8 16.7 1.0
O3A A:ANP401 3.9 18.7 1.0
MG A:MG403 3.9 16.4 1.0
OD1 A:ASP309 4.0 14.5 1.0
ND2 A:ASN323 4.1 12.9 1.0
O A:HOH501 4.1 30.5 1.0
O2G A:ANP401 4.2 19.2 1.0
O3' A:ANP401 4.2 18.2 1.0
CB A:ASP309 4.2 13.5 1.0
OD1 A:ASP321 4.3 14.9 1.0
O1A A:ANP401 4.3 18.7 1.0
O5' A:ANP401 4.4 18.8 1.0
C5' A:ANP401 4.5 18.7 1.0
NZ A:LYS248 4.5 24.9 1.0
OD1 A:ASN323 4.7 14.6 1.0
C3' A:ANP401 4.8 18.0 1.0
CG A:ASN323 4.9 13.6 1.0
O A:HOH708 5.0 29.2 1.0

Magnesium binding site 3 out of 5 in 5dgh

Go back to Magnesium Binding Sites List in 5dgh
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 Amp-Pnp and 5- (Pcp)-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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:23.9
occ:1.00
 O A:SER68 2.2 23.0 1.0
O A:PHE70 2.2 21.7 1.0
O A:ILE73 2.2 21.0 1.0
O A:HOH540 2.3 46.6 1.0
O A:HOH654 2.5 26.3 1.0
O A:HOH701 2.5 22.6 1.0
C A:SER68 3.2 22.5 1.0
C A:ILE73 3.4 20.4 1.0
C A:PHE70 3.4 23.6 1.0
CA A:SER68 3.8 21.1 1.0
N A:ILE73 3.9 21.4 1.0
O A:HOH635 4.0 35.0 1.0
O A:LYS71 4.1 26.0 1.0
N A:PHE70 4.1 22.3 1.0
CA A:ILE73 4.1 20.2 1.0
C A:LEU69 4.2 23.5 1.0
N A:LEU69 4.2 21.6 1.0
C A:LYS71 4.2 25.5 1.0
CA A:PHE70 4.3 22.3 1.0
N A:LYS71 4.3 24.6 1.0
N A:THR74 4.5 20.5 1.0
CA A:LYS71 4.5 27.0 1.0
CA A:LEU69 4.5 23.6 1.0
CB A:SER68 4.5 21.3 1.0
CB A:ILE73 4.5 19.4 1.0
O A:LEU69 4.6 23.4 1.0
OE1 A:GLN43 4.6 38.0 1.0
O A:ILE67 4.6 19.4 1.0
O A:HOH558 4.8 31.0 1.0
N A:TYR72 4.8 25.2 1.0
CA A:THR74 4.8 22.5 1.0
NE2 A:GLN43 4.8 37.9 1.0
CB A:PHE70 4.9 21.0 1.0

Magnesium binding site 4 out of 5 in 5dgh

Go back to Magnesium Binding Sites List in 5dgh
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 Amp-Pnp and 5- (Pcp)-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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:49.9
occ:1.00
 O A:HOH731 2.1 30.1 1.0
O A:HOH520 2.2 32.0 1.0
O A:HOH697 2.3 32.7 1.0
O A:HOH571 2.3 33.7 1.0
O A:HOH587 2.4 32.6 1.0
O A:HOH506 2.4 33.6 1.0
O A:ASN323 3.7 12.9 1.0
O A:HOH605 4.1 16.9 1.0
O A:HIS101 4.2 14.8 1.0
O A:HOH557 4.2 35.1 1.0
O A:HOH593 4.3 21.6 1.0
OE2 A:GLU192 4.4 33.7 1.0
O33 A:5A3402 4.4 29.2 1.0
O A:HOH533 4.5 28.5 1.0
O A:HOH740 4.5 28.9 1.0
O A:PHE325 4.5 12.1 1.0
O A:HOH580 4.7 23.1 1.0
O22 A:5A3402 4.7 30.6 1.0
C A:ASN323 4.7 12.2 1.0
O A:HOH579 4.7 25.1 1.0
O A:HOH712 4.9 21.3 1.0
CB A:ASN323 4.9 12.3 1.0

Magnesium binding site 5 out of 5 in 5dgh

Go back to Magnesium Binding Sites List in 5dgh
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 Amp-Pnp and 5- (Pcp)-IP5


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 Amp-Pnp and 5- (Pcp)-IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:48.4
occ:1.00
 O A:HOH651 2.0 47.9 1.0
O A:HOH559 2.1 28.3 1.0
O35 A:5A3402 2.1 36.5 1.0
O44 A:5A3402 2.2 32.4 1.0
O A:HOH728 2.3 35.8 1.0
O A:HOH568 2.8 53.3 1.0
PA5 A:5A3402 3.4 35.9 1.0
O25 A:5A3402 3.6 31.4 1.0
PA4 A:5A3402 3.6 33.6 1.0
O75 A:5A3402 4.0 45.0 1.0
O14 A:5A3402 4.1 32.1 1.0
O34 A:5A3402 4.1 31.9 1.0
O A:LYS214 4.2 22.5 1.0
O65 A:5A3402 4.3 43.4 1.0
O A:HOH608 4.3 37.5 1.0
O15 A:5A3402 4.4 32.1 1.0
PB5 A:5A3402 4.5 42.5 1.0
CB5 A:5A3402 4.7 38.6 1.0
O24 A:5A3402 4.7 33.0 1.0

Reference:

A.Hager, M.Wu, H.Wang, N.W.Brown, S.B.Shears, N.Veiga, D.Fiedler. Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues. Chemistry V. 22 12406 2016.
ISSN: ISSN 0947-6539
PubMed: 27460418
DOI: 10.1002/CHEM.201601754
Page generated: Sun Sep 29 02:46:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy