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

Magnesium in PDB 5dgi: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 3,5- (Pcp)2-IP4

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 3,5- (Pcp)2-IP4

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 3,5- (Pcp)2-IP4:
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 3,5- (Pcp)2-IP4, PDB code: 5dgi 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) 29.08 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.268, 110.205, 41.236, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 20.3

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 3,5- (Pcp)2-IP4 (pdb code 5dgi). 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 Adp and 3,5- (Pcp)2-IP4, PDB code: 5dgi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5dgi

Go back to Magnesium Binding Sites List in 5dgi
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 Adp and 3,5- (Pcp)2-IP4


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 3,5- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:10.7
occ:1.00
 O1B A:ADP401 2.2 13.6 1.0
O A:HOH515 2.2 16.1 1.0
OD1 A:ASN323 2.2 12.8 1.0
O A:HOH705 2.2 13.6 1.0
OD2 A:ASP321 2.2 12.0 1.0
OD1 A:ASP321 2.2 12.2 1.0
CG A:ASP321 2.5 13.0 1.0
CG A:ASN323 3.2 12.5 1.0
PB A:ADP401 3.2 14.7 1.0
O3B A:ADP401 3.4 14.0 1.0
ND2 A:ASN323 3.6 13.2 1.0
MG A:MG404 3.8 14.9 1.0
CB A:ASP321 4.1 13.5 1.0
O A:HOH742 4.1 16.1 1.0
NH1 A:ARG134 4.1 16.1 0.7
O3A A:ADP401 4.2 14.4 1.0
CE1 A:HIS194 4.2 19.3 1.0
O A:HOH710 4.2 24.4 1.0
O A:HOH503 4.3 23.2 1.0
O2B A:ADP401 4.3 16.9 1.0
O A:ALA191 4.4 17.0 1.0
CB A:ASN323 4.5 13.1 1.0
ND1 A:HIS194 4.6 17.4 1.0
NH2 A:ARG134 4.6 15.8 0.3
O A:HOH808 4.6 35.5 1.0
O A:HOH736 4.7 39.5 1.0
O A:HOH676 4.7 19.0 1.0
O2A A:ADP401 4.8 13.4 1.0
O A:HOH743 4.9 31.7 1.0
CA A:ASN323 4.9 13.2 1.0
NH2 A:ARG134 4.9 15.3 0.7
CA A:ASP321 5.0 13.5 1.0
PA A:ADP401 5.0 14.8 1.0
CZ A:ARG134 5.0 16.0 0.7
O A:VAL322 5.0 14.0 1.0

Magnesium binding site 2 out of 3 in 5dgi

Go back to Magnesium Binding Sites List in 5dgi
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 Adp and 3,5- (Pcp)2-IP4


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 3,5- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:14.9
occ:1.00
 OD2 A:ASP309 2.1 15.7 1.0
O3B A:ADP401 2.2 14.0 1.0
O2A A:ADP401 2.2 13.4 1.0
OD2 A:ASP321 2.2 12.0 1.0
O A:HOH742 2.2 16.1 1.0
O A:HOH549 2.2 15.2 1.0
CG A:ASP321 3.2 13.0 1.0
PB A:ADP401 3.3 14.7 1.0
CG A:ASP309 3.3 16.9 1.0
PA A:ADP401 3.3 14.8 1.0
CB A:ASP321 3.6 13.5 1.0
O3A A:ADP401 3.6 14.4 1.0
MG A:MG403 3.8 10.7 1.0
O1B A:ADP401 3.9 13.6 1.0
O A:HOH774 3.9 37.4 1.0
OD1 A:ASP309 3.9 19.9 1.0
O A:HOH705 4.0 13.6 1.0
NZ A:LYS248 4.1 33.4 1.0
O A:HOH736 4.1 39.5 1.0
O3' A:ADP401 4.2 16.0 1.0
OD1 A:ASP321 4.2 12.2 1.0
ND2 A:ASN323 4.2 13.2 1.0
C5' A:ADP401 4.3 15.4 1.0
O5' A:ADP401 4.3 14.0 1.0
CB A:ASP309 4.4 15.8 1.0
O1A A:ADP401 4.5 15.9 1.0
O2B A:ADP401 4.6 16.9 1.0
C3' A:ADP401 4.7 15.4 1.0
OD1 A:ASN323 4.9 12.8 1.0

Magnesium binding site 3 out of 3 in 5dgi

Go back to Magnesium Binding Sites List in 5dgi
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 Adp and 3,5- (Pcp)2-IP4


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 3,5- (Pcp)2-IP4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:27.4
occ:1.00
 O A:HOH653 2.2 40.8 1.0
O A:HOH750 2.2 39.6 1.0
O A:HOH598 2.2 31.5 1.0
O A:PHE70 2.2 24.8 1.0
O A:SER68 2.2 23.6 1.0
O A:ILE73 2.2 25.7 1.0
C A:SER68 3.2 21.5 1.0
C A:PHE70 3.4 24.0 1.0
C A:ILE73 3.4 21.9 1.0
CA A:SER68 3.9 20.3 1.0
N A:ILE73 3.9 23.4 1.0
N A:PHE70 4.1 25.1 1.0
CA A:ILE73 4.1 21.0 1.0
O A:HOH593 4.1 47.9 1.0
O A:LYS71 4.2 31.3 1.0
OE1 A:GLN43 4.2 46.4 1.0
C A:LEU69 4.2 25.8 1.0
C A:LYS71 4.2 29.6 1.0
N A:LEU69 4.3 22.0 1.0
CA A:PHE70 4.3 24.0 1.0
N A:LYS71 4.3 26.5 1.0
CA A:LYS71 4.4 29.1 1.0
N A:THR74 4.5 22.8 1.0
CA A:LEU69 4.6 25.4 1.0
CB A:ILE73 4.6 20.6 1.0
O A:LEU69 4.6 26.3 1.0
CB A:SER68 4.6 20.8 1.0
O A:ILE67 4.7 19.7 1.0
N A:TYR72 4.8 28.6 1.0
CA A:THR74 4.8 22.8 0.3
CA A:THR74 4.8 23.5 0.7
CB A:PHE70 4.9 21.6 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 02:46:17 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy