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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

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