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Magnesium in PDB 3t7a: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp at pH 5.2

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp at pH 5.2

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp at pH 5.2:
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 at pH 5.2, PDB code: 3t7a was solved by H.Wang, J.Falck, T.M.T.Hall, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.28 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.973, 110.807, 41.381, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.6

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 at pH 5.2 (pdb code 3t7a). 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 at pH 5.2, PDB code: 3t7a:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3t7a

Go back to Magnesium Binding Sites List in 3t7a
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 at pH 5.2


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 at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:2.3
occ:1.00
O A:HOH465 1.9 17.5 1.0
O A:HOH22 1.9 15.9 1.0
O2B A:ADP401 2.0 11.0 1.0
OD1 A:ASN323 2.1 12.3 1.0
OD2 A:ASP321 2.4 9.6 1.0
OD1 A:ASP321 2.4 12.9 1.0
CG A:ASP321 2.7 9.2 1.0
CG A:ASN323 3.2 11.1 1.0
PB A:ADP401 3.2 11.2 1.0
O3B A:ADP401 3.4 9.2 1.0
ND2 A:ASN323 3.6 11.1 1.0
MG A:MG602 3.9 11.1 1.0
O A:HOH462 3.9 14.0 1.0
O A:HOH711 4.1 41.0 1.0
NH1 A:ARG134 4.2 8.8 0.7
CE1 A:HIS194 4.2 15.8 1.0
CB A:ASP321 4.2 8.1 1.0
O1B A:ADP401 4.3 13.4 1.0
O3A A:ADP401 4.3 11.4 1.0
O A:ALA191 4.3 12.9 1.0
O A:HOH487 4.4 21.8 1.0
CB A:ASN323 4.4 8.8 1.0
NH2 A:ARG134 4.5 9.1 0.3
ND1 A:HIS194 4.5 14.4 1.0
O A:HOH697 4.6 44.0 1.0
O2A A:ADP401 4.8 10.0 1.0
O A:HOH20 4.8 11.2 1.0
NH2 A:ARG134 4.9 8.8 0.7
CA A:ASN323 4.9 8.4 1.0
O A:VAL322 4.9 8.3 1.0
CZ A:ARG134 5.0 9.0 0.7

Magnesium binding site 2 out of 3 in 3t7a

Go back to Magnesium Binding Sites List in 3t7a
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 at pH 5.2


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 at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:11.1
occ:1.00
OD2 A:ASP309 2.0 13.5 1.0
O2A A:ADP401 2.1 10.0 1.0
OD2 A:ASP321 2.1 9.6 1.0
O3B A:ADP401 2.1 9.2 1.0
O A:HOH462 2.1 14.0 1.0
O A:HOH16 2.2 11.8 1.0
CG A:ASP321 3.1 9.2 1.0
PB A:ADP401 3.2 11.2 1.0
CG A:ASP309 3.2 12.2 1.0
PA A:ADP401 3.3 10.2 1.0
CB A:ASP321 3.6 8.1 1.0
O3A A:ADP401 3.6 11.4 1.0
OD1 A:ASP309 3.8 15.7 1.0
O2B A:ADP401 3.8 11.0 1.0
MG A:MG601 3.9 2.3 1.0
O A:HOH465 4.0 17.5 1.0
O3' A:ADP401 4.1 12.7 1.0
OD1 A:ASP321 4.2 12.9 1.0
ND2 A:ASN323 4.2 11.1 1.0
O A:HOH670 4.3 33.1 1.0
O1A A:ADP401 4.3 11.9 1.0
CB A:ASP309 4.3 8.9 1.0
C5' A:ADP401 4.3 10.2 1.0
NZ A:LYS248 4.3 22.4 1.0
O5' A:ADP401 4.3 9.0 1.0
O A:HOH404 4.5 41.5 1.0
O2 A:EDO4 4.6 30.9 1.0
O1B A:ADP401 4.6 13.4 1.0
C3' A:ADP401 4.7 12.0 1.0
OD1 A:ASN323 4.8 12.3 1.0
CG A:ASN323 5.0 11.1 1.0

Magnesium binding site 3 out of 3 in 3t7a

Go back to Magnesium Binding Sites List in 3t7a
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 at pH 5.2


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 at pH 5.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:15.6
occ:1.00
O A:ILE73 2.3 11.7 1.0
O A:HOH674 2.3 36.0 1.0
O A:SER68 2.3 12.3 1.0
O A:PHE70 2.4 13.3 1.0
O A:HOH491 2.5 21.7 1.0
O A:HOH528 2.6 27.9 1.0
C A:SER68 3.3 11.9 1.0
C A:ILE73 3.4 11.1 1.0
C A:PHE70 3.5 13.5 1.0
CA A:SER68 3.9 11.4 1.0
N A:ILE73 4.0 11.4 1.0
O A:LYS71 4.1 15.8 1.0
OE1 A:GLN43 4.1 29.2 1.0
CA A:ILE73 4.2 11.1 1.0
C A:LYS71 4.2 14.8 1.0
N A:PHE70 4.2 13.4 1.0
C A:LEU69 4.4 14.0 1.0
N A:LYS71 4.4 13.8 1.0
N A:LEU69 4.4 12.8 1.0
CA A:LYS71 4.4 15.4 1.0
CA A:PHE70 4.4 13.1 1.0
N A:THR74 4.5 11.4 1.0
O A:HOH656 4.5 32.0 1.0
O A:HOH725 4.6 42.3 1.0
CB A:SER68 4.6 11.3 1.0
CB A:ILE73 4.7 10.2 1.0
CA A:THR74 4.7 11.0 0.3
CA A:LEU69 4.7 14.0 1.0
O A:ILE67 4.7 10.7 1.0
CA A:THR74 4.8 11.6 0.7
N A:TYR72 4.8 14.0 1.0
O A:LEU69 4.8 15.2 1.0
CG2 A:THR74 4.8 11.1 0.3
C A:TYR72 5.0 12.5 1.0

Reference:

H.Wang, J.R.Falck, T.M.Hall, S.B.Shears. Structural Basis For An Inositol Pyrophosphate Kinase Surmounting Phosphate Crowding. Nat.Chem.Biol. V. 8 111 2011.
ISSN: ISSN 1552-4450
PubMed: 22119861
DOI: 10.1038/NCHEMBIO.733
Page generated: Mon Dec 14 08:53:41 2020

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