Magnesium in PDB 6pck: Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7

Enzymatic activity of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7

All present enzymatic activity of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7:
3.6.1.52;

Protein crystallography data

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7, PDB code: 6pck was solved by D.E.Dollins, J.Neubauer, J.Dong, J.D.York, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.38 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.411, 56.612, 62.556, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.3

Other elements in 6pck:

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7 (pdb code 6pck). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7, PDB code: 6pck:

Magnesium binding site 1 out of 1 in 6pck

Go back to Magnesium Binding Sites List in 6pck
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7


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 Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:11.8
occ:1.00
 O21 A:O81201 1.9 11.7 1.0
O46 A:O81201 2.0 13.0 1.0
OE2 A:GLU70 2.0 10.2 1.0
O47 A:O81201 2.0 11.7 1.0
O A:GLY50 2.2 10.1 1.0
O A:HOH313 2.2 11.6 1.0
CD A:GLU70 2.9 10.3 1.0
P1 A:O81201 3.1 12.5 1.0
P6 A:O81201 3.3 14.0 1.0
P7 A:O81201 3.3 13.1 1.0
OE1 A:GLU70 3.3 10.6 1.0
C A:GLY50 3.3 9.6 1.0
O41 A:O81201 3.5 12.8 1.0
O16 A:O81201 3.6 13.0 1.0
CA A:GLY51 3.7 10.7 1.0
O36 A:O81201 3.8 14.4 1.0
O11 A:O81201 3.8 13.3 1.0
O A:HOH364 3.8 20.9 1.0
NH1 A:ARG20 4.0 9.9 1.0
N A:GLY51 4.0 9.6 1.0
OE1 A:GLU66 4.1 14.0 1.0
O A:HOH373 4.1 14.0 1.0
O37 A:O81201 4.2 14.6 1.0
CG A:GLU70 4.3 11.5 1.0
NH2 A:ARG115 4.3 15.5 1.0
O31 A:O81201 4.3 12.4 1.0
O27 A:O81201 4.4 12.5 1.0
O A:HOH371 4.4 18.6 1.0
N A:GLY50 4.5 9.5 1.0
C1 A:O81201 4.5 13.4 1.0
O26 A:O81201 4.5 15.9 1.0
CA A:GLY50 4.5 9.8 1.0
C6 A:O81201 4.6 13.8 1.0

Reference:

D.E.Dollins, W.Bai, P.C.Fridy, J.C.Otto, J.L.Neubauer, S.G.Gattis, K.P.M.Mehta, J.D.York. VIP1 Is A Kinase and Pyrophosphatase Switch That Regulates Inositol Diphosphate Signaling. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32303658
DOI: 10.1073/PNAS.1908875117
Page generated: Mon Dec 14 23:47:28 2020

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