Magnesium in PDB 7a17: Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody

All present enzymatic activity of Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody:
3.1.3.36;

The structure of Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody, PDB code: 7a17 was solved by J.Paesmans, C.Galicia, E.Martin, W.Versees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.39 / 2.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.323, 109.205, 100.902, 90, 120.62, 90
R / Rfree (%)	19.6 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody (pdb code 7a17). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody, PDB code: 7a17:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody


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 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:46.9 occ:1.00 O A:HOH1011 2.5 21.9 1.0 O A:HOH1007 2.7 31.9 1.0 OD1 A:ASN543 2.8 36.1 1.0 OE1 A:GLU591 2.9 36.0 1.0 OE2 A:GLU591 3.1 33.6 1.0 OD2 A:ASP858 3.4 29.7 1.0 CD A:GLU591 3.4 37.0 1.0 O9P A:IP9901 3.6 65.9 1.0 CG A:ASN543 4.0 35.8 1.0 O5 A:IP9901 4.0 57.3 1.0 O A:HOH1010 4.4 18.7 1.0 CG A:ASP858 4.5 29.8 1.0 OPF A:IP9901 4.7 63.7 1.0 OD1 A:ASP858 4.7 36.3 1.0 ND2 A:ASN543 4.8 37.1 1.0 C4 A:IP9901 4.8 61.5 1.0 CA A:ASN543 4.9 34.5 1.0 C5 A:IP9901 4.9 55.1 1.0 CB A:ASN543 5.0 34.1 1.0 CG A:GLU591 5.0 37.8 1.0 P4 A:IP9901 5.0 67.3 1.0 OD1 A:ASN541 5.0 36.0 1.0 P5 A:IP9901 5.0 63.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody


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 5-Phosphatase Domain of SYNAPTOJANIN1 Bound to Its Substrate DIC8-Pi(3,4,5)P3 in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:38.3 occ:1.00 OE1 C:GLU591 2.7 67.5 1.0 OE2 C:GLU591 2.8 54.7 1.0 CD C:GLU591 3.1 63.1 1.0 O3 C:PO4902 3.2 78.3 1.0 OD1 C:ASN543 3.2 56.9 1.0 OD2 C:ASP858 4.0 52.3 1.0 O1 C:PO4901 4.4 79.7 1.0 CG C:ASN543 4.4 48.0 1.0 P C:PO4902 4.5 88.3 1.0 CG C:GLU591 4.7 62.6 1.0 O1 C:PO4902 4.7 97.5 1.0 CG C:ASP858 5.0 43.5 1.0

J.Paesmans, E.Martin, B.Deckers, M.Berghmans, R.Sethi, Y.Loeys, E.Pardon, J.Steyaert, P.Verstreken, C.Galicia, W.Versees. A Structure of Substrate-Bound SYNAPTOJANIN1 Provides New Insights in Its Mechanism and the Effect of Disease Mutations. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 33349335
DOI: 10.7554/ELIFE.64922