Magnesium in PDB 7a0v: Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody

All present enzymatic activity of Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody:
3.1.3.36;

The structure of Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody, PDB code: 7a0v 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)	86.81 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.874, 108.793, 100.974, 90, 120.72, 90
R / Rfree (%)	19.6 / 25.2

The binding sites of Magnesium atom in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody (pdb code 7a0v). 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 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody, PDB code: 7a0v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 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 in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:46.2 occ:1.00 O A:HOH1004 2.4 31.2 1.0 OE1 A:GLU591 2.5 34.4 1.0 OD1 A:ASN543 2.6 42.1 1.0 OE2 A:GLU591 2.9 33.3 1.0 CD A:GLU591 3.1 32.4 1.0 O A:HOH1078 3.1 38.7 1.0 CG A:ASN543 3.7 41.6 1.0 OD2 A:ASP858 3.8 46.6 1.0 O A:HOH1086 3.9 39.1 1.0 CB A:ASN543 4.3 35.9 1.0 CA A:ASN543 4.3 35.8 1.0 O A:HOH1136 4.5 52.2 1.0 OD1 A:ASP858 4.5 42.0 1.0 OD1 A:ASN541 4.5 31.4 1.0 CG A:GLU591 4.6 30.8 1.0 CG A:ASP858 4.6 36.4 1.0 ND2 A:ASN543 4.7 36.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 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 in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:72.0 occ:1.00 OE1 C:GLU591 2.6 68.8 1.0 O C:HOH1059 2.8 55.7 1.0 OE2 C:GLU591 3.2 59.1 1.0 CD C:GLU591 3.3 61.5 1.0 OD1 C:ASN543 3.6 75.3 1.0 OD2 C:ASP858 4.0 63.9 1.0 CG C:ASN543 4.0 61.3 1.0 O C:HOH1065 4.3 43.2 1.0 ND2 C:ASN543 4.3 56.3 1.0 OD1 C:ASP858 4.7 57.7 1.0 O C:HOH1068 4.7 53.7 1.0 CG C:ASP858 4.8 60.5 1.0 CG C:GLU591 4.8 51.8 1.0 OD1 C:ASN541 4.8 53.4 1.0 CB C:ASN543 4.9 61.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 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 3 of Crystal Structure of the 5-Phosphatase Domain of SYNAPTOJANIN1 in Complex with A Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg903 b:67.0 occ:1.00 O3 E:PO4901 2.2 75.9 1.0 O E:HOH1002 2.6 56.4 1.0 OE1 E:GLU591 2.8 44.0 1.0 O4 E:PO4901 2.8 86.3 1.0 O E:HOH1036 2.9 43.6 1.0 P E:PO4901 3.0 106.4 1.0 OE2 E:GLU591 3.2 50.6 1.0 CD E:GLU591 3.2 48.5 1.0 O E:HOH1065 3.3 43.2 1.0 O E:HOH1030 3.6 40.7 1.0 O E:HOH1063 3.7 51.8 1.0 O2 E:PO4901 3.9 78.2 1.0 O1 E:PO4901 4.2 84.8 1.0 CG E:GLU591 4.6 39.0 1.0 OD1 E:ASN543 4.8 47.8 1.0 O E:HOH1033 4.8 44.2 1.0 ND2 E:ASN541 4.9 43.0 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