Magnesium in PDB 8omi: Crystal Structure of the Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+

The structure of Crystal Structure of the Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+, PDB code: 8omi was solved by A.Schuetz, T.Aguirre, D.Fiedler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.81 / 1.77
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.82, 102.82, 111.61, 90, 90, 90
R / Rfree (%)	23.1 / 25.4

The binding sites of Magnesium atom in the Crystal Structure of the Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+ (pdb code 8omi). 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 Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+, PDB code: 8omi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+


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 Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:42.0 occ:1.00 O A:HOH402 2.0 53.9 1.0 O A:HOH455 2.1 27.0 1.0 O A:HOH453 2.1 42.7 1.0 OD2 A:ASP231 2.1 31.9 1.0 O A:HOH533 2.2 51.6 1.0 O1G A:ATP303 2.4 65.6 1.0 CG A:ASP231 3.2 37.0 1.0 PG A:ATP303 3.4 67.0 1.0 O2G A:ATP303 3.5 56.6 1.0 CB A:ASP231 3.6 29.0 1.0 O2A A:ATP303 3.8 68.5 1.0 O3A A:ATP303 4.0 67.9 1.0 O A:SER207 4.0 25.1 1.0 MG A:MG302 4.1 47.5 1.0 NZ A:LYS101 4.1 41.1 1.0 O3B A:ATP303 4.3 72.7 1.0 OD1 A:ASP231 4.3 28.4 1.0 OG A:SER209 4.3 27.0 1.0 O A:HOH495 4.4 43.3 1.0 PA A:ATP303 4.4 61.8 1.0 O2B A:ATP303 4.4 57.4 1.0 PB A:ATP303 4.6 78.2 1.0 O3G A:ATP303 4.6 79.3 1.0 OD2 A:ASP99 4.7 43.6 1.0 CE A:LYS101 4.8 33.1 1.0 CB A:SER209 5.0 27.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+


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 Inositol Hexakisphosphate Kinase EHIP6KA M85 Variant in Complex with Atp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:47.5 occ:1.00 O2B A:ATP303 2.2 57.4 1.0 O A:HOH557 2.2 54.0 1.0 O A:HOH495 2.2 43.3 1.0 O2G A:ATP303 2.2 56.6 1.0 OD1 A:ASP231 2.3 28.4 1.0 OD2 A:ASP231 2.3 31.9 1.0 CG A:ASP231 2.7 37.0 1.0 PB A:ATP303 3.2 78.2 1.0 PG A:ATP303 3.4 67.0 1.0 O3B A:ATP303 3.5 72.7 1.0 O A:HOH453 3.9 42.7 1.0 MG A:MG301 4.1 42.0 1.0 O3A A:ATP303 4.2 67.9 1.0 O1G A:ATP303 4.2 65.6 1.0 CB A:ASP231 4.2 29.0 1.0 CB A:ALA233 4.3 24.7 1.0 O A:HOH494 4.4 36.2 1.0 O1B A:ATP303 4.5 76.2 1.0 O A:HOH432 4.6 28.3 1.0 NZ A:LYS38 4.6 41.0 1.0 O A:HOH580 4.6 42.5 1.0 O3G A:ATP303 4.6 79.3 1.0 PA A:ATP303 4.8 61.8 1.0 CA A:ASP231 5.0 24.9 1.0

T.Aguirre, G.L.Dornan, S.Hostachy, M.Neuenschwander, C.Seyffarth, V.Haucke, A.Schutz, J.P.Von Kries, D.Fiedler. An Unconventional Gatekeeper Mutation Sensitizes Inositol Hexakisphosphate Kinases to An Allosteric Inhibitor. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 37843983
DOI: 10.7554/ELIFE.88982