Magnesium in PDB 8oxe: Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+

The structure of Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+, PDB code: 8oxe was solved by R.Faba-Rodriguez, A.W.H.Li, C.A.Brearley, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.59 / 2.26
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.61, 140.77, 55.56, 90, 90, 90
R / Rfree (%)	19 / 24.1

The binding sites of Magnesium atom in the Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+ (pdb code 8oxe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+, PDB code: 8oxe:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.1 occ:0.50 OD1 A:ASP44 2.1 27.4 1.0 OD2 A:ASP46 2.2 30.3 1.0 O A:HOH608 2.7 32.5 1.0 CG A:ASP44 3.2 27.7 1.0 CG A:ASP46 3.3 29.0 1.0 CB A:ASP46 3.8 29.8 1.0 OD2 A:ASP44 3.9 29.2 1.0 CB A:ASP44 4.1 26.5 1.0 N A:ASP46 4.1 26.9 1.0 CA A:ASP44 4.2 27.8 1.0 N A:THR45 4.3 24.3 1.0 O A:HOH514 4.3 28.9 1.0 OD1 A:ASP46 4.4 29.1 1.0 C A:ASP44 4.6 24.7 1.0 CA A:ASP46 4.6 28.9 1.0

Magnesium binding site 2 out of 3 in the Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:13.9 occ:1.00 O2A A:ADP401 2.1 22.2 1.0 O3B A:ADP401 2.2 22.8 1.0 OD2 A:ASP289 2.2 22.7 1.0 OD2 A:ASP274 2.2 24.0 1.0 O A:HOH522 2.3 25.7 1.0 CG A:ASP289 3.2 22.7 1.0 PB A:ADP401 3.4 20.8 1.0 PA A:ADP401 3.5 20.6 1.0 CG A:ASP274 3.5 27.2 1.0 CB A:ASP289 3.6 20.4 1.0 O A:HOH531 3.7 26.3 1.0 O3A A:ADP401 3.7 22.9 1.0 O2B A:ADP401 3.9 22.5 1.0 MG A:MG404 4.3 13.7 1.0 OD1 A:ASP289 4.3 21.6 1.0 OD1 A:ASP274 4.4 28.4 1.0 O3' A:ADP401 4.4 25.1 1.0 ND2 A:ASN291 4.4 27.4 1.0 CB A:ASP274 4.4 21.6 1.0 O5' A:ADP401 4.5 21.6 1.0 C5' A:ADP401 4.5 26.7 1.0 O1A A:ADP401 4.5 21.1 1.0 NZ A:LYS189 4.5 40.4 1.0 O1B A:ADP401 4.7 27.7 1.0 C3' A:ADP401 4.8 24.6 1.0

Magnesium binding site 3 out of 3 in the Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inositol 1,3,4-Trisphosphate 5/6-Kinase 1 From Solanum Tuberosum (STITPK1) in Complex with Adp/MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:13.7 occ:1.00 O A:HOH531 1.9 26.3 1.0 O2B A:ADP401 2.1 22.5 1.0 OD1 A:ASN291 2.2 24.4 1.0 OD1 A:ASP289 2.4 21.6 1.0 O A:HOH576 2.6 26.2 1.0 O A:HOH577 2.6 29.8 1.0 OD2 A:ASP289 2.6 22.7 1.0 CG A:ASP289 2.9 22.7 1.0 CG A:ASN291 3.2 28.9 1.0 PB A:ADP401 3.4 20.8 1.0 ND2 A:ASN291 3.6 27.4 1.0 O3B A:ADP401 3.7 22.8 1.0 O A:HOH556 3.9 29.2 1.0 O A:HOH520 4.2 20.2 1.0 NH2 A:ARG96 4.3 25.0 1.0 MG A:MG403 4.3 13.9 1.0 CB A:ASP289 4.4 20.4 1.0 O1B A:ADP401 4.4 27.7 1.0 O3A A:ADP401 4.5 22.9 1.0 CB A:ASN291 4.6 27.1 1.0 O A:HOH615 4.6 32.2 1.0 O A:HOH559 4.7 31.6 1.0 CE1 A:HIS157 4.7 38.5 1.0 O A:ILE290 4.9 22.8 1.0

H.L.Whitfield, R.F.Rodriguez, M.L.Shipton, A.W.H.Li, A.M.Riley, B.V.L.Potter, A.M.Hemmings, C.A.Brearley. Crystal Structure and Enzymology of Solanum Tuberosum Inositol Tris/Tetrakisphosphate Kinase 1 ( St ITPK1). Biochemistry V. 63 42 2024.
ISSN: ISSN 0006-2960
PubMed: 38146842
DOI: 10.1021/ACS.BIOCHEM.3C00404