Manganese in PDB 8ppc: Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn

All present enzymatic activity of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn:
2.7.1.127;

The structure of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn, PDB code: 8ppc was solved by M.A.Marquez-Monino, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 1.92
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.915, 97.904, 191.881, 90, 90, 90
R / Rfree (%)	19.3 / 21.9

The binding sites of Manganese atom in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn (pdb code 8ppc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn, PDB code: 8ppc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:40.6 occ:0.50 OD2 A:ASP416 2.1 33.0 1.0 O A:HOH665 2.2 44.4 1.0 O1B A:ATP502 2.3 42.1 1.0 O A:HOH604 2.4 55.0 1.0 O A:HOH616 2.4 40.5 1.0 O2G A:ATP502 2.6 53.0 1.0 CG A:ASP416 3.0 28.4 1.0 OD1 A:ASP416 3.2 31.2 1.0 PG A:ATP502 3.4 61.3 1.0 O1G A:ATP502 3.4 58.1 1.0 PB A:ATP502 3.6 43.0 1.0 O3B A:ATP502 3.8 48.5 1.0 O32 A:2KM501 4.2 50.9 1.0 O1A A:ATP502 4.2 32.0 1.0 O22 A:2KM501 4.3 47.4 1.0 CB A:ASP416 4.4 27.0 1.0 O A:GLY397 4.4 29.4 1.0 O A:HOH652 4.5 32.5 1.0 O3A A:ATP502 4.5 38.4 1.0 P2 A:2KM501 4.7 54.3 1.0 O2B A:ATP502 4.7 47.2 1.0 O3G A:ATP502 4.8 60.0 1.0 PA A:ATP502 4.9 32.6 1.0 O2 A:2KM501 5.0 47.6 1.0

Manganese binding site 2 out of 2 in the Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Inositol 1,4,5-Trisphosphate 3-Kinase A (IP3K) Catalytic Domain in Complex with L-Chiro-Inositol 2,3,5-Trisphosphate/Atp/Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:90.5 occ:1.00 OD2 B:ASP416 2.6 42.4 1.0 O B:HOH603 2.7 70.6 1.0 O1B B:ATP502 2.7 58.1 1.0 O1G B:ATP502 2.9 72.0 1.0 OD1 B:ASP416 3.2 36.8 1.0 CG B:ASP416 3.2 38.0 1.0 O3G B:ATP502 3.2 68.0 1.0 PG B:ATP502 3.6 79.5 1.0 O22 B:2KM501 3.9 44.7 1.0 PB B:ATP502 4.0 57.9 1.0 O3B B:ATP502 4.1 60.3 1.0 O12 B:2KM501 4.2 48.8 1.0 P2 B:2KM501 4.5 50.1 1.0 CB B:ASP416 4.7 34.3 1.0 O1A B:ATP502 4.7 43.5 1.0 O2 B:2KM501 4.7 47.3 1.0 O B:GLY397 4.8 29.8 1.0 O B:HOH663 4.9 39.1 1.0 O3A B:ATP502 4.9 57.8 1.0 O2G B:ATP502 5.0 75.0 1.0

M.A.Marquez-Monino, R.Ortega-Garcia, H.Whitfield, A.M.Riley, L.Infantes, S.W.Garrett, M.L.Shipton, C.A.Brearley, B.V.L.Potter, B.Gonzalez. Substrate Promiscuity of Inositol 1,4,5-Trisphosphate Kinase Driven By Structurally-Modified Ligands and Active Site Plasticity Nat Commun V. 15 1502 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-45917-5