Fluorine in PDB 7bi2: PI3KC2ADELTAN and Deltac-C2

All present enzymatic activity of PI3KC2ADELTAN and Deltac-C2:
2.7.1.154;

The structure of PI3KC2ADELTAN and Deltac-C2, PDB code: 7bi2 was solved by W.T.Lo, Y.Roske, O.Daumke, V.Haucke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.20 / 3.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.557, 115.887, 144.365, 90, 90, 90
R / Rfree (%)	26.6 / 31.2

The structure of PI3KC2ADELTAN and Deltac-C2 also contains other interesting chemical elements:

Iodine

(I)

5 atoms

The binding sites of Fluorine atom in the PI3KC2ADELTAN and Deltac-C2 (pdb code 7bi2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the PI3KC2ADELTAN and Deltac-C2, PDB code: 7bi2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:250.0 occ:1.00 F3 A:17G1202 0.0 250.0 1.0 C24 A:17G1202 1.4 241.6 1.0 F1 A:17G1202 2.2 241.9 1.0 F2 A:17G1202 2.2 240.9 1.0 C16 A:17G1202 2.4 235.9 1.0 C20 A:17G1202 2.7 232.8 1.0 CG A:PRO736 3.1 158.5 1.0 CG A:PHE730 3.2 143.1 1.0 CB A:PHE730 3.2 148.7 1.0 CB A:PRO736 3.5 157.1 1.0 SD A:MET754 3.6 123.5 1.0 CD2 A:PHE730 3.6 139.6 1.0 C15 A:17G1202 3.6 232.0 1.0 CD1 A:PHE730 3.7 141.3 1.0 CD A:PRO736 3.8 161.3 1.0 C19 A:17G1202 4.1 231.3 1.0 CE2 A:PHE730 4.3 138.2 1.0 CE1 A:PHE730 4.4 140.3 1.0 CG A:MET754 4.5 122.4 1.0 CE A:MET754 4.6 122.1 1.0 CZ A:PHE730 4.7 139.7 1.0 CA A:PHE730 4.7 153.9 1.0 C18 A:17G1202 4.8 230.4 1.0 CA A:PRO736 4.8 157.2 1.0 N A:PRO736 4.9 160.7 1.0 C21 A:17G1202 4.9 231.7 1.0 OG A:SER732 5.0 180.8 1.0

Fluorine binding site 2 out of 3 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:240.9 occ:1.00 F2 A:17G1202 0.0 240.9 1.0 C24 A:17G1202 1.4 241.6 1.0 F1 A:17G1202 2.2 241.9 1.0 F3 A:17G1202 2.2 250.0 1.0 C16 A:17G1202 2.3 235.9 1.0 C15 A:17G1202 2.8 232.0 1.0 CG A:PRO736 3.4 158.5 1.0 C20 A:17G1202 3.5 232.8 1.0 C18 A:17G1202 4.2 230.4 1.0 C38 A:17G1202 4.2 195.9 1.0 CE A:LYS756 4.2 150.6 1.0 CD A:PRO736 4.2 161.3 1.0 OG A:SER732 4.2 180.8 1.0 NZ A:LYS756 4.3 150.5 1.0 C40 A:17G1202 4.3 190.4 1.0 SD A:MET754 4.4 123.5 1.0 CB A:PRO736 4.4 157.1 1.0 CB A:SER732 4.6 182.8 1.0 C19 A:17G1202 4.6 231.3 1.0 C21 A:17G1202 4.9 231.7 1.0 CE A:MET754 4.9 122.1 1.0

Fluorine binding site 3 out of 3 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:241.9 occ:1.00 F1 A:17G1202 0.0 241.9 1.0 C24 A:17G1202 1.4 241.6 1.0 F2 A:17G1202 2.2 240.9 1.0 F3 A:17G1202 2.2 250.0 1.0 C16 A:17G1202 2.4 235.9 1.0 C15 A:17G1202 3.0 232.0 1.0 OG A:SER732 3.3 180.8 1.0 CB A:SER732 3.3 182.8 1.0 C20 A:17G1202 3.4 232.8 1.0 CB A:PHE730 3.5 148.7 1.0 CG A:PRO736 3.8 158.5 1.0 CD A:PRO736 3.8 161.3 1.0 CG A:PHE730 4.2 143.1 1.0 C18 A:17G1202 4.3 230.4 1.0 CD1 A:PHE730 4.4 141.3 1.0 N A:SER732 4.4 183.6 1.0 CA A:SER732 4.5 185.2 1.0 C A:PHE730 4.5 159.4 1.0 C19 A:17G1202 4.5 231.3 1.0 O A:PHE730 4.6 157.7 1.0 CA A:PHE730 4.6 153.9 1.0 CB A:PRO736 4.7 157.1 1.0 C A:SER731 4.8 178.2 1.0 N A:SER731 4.8 168.2 1.0 C21 A:17G1202 4.9 231.7 1.0

W.T.Lo, Y.Zhang, O.Vadas, Y.Roske, F.Gulluni, M.C.De Santis, A.V.Zagar, H.Stephanowitz, E.Hirsch, F.Liu, O.Daumke, M.Kudryashev, V.Haucke. Structural Basis of Phosphatidylinositol 3-Kinase C2 Alpha Function. Nat.Struct.Mol.Biol. V. 29 218 2022.
ISSN: ESSN 1545-9985
PubMed: 35256802
DOI: 10.1038/S41594-022-00730-W