Iodine 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:

Fluorine

(F)

3 atoms

The binding sites of Iodine atom in the PI3KC2ADELTAN and Deltac-C2 (pdb code 7bi2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the PI3KC2ADELTAN and Deltac-C2, PDB code: 7bi2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1203 b:278.9 occ:1.00 OG1 A:THR307 2.7 98.5 1.0 O A:ASP457 3.5 93.4 1.0 N A:THR307 3.7 90.4 1.0 CB A:THR307 3.8 94.5 1.0 N A:PRO459 4.0 93.4 1.0 CD1 A:LEU362 4.1 90.5 1.0 CA A:PHE306 4.1 86.8 1.0 C A:PHE306 4.1 88.3 1.0 CD A:PRO459 4.1 94.6 1.0 C A:ASP457 4.3 90.6 1.0 C A:PHE458 4.3 89.6 1.0 CA A:THR307 4.4 92.8 1.0 CA A:PRO459 4.4 94.6 1.0 CA A:PHE458 4.6 87.0 1.0 CB A:PRO459 4.6 94.4 1.0 N A:PHE306 4.8 85.7 1.0 N A:PHE458 4.8 87.5 1.0 CG A:PRO459 4.9 93.9 1.0 O A:GLN305 4.9 83.5 1.0 O A:PHE306 4.9 89.1 1.0 O A:PHE458 5.0 88.2 1.0

Iodine binding site 2 out of 5 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1204 b:296.7 occ:1.00 CD2 A:LEU804 3.7 133.3 1.0 C31 A:17G1202 3.9 228.8 1.0 CG A:LEU804 4.0 129.9 1.0 C34 A:17G1202 4.1 215.6 1.0 O A:VAL805 4.2 147.1 1.0 CD1 A:LEU804 4.4 128.8 1.0 C26 A:17G1202 4.5 221.5 1.0 CE A:LYS738 4.5 128.9 1.0 ND2 A:ASN752 4.5 129.9 1.0 CA A:PRO806 4.9 138.1 1.0 C32 A:17G1202 4.9 231.6 1.0 C A:VAL805 5.0 137.5 1.0

Iodine binding site 3 out of 5 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1205 b:324.4 occ:1.00 O A:LEU60 2.8 139.8 1.0 O A:ILE57 2.8 113.7 1.0 OE1 A:GLU56 3.5 132.8 1.0 C A:ILE57 3.8 114.9 1.0 C A:LEU60 4.0 134.1 1.0 CA A:GLU58 4.3 122.2 1.0 N A:LEU60 4.4 128.7 1.0 N A:GLY59 4.4 125.8 1.0 N A:GLU58 4.4 119.0 1.0 N A:ILE57 4.4 110.6 1.0 CD A:GLU56 4.5 125.4 1.0 C A:GLU58 4.7 124.0 1.0 CA A:LEU60 4.7 130.4 1.0 CA A:ILE57 4.8 110.6 1.0 O A:GLN61 4.8 134.6 1.0 CB A:GLU56 5.0 113.8 1.0

Iodine binding site 4 out of 5 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1206 b:336.6 occ:1.00 CB A:HIS523 3.6 133.2 1.0 CB A:ASN525 3.7 111.2 1.0 CA A:HIS523 3.9 132.2 1.0 N A:ASN525 3.9 113.1 1.0 C A:HIS523 4.0 128.0 1.0 CA A:ASN525 4.2 111.3 1.0 ND1 A:HIS523 4.3 135.2 1.0 O A:HIS523 4.3 129.4 1.0 CG A:HIS523 4.4 135.0 1.0 N A:PRO524 4.5 123.6 1.0 N A:CYS526 4.5 109.9 1.0 CG A:ASN525 4.6 109.0 1.0 C A:ASN525 4.6 110.7 1.0 CD A:PRO524 4.7 124.2 1.0 C A:PRO524 5.0 115.0 1.0

Iodine binding site 5 out of 5 in the PI3KC2ADELTAN and Deltac-C2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of PI3KC2ADELTAN and Deltac-C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1207 b:545.7 occ:1.00 CG A:PRO459 3.6 93.9 1.0 O A:GLN305 3.6 83.5 1.0 CD1 A:ILE369 3.9 103.5 1.0 N A:GLN305 3.9 89.2 1.0 CD1 A:LEU304 4.0 89.3 1.0 CD A:PRO459 4.1 94.6 1.0 CG1 A:ILE369 4.2 102.0 1.0 CA A:LEU304 4.2 92.8 1.0 O A:GLN303 4.4 98.3 1.0 CD2 A:LEU420 4.4 99.4 1.0 C A:GLN305 4.6 86.2 1.0 C A:LEU304 4.6 89.9 1.0 CG A:GLN305 4.9 91.3 1.0 CA A:GLN305 4.9 88.9 1.0 CB A:PRO459 5.0 94.4 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