Zinc in PDB 6gfh: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp:
2.7.1.158;

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp, PDB code: 6gfh was solved by H.L.Whitfield, 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)	29.34 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.632, 60.563, 84.482, 87.81, 88.43, 63.01
R / Rfree (%)	19.9 / 26.8

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp (pdb code 6gfh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp, PDB code: 6gfh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:48.5 occ:1.00 NE2 A:HIS346 1.9 40.4 1.0 SG A:CYS330 2.2 46.4 1.0 SG A:CYS333 2.3 57.0 1.0 ND1 A:HIS320 2.5 37.0 1.0 CE1 A:HIS346 2.9 37.0 1.0 CD2 A:HIS346 2.9 43.3 1.0 CB A:CYS330 3.1 52.4 1.0 CB A:CYS333 3.3 63.2 1.0 CG A:HIS320 3.3 37.7 1.0 CB A:HIS320 3.4 30.6 1.0 CE1 A:HIS320 3.6 40.3 1.0 N A:CYS333 3.9 60.0 1.0 ND1 A:HIS346 4.0 40.4 1.0 CA A:HIS320 4.1 30.4 1.0 CG A:HIS346 4.1 44.1 1.0 CA A:CYS333 4.2 70.1 1.0 CD2 A:HIS320 4.5 38.7 1.0 CA A:CYS330 4.6 56.2 1.0 N A:GLU342 4.6 70.9 1.0 NE2 A:HIS320 4.6 39.1 1.0 CB A:ILE332 4.7 49.0 1.0 CB A:GLU342 4.8 67.5 1.0 O A:HIS320 4.9 32.0 1.0 C A:HIS320 4.9 36.9 1.0

Zinc binding site 2 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:44.8 occ:1.00 NE2 B:HIS346 2.0 39.2 1.0 SG B:CYS333 2.2 56.5 1.0 SG B:CYS330 2.3 41.0 1.0 ND1 B:HIS320 2.3 41.7 1.0 CD2 B:HIS346 3.0 36.5 1.0 CB B:CYS330 3.1 41.7 1.0 CE1 B:HIS346 3.1 34.7 1.0 CG B:HIS320 3.2 37.1 1.0 CE1 B:HIS320 3.3 36.7 1.0 CB B:HIS320 3.4 29.9 1.0 CB B:CYS333 3.5 55.0 1.0 N B:CYS333 4.0 56.7 1.0 CA B:HIS320 4.1 31.2 1.0 CG B:HIS346 4.2 38.2 1.0 ND1 B:HIS346 4.2 40.5 1.0 CA B:CYS333 4.2 59.0 1.0 CD2 B:HIS320 4.4 33.4 1.0 NE2 B:HIS320 4.4 37.2 1.0 CA B:CYS330 4.5 42.2 1.0 N B:GLU342 4.5 64.2 1.0 CB B:ILE332 4.6 45.5 1.0 CB B:GLU342 4.7 50.8 1.0 C B:ILE332 4.7 55.4 1.0 O B:HIS320 5.0 36.4 1.0

H.Whitfield, M.Gilmartin, K.Baker, A.M.Riley, H.Y.Godage, B.V.L.Potter, A.M.Hemmings, C.A.Brearley. A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. J. Med. Chem. V. 61 8838 2018.
ISSN: ISSN 1520-4804
PubMed: 30160967
DOI: 10.1021/ACS.JMEDCHEM.8B01022