Zinc in PDB 6fl3: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp

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

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp, PDB code: 6fl3 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)	52.87 / 2.36
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.950, 59.010, 83.360, 88.98, 89.56, 63.65
R / Rfree (%)	15.4 / 21.7

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

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP5 and Adp (pdb code 6fl3). 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 Myo-IP5 and Adp, PDB code: 6fl3:
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 Myo-IP5 and Adp


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 Myo-IP5 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:29.7 occ:1.00 NE2 A:HIS346 1.9 28.7 1.0 ND1 A:HIS320 2.1 18.2 1.0 SG A:CYS330 2.3 33.4 1.0 SG A:CYS333 2.4 40.8 1.0 CE1 A:HIS346 2.8 24.0 1.0 CE1 A:HIS320 3.0 20.1 1.0 CD2 A:HIS346 3.0 33.7 1.0 CB A:CYS330 3.2 30.5 1.0 CG A:HIS320 3.2 19.0 1.0 CB A:CYS333 3.5 32.9 1.0 CB A:HIS320 3.6 16.5 1.0 N A:CYS333 3.8 35.0 1.0 ND1 A:HIS346 3.9 26.5 1.0 CG A:HIS346 4.1 32.4 1.0 NE2 A:HIS320 4.1 17.1 1.0 CA A:HIS320 4.2 25.6 1.0 CA A:CYS333 4.2 36.5 1.0 CD2 A:HIS320 4.3 14.8 1.0 CB A:ILE332 4.5 27.4 1.0 CA A:CYS330 4.6 31.9 1.0 C A:ILE332 4.8 35.0 1.0 CG1 A:ILE332 5.0 29.6 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 Myo-IP5 and Adp


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 Myo-IP5 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:27.9 occ:1.00 NE2 B:HIS346 1.9 26.3 1.0 ND1 B:HIS320 2.1 24.1 1.0 SG B:CYS330 2.2 26.6 1.0 SG B:CYS333 2.3 38.7 1.0 CE1 B:HIS346 2.9 28.5 1.0 CE1 B:HIS320 2.9 20.9 1.0 CD2 B:HIS346 2.9 25.5 1.0 CB B:CYS330 3.0 23.2 1.0 CG B:HIS320 3.1 20.8 1.0 CB B:CYS333 3.3 30.1 1.0 CB B:HIS320 3.6 17.0 1.0 N B:CYS333 3.6 41.4 1.0 ND1 B:HIS346 4.0 28.2 1.0 CA B:CYS333 4.0 38.3 1.0 CG B:HIS346 4.1 32.3 1.0 NE2 B:HIS320 4.1 23.6 1.0 CA B:HIS320 4.2 14.6 1.0 CD2 B:HIS320 4.2 15.1 1.0 CB B:ILE332 4.4 34.9 1.0 CA B:CYS330 4.4 28.5 1.0 C B:ILE332 4.7 35.1 1.0 CB B:GLU342 4.7 54.1 1.0 CA B:ILE332 4.9 37.4 1.0 C B:CYS330 4.9 31.8 1.0 CG1 B:ILE332 4.9 36.0 1.0 O B:CYS330 4.9 42.9 1.0 N B:ILE332 5.0 39.1 1.0 O B:HIS320 5.0 25.5 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