Zinc in PDB 6fjk: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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-IP6 and Adp, PDB code: 6fjk 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)	83.95 / 2.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.810, 60.340, 83.980, 88.53, 89.18, 63.36
R / Rfree (%)	17.8 / 22.5

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp 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 Myo-IP6 and Adp (pdb code 6fjk). 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-IP6 and Adp, PDB code: 6fjk:
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-IP6 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-IP6 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:32.4 occ:1.00 NE2 A:HIS346 1.9 28.4 1.0 SG A:CYS330 2.2 33.5 1.0 ND1 A:HIS320 2.3 26.3 1.0 SG A:CYS333 2.4 38.3 1.0 CE1 A:HIS346 2.9 36.1 1.0 CD2 A:HIS346 3.0 32.7 1.0 CB A:CYS330 3.1 32.8 1.0 CE1 A:HIS320 3.2 32.4 1.0 CG A:HIS320 3.3 22.5 1.0 CB A:CYS333 3.4 37.9 1.0 CB A:HIS320 3.6 23.5 1.0 N A:CYS333 3.9 42.9 1.0 ND1 A:HIS346 4.0 29.9 1.0 CG A:HIS346 4.1 36.0 1.0 CA A:HIS320 4.2 25.9 1.0 CA A:CYS333 4.3 44.3 1.0 NE2 A:HIS320 4.3 27.7 1.0 CD2 A:HIS320 4.4 24.6 1.0 CA A:CYS330 4.5 35.7 1.0 CB A:ILE332 4.5 45.8 1.0 OE1 A:GLU342 4.5 63.6 1.0 C A:ILE332 4.8 48.3 1.0 CB A:GLU342 4.9 68.0 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-IP6 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-IP6 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:25.2 occ:1.00 NE2 B:HIS346 2.0 24.9 1.0 ND1 B:HIS320 2.1 17.9 1.0 SG B:CYS330 2.3 28.2 1.0 SG B:CYS333 2.3 31.1 1.0 CE1 B:HIS346 2.9 22.4 1.0 CE1 B:HIS320 3.0 20.8 1.0 CB B:CYS330 3.1 30.8 1.0 CD2 B:HIS346 3.1 23.8 1.0 CG B:HIS320 3.2 27.4 1.0 CB B:CYS333 3.5 27.5 1.0 CB B:HIS320 3.6 18.3 1.0 N B:CYS333 3.9 35.4 1.0 ND1 B:HIS346 4.1 22.0 1.0 CA B:HIS320 4.2 18.6 1.0 NE2 B:HIS320 4.2 24.0 1.0 CG B:HIS346 4.2 27.9 1.0 CA B:CYS333 4.2 38.7 1.0 CD2 B:HIS320 4.3 22.2 1.0 CA B:CYS330 4.6 27.5 1.0 CB B:ILE332 4.6 43.1 1.0 N B:GLU342 4.9 68.6 1.0 CA B:GLU342 4.9 75.1 1.0 C B:ILE332 4.9 40.7 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