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

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

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5., PDB code: 3udt was solved by V.Gosein, T.-F.Leung, O.Krajden, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.63 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.362, 59.913, 83.146, 90.02, 97.04, 116.81
R / Rfree (%)	21 / 27.6

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

Magnesium

(Mg)

2 atoms

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


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 Adp and IP5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn914 b:39.8 occ:1.00 NE2 A:HIS346 2.1 18.2 1.0 SG A:CYS330 2.2 29.1 1.0 ND1 A:HIS320 2.2 18.2 1.0 SG A:CYS333 2.5 13.7 1.0 CE1 A:HIS346 3.0 13.8 1.0 CB A:CYS330 3.1 20.0 1.0 CE1 A:HIS320 3.2 22.3 1.0 CD2 A:HIS346 3.2 11.8 1.0 CG A:HIS320 3.2 13.4 1.0 CB A:HIS320 3.5 12.9 1.0 CB A:CYS333 3.9 23.3 1.0 CA A:HIS320 3.9 13.3 1.0 N A:CYS333 4.1 21.5 1.0 ND1 A:HIS346 4.1 16.7 1.0 CG A:HIS346 4.3 14.0 1.0 NE2 A:HIS320 4.3 14.8 1.0 CD2 A:HIS320 4.4 13.9 1.0 CB A:ILE332 4.5 18.6 1.0 CA A:CYS330 4.5 16.9 1.0 CA A:CYS333 4.6 25.7 1.0 O A:HIS320 4.7 14.3 1.0 C A:HIS320 4.8 13.1 1.0 C A:ILE332 4.9 22.2 1.0 O A:CYS330 4.9 18.8 1.0 C A:CYS330 4.9 16.3 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 Adp and IP5.


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 Adp and IP5. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn914 b:33.5 occ:1.00 NE2 B:HIS346 2.1 15.8 1.0 ND1 B:HIS320 2.2 11.5 1.0 SG B:CYS330 2.2 21.0 1.0 SG B:CYS333 2.5 14.8 1.0 CE1 B:HIS346 2.9 13.4 1.0 CB B:CYS330 2.9 16.1 1.0 CE1 B:HIS320 3.1 12.7 1.0 CG B:HIS320 3.2 10.0 1.0 CD2 B:HIS346 3.2 9.7 1.0 CB B:HIS320 3.5 9.7 1.0 CB B:CYS333 3.9 26.1 1.0 CA B:HIS320 3.9 9.8 1.0 ND1 B:HIS346 4.0 12.2 1.0 N B:CYS333 4.2 21.7 1.0 CG B:HIS346 4.2 11.8 1.0 NE2 B:HIS320 4.2 9.7 1.0 CD2 B:HIS320 4.3 10.8 1.0 CA B:CYS330 4.4 12.9 1.0 CB B:ILE332 4.5 14.5 1.0 CA B:CYS333 4.6 21.0 1.0 C B:ILE332 4.8 22.2 1.0 C B:HIS320 4.9 9.7 1.0 O B:HIS320 4.9 12.9 1.0 C B:CYS330 4.9 15.5 1.0 O B:CYS330 4.9 16.2 1.0 N B:HIS320 5.0 10.6 1.0

V.Gosein, T.F.Leung, O.Krajden, G.J.Miller. Inositol Phosphate-Induced Stabilization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase and Its Role in Substrate Specificity. Protein Sci. V. 21 737 2012.
ISSN: ISSN 0961-8368
PubMed: 22362712
DOI: 10.1002/PRO.2049