Zinc in PDB 4lv7: Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C

All present enzymatic activity of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C:
2.7.1.158;

The structure of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C, PDB code: 4lv7 was solved by V.Gosein, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.55 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.763, 59.353, 82.232, 83.01, 89.92, 63.41
R / Rfree (%)	22.4 / 29.4

The structure of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C (pdb code 4lv7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C, PDB code: 4lv7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:23.1 occ:1.00 NE2 A:HIS346 2.1 20.8 1.0 ND1 A:HIS320 2.1 22.8 1.0 SG A:CYS330 2.2 23.5 1.0 SG A:CYS333 2.4 39.5 1.0 CE1 A:HIS346 2.8 18.9 1.0 CB A:CYS330 3.0 20.9 1.0 CE1 A:HIS320 3.0 17.7 1.0 CG A:HIS320 3.1 17.7 1.0 CD2 A:HIS346 3.3 17.5 1.0 CB A:HIS320 3.5 18.6 1.0 CB A:CYS333 3.7 32.2 1.0 ND1 A:HIS346 4.0 18.5 1.0 N A:CYS333 4.1 30.6 1.0 CA A:HIS320 4.1 15.8 1.0 NE2 A:HIS320 4.1 16.7 1.0 CD2 A:HIS320 4.2 16.4 1.0 CG A:HIS346 4.2 24.0 1.0 CA A:CYS333 4.5 35.2 1.0 CA A:CYS330 4.5 24.2 1.0 CB A:ILE332 4.5 27.0 1.0 C A:ILE332 4.8 32.2 1.0 C A:CYS330 4.9 25.1 1.0 O A:CYS330 4.9 33.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase E82C/S142C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:27.9 occ:1.00 NE2 B:HIS346 2.0 18.5 1.0 ND1 B:HIS320 2.2 23.1 1.0 SG B:CYS333 2.3 32.7 1.0 SG B:CYS330 2.3 31.7 1.0 CD2 B:HIS346 2.9 21.7 1.0 CE1 B:HIS346 3.0 20.4 1.0 CB B:CYS330 3.1 30.9 1.0 CG B:HIS320 3.1 15.9 1.0 CE1 B:HIS320 3.2 26.4 1.0 CB B:HIS320 3.4 17.3 1.0 CB B:CYS333 3.7 38.2 1.0 N B:CYS333 3.9 34.1 1.0 CA B:HIS320 4.0 17.7 1.0 CG B:HIS346 4.0 22.4 1.0 ND1 B:HIS346 4.1 23.4 1.0 NE2 B:HIS320 4.3 17.7 1.0 CD2 B:HIS320 4.3 19.6 1.0 CA B:CYS333 4.4 39.0 1.0 CA B:CYS330 4.5 31.0 1.0 CB B:ILE332 4.6 28.2 1.0 O B:CYS330 4.8 40.0 1.0 C B:HIS320 4.9 18.1 1.0 C B:ILE332 4.9 32.1 1.0 O B:HIS320 4.9 21.4 1.0 C B:CYS330 5.0 32.8 1.0

V.Gosein, G.J.Miller. Conformational Stability of IPK1 Dictates Its Substrate Selectivity J.Biol.Chem. 2013.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M113.512731