Zinc in PDB 3vov: Crystal Structure of Rok Hexokinase From Thermus Thermophilus

All present enzymatic activity of Crystal Structure of Rok Hexokinase From Thermus Thermophilus:
2.7.1.1;

The structure of Crystal Structure of Rok Hexokinase From Thermus Thermophilus, PDB code: 3vov was solved by T.Nakamura, Y.Kashima, S.Mine, T.Oku, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.60 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.926, 138.144, 75.156, 90.00, 95.41, 90.00
R / Rfree (%)	18.1 / 22.5

The binding sites of Zinc atom in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus (pdb code 3vov). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus, PDB code: 3vov:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus


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 Rok Hexokinase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.3 occ:1.00 ND1 A:HIS159 2.1 19.0 1.0 SG A:CYS169 2.3 19.8 1.0 SG A:CYS176 2.3 20.5 1.0 SG A:CYS171 2.3 21.2 1.0 CE1 A:HIS159 2.9 21.9 1.0 CB A:CYS169 3.1 18.6 1.0 CB A:CYS176 3.1 18.3 1.0 CG A:HIS159 3.1 18.8 1.0 CB A:CYS171 3.3 21.3 1.0 CB A:HIS159 3.6 18.0 1.0 NE2 A:HIS159 4.1 22.2 1.0 N A:CYS171 4.1 20.5 1.0 CA A:HIS159 4.1 18.4 1.0 CD2 A:HIS159 4.2 20.7 1.0 CA A:CYS171 4.2 21.5 1.0 CA A:CYS169 4.6 18.2 1.0 CA A:CYS176 4.6 18.4 1.0 CB A:LEU173 4.6 18.8 1.0 O A:GLY158 4.7 19.3 1.0 CG A:LEU173 4.9 19.8 1.0 N A:LEU173 4.9 20.0 1.0 C A:CYS169 4.9 19.3 1.0 O A:HIS159 4.9 17.3 1.0 CZ2 B:TRP270 4.9 22.1 1.0 CD1 A:LEU173 4.9 17.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus


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 Rok Hexokinase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.3 occ:1.00 ND1 B:HIS159 2.2 20.2 1.0 SG B:CYS169 2.3 20.1 1.0 SG B:CYS171 2.3 21.2 1.0 SG B:CYS176 2.4 20.6 1.0 CE1 B:HIS159 3.1 21.4 1.0 CB B:CYS169 3.1 18.7 1.0 CB B:CYS176 3.1 15.9 1.0 CB B:CYS171 3.2 21.3 1.0 CG B:HIS159 3.2 19.6 1.0 CB B:HIS159 3.6 19.3 1.0 N B:CYS171 4.1 20.9 1.0 CA B:HIS159 4.1 18.8 1.0 CA B:CYS171 4.2 21.0 1.0 NE2 B:HIS159 4.2 19.4 1.0 CD2 B:HIS159 4.3 21.2 1.0 CA B:CYS169 4.6 18.9 1.0 CB B:LEU173 4.6 19.2 1.0 CA B:CYS176 4.6 15.9 1.0 O B:GLY158 4.7 18.1 1.0 CD1 B:LEU173 4.8 19.8 1.0 O B:HIS159 4.9 19.8 1.0 N B:LEU173 4.9 19.6 1.0 C B:CYS169 4.9 19.7 1.0 C B:CYS171 4.9 21.3 1.0 CG B:LEU173 4.9 20.4 1.0 C B:HIS159 4.9 19.1 1.0 CZ2 A:TRP270 5.0 22.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rok Hexokinase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:22.0 occ:1.00 ND1 C:HIS159 2.2 24.0 1.0 SG C:CYS169 2.3 21.2 1.0 SG C:CYS171 2.3 21.4 1.0 SG C:CYS176 2.4 22.5 1.0 CE1 C:HIS159 3.0 25.5 1.0 CB C:CYS169 3.1 19.4 1.0 CB C:CYS176 3.1 18.1 1.0 CG C:HIS159 3.2 23.0 1.0 CB C:CYS171 3.3 21.3 1.0 CB C:HIS159 3.7 20.1 1.0 N C:CYS171 4.1 21.2 1.0 CA C:HIS159 4.2 20.8 1.0 NE2 C:HIS159 4.2 23.6 1.0 CA C:CYS171 4.2 22.2 1.0 CD2 C:HIS159 4.3 23.1 1.0 CA C:CYS169 4.5 19.5 1.0 CB C:LEU173 4.6 20.6 1.0 CA C:CYS176 4.6 18.6 1.0 O C:GLY158 4.7 20.1 1.0 N C:LEU173 4.8 20.8 1.0 C C:CYS169 4.9 19.6 1.0 CZ2 D:TRP270 4.9 22.7 1.0 CD1 C:LEU173 5.0 18.4 1.0 CG C:LEU173 5.0 21.1 1.0 O C:HIS159 5.0 21.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Rok Hexokinase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rok Hexokinase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:22.6 occ:1.00 ND1 D:HIS159 2.1 21.1 1.0 SG D:CYS169 2.2 22.2 1.0 SG D:CYS171 2.3 23.0 1.0 SG D:CYS176 2.4 20.9 1.0 CE1 D:HIS159 3.0 21.4 1.0 CB D:CYS176 3.2 18.0 1.0 CB D:CYS171 3.2 23.3 1.0 CB D:CYS169 3.2 20.6 1.0 CG D:HIS159 3.2 17.2 1.0 CB D:HIS159 3.6 19.9 1.0 CA D:HIS159 4.2 18.5 1.0 NE2 D:HIS159 4.2 21.7 1.0 N D:CYS171 4.2 23.2 1.0 CA D:CYS171 4.3 23.8 1.0 CD2 D:HIS159 4.3 19.5 1.0 CA D:CYS169 4.6 21.1 1.0 CB D:LEU173 4.6 20.2 1.0 CA D:CYS176 4.6 17.0 1.0 O D:GLY158 4.7 19.7 1.0 CD1 D:LEU173 4.8 17.8 1.0 O D:HIS159 4.9 17.1 1.0 CZ2 C:TRP270 4.9 20.7 1.0 C D:CYS169 4.9 21.5 1.0 CG D:LEU173 4.9 21.8 1.0 N D:LEU173 5.0 21.7 1.0

T.Nakamura, Y.Kashima, S.Mine, T.Oku, K.Uegaki. Characterization and Crystal Structure of the Thermophilic Rok Hexokinase From Thermus Thermophilus J.Biosci.Bioeng. 2012.
ISSN: ISSN 1389-1723
PubMed: 22591843
DOI: 10.1016/J.JBIOSC.2012.03.018