Sodium in PDB 4f9o: Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate

All present enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate:
2.7.1.1;

The structure of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate, PDB code: 4f9o was solved by L.Shen, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.36 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.980, 122.090, 120.350, 90.00, 92.97, 90.00
R / Rfree (%)	24 / 25.8

The binding sites of Sodium atom in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate (pdb code 4f9o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate, PDB code: 4f9o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:58.0 occ:1.00 O A:LEU242 2.3 64.0 1.0 O A:GLY250 2.6 64.1 1.0 O A:VAL248 2.6 54.4 1.0 O A:ILE245 2.9 56.2 1.0 C A:ILE245 3.5 56.5 1.0 C A:LEU242 3.5 64.2 1.0 C A:GLY250 3.8 64.3 1.0 C A:VAL248 3.8 54.8 1.0 CD1 A:LEU242 4.0 62.8 1.0 N A:GLY250 4.0 60.5 1.0 CG A:LEU242 4.1 63.6 1.0 N A:ILE245 4.1 58.9 1.0 CA A:ILE245 4.1 56.9 1.0 CB A:ILE245 4.2 56.2 1.0 N A:ASP246 4.2 55.8 1.0 CA A:LEU242 4.4 63.7 1.0 CA A:GLY250 4.4 62.7 1.0 N A:ARG243 4.4 64.9 1.0 N A:VAL248 4.5 53.4 1.0 CA A:ARG243 4.5 65.4 1.0 CA A:ASP246 4.5 55.2 1.0 CA A:VAL248 4.5 53.9 1.0 CB A:VAL248 4.7 53.6 1.0 CB A:LEU242 4.7 63.5 1.0 N A:HIS244 4.7 64.0 1.0 C A:ASP246 4.7 54.4 1.0 C A:ARG243 4.7 65.0 1.0 C A:GLU249 4.8 58.9 1.0 O A:ASP246 4.8 54.1 1.0 N A:ASP251 4.8 65.8 1.0 N A:GLU249 4.9 56.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:46.6 occ:1.00 O A:VAL696 2.3 54.1 1.0 O A:VAL693 2.3 44.6 1.0 O A:MET690 2.5 52.6 1.0 O A:GLY698 2.6 58.9 1.0 C A:VAL693 3.2 44.5 1.0 C A:VAL696 3.5 53.9 1.0 C A:MET690 3.6 52.4 1.0 C A:GLY698 3.8 58.7 1.0 CE A:MET690 3.8 55.6 1.0 N A:GLU694 4.0 44.9 1.0 CA A:VAL693 4.0 44.4 1.0 N A:GLY698 4.1 57.9 1.0 N A:VAL693 4.1 45.5 1.0 CB A:VAL693 4.1 44.0 1.0 CA A:GLU694 4.1 45.5 1.0 N A:VAL696 4.3 50.7 1.0 CA A:VAL696 4.3 52.5 1.0 C A:GLU697 4.4 57.6 1.0 CA A:MET690 4.4 52.5 1.0 N A:GLU697 4.5 55.8 1.0 CA A:GLY698 4.5 58.4 1.0 C A:GLU694 4.5 46.3 1.0 SD A:MET690 4.6 54.6 1.0 CB A:MET690 4.6 52.7 1.0 CA A:GLU697 4.6 57.6 1.0 CB A:VAL696 4.6 52.5 1.0 N A:LYS691 4.6 52.2 1.0 C A:LYS691 4.7 51.0 1.0 CA A:LYS691 4.7 52.0 1.0 CG1 A:VAL693 4.8 43.3 1.0 N A:ASP699 4.8 59.0 1.0 CA A:ASP699 4.9 59.2 1.0 N A:MET695 4.9 47.4 1.0 O A:GLU697 5.0 57.6 1.0 O A:LYS691 5.0 51.2 1.0 O A:GLU694 5.0 46.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1005 b:56.1 occ:1.00 O B:ILE245 2.4 54.3 1.0 O B:VAL248 2.8 52.2 1.0 O B:LEU242 2.8 62.5 1.0 O B:GLY250 2.8 61.8 1.0 C B:ILE245 3.3 54.4 1.0 C B:VAL248 3.9 52.5 1.0 C B:GLY250 3.9 61.7 1.0 C B:LEU242 4.0 62.3 1.0 N B:ASP246 4.0 53.7 1.0 N B:GLY250 4.0 58.0 1.0 N B:ILE245 4.1 56.9 1.0 CA B:ASP246 4.1 53.3 1.0 CA B:ILE245 4.1 55.0 1.0 O B:ASP246 4.3 52.4 1.0 C B:ARG243 4.4 63.3 1.0 C B:ASP246 4.4 52.4 1.0 O B:ARG243 4.4 63.8 1.0 CA B:ARG243 4.4 64.0 1.0 CB B:ILE245 4.5 55.0 1.0 CA B:GLY250 4.6 60.2 1.0 C B:GLU249 4.6 56.4 1.0 CA B:GLU249 4.6 55.6 1.0 N B:VAL248 4.7 51.2 1.0 N B:ARG243 4.7 63.2 1.0 N B:GLU249 4.7 53.9 1.0 CG B:LEU242 4.7 64.3 1.0 CD1 B:LEU242 4.8 65.8 1.0 CA B:VAL248 4.8 51.8 1.0 N B:HIS244 4.9 62.3 1.0 C B:HIS244 4.9 59.1 1.0 N B:ASP251 5.0 63.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Recombinant Human Hexokinase Type I with 2-Deoxy- Glucose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:47.4 occ:1.00 O B:GLY698 2.3 60.1 1.0 O B:VAL696 2.4 55.1 1.0 O B:MET690 2.6 53.3 1.0 O B:VAL693 2.9 45.4 1.0 C B:GLY698 3.4 60.2 1.0 C B:VAL693 3.6 45.5 1.0 C B:VAL696 3.6 55.1 1.0 C B:MET690 3.7 53.2 1.0 CE B:MET690 3.7 53.3 1.0 N B:GLY698 3.8 59.4 1.0 C B:GLU697 4.1 59.1 1.0 CA B:GLY698 4.2 59.8 1.0 N B:GLU694 4.3 45.7 1.0 CA B:VAL693 4.4 45.4 1.0 CA B:MET690 4.4 53.3 1.0 CA B:GLU694 4.4 46.2 1.0 CB B:VAL693 4.4 44.9 1.0 CA B:GLU697 4.4 59.0 1.0 N B:ASP699 4.4 60.4 1.0 N B:VAL693 4.4 46.6 1.0 CB B:MET690 4.4 53.2 1.0 N B:GLU697 4.5 57.1 1.0 N B:VAL696 4.6 51.8 1.0 O B:GLU697 4.6 58.9 1.0 CA B:VAL696 4.6 53.4 1.0 CA B:ASP699 4.6 60.5 1.0 N B:LYS691 4.6 53.0 1.0 C B:GLU694 4.8 47.0 1.0 CA B:LYS691 4.8 52.7 1.0 SD B:MET690 4.9 54.1 1.0 C B:LYS691 4.9 51.9 1.0

L.Shen, Y.Gao, R.B.Honzatko. Inhibitor Sites of Unequal Affinity Linked By Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I To Be Published.