Sodium in PDB 4foe: Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 6-Phosphate

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

The structure of Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 6-Phosphate, PDB code: 4foe 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)	45.78 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.440, 122.090, 118.950, 90.00, 92.65, 90.00
R / Rfree (%)	24.4 / 25.4

The binding sites of Sodium atom in the Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 6-Phosphate (pdb code 4foe). 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 Mannose 6-Phosphate, PDB code: 4foe:
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 Mannose 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 Mannose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:58.0 occ:1.00 O A:LEU242 2.4 61.0 1.0 O A:VAL248 2.6 51.8 1.0 O A:ILE245 2.6 53.5 1.0 O A:GLY250 2.8 62.4 1.0 C A:ILE245 3.3 53.6 1.0 C A:LEU242 3.6 61.3 1.0 C A:VAL248 3.8 52.1 1.0 C A:GLY250 3.8 62.5 1.0 N A:ILE245 4.0 56.1 1.0 CA A:ILE245 4.1 54.1 1.0 N A:GLY250 4.1 58.7 1.0 N A:ASP246 4.1 52.7 1.0 CD1 A:LEU242 4.2 60.2 1.0 CB A:ILE245 4.3 53.6 1.0 CG A:LEU242 4.3 60.7 1.0 CA A:ASP246 4.4 51.7 1.0 CA A:ARG243 4.4 62.2 1.0 N A:ARG243 4.5 61.8 1.0 N A:VAL248 4.5 50.2 1.0 CA A:GLY250 4.5 61.0 1.0 CA A:VAL248 4.6 50.9 1.0 C A:ARG243 4.6 61.9 1.0 CA A:LEU242 4.6 60.8 1.0 C A:ASP246 4.6 51.0 1.0 N A:HIS244 4.6 61.0 1.0 C A:GLU249 4.7 56.9 1.0 O A:ASP246 4.7 50.8 1.0 N A:GLU249 4.7 53.8 1.0 CB A:VAL248 4.8 50.6 1.0 N A:ASP251 4.8 63.8 1.0 CA A:GLU249 4.8 55.6 1.0 C A:HIS244 4.9 58.1 1.0 CB A:LEU242 5.0 60.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 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 Mannose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:52.9 occ:1.00 O A:VAL693 2.3 43.8 1.0 O A:MET690 2.4 52.7 1.0 O A:VAL696 2.5 51.6 1.0 O A:GLY698 2.6 58.7 1.0 C A:VAL693 3.0 43.8 1.0 C A:MET690 3.6 52.5 1.0 C A:VAL696 3.6 51.6 1.0 CA A:VAL693 3.7 43.6 1.0 C A:GLY698 3.8 58.5 1.0 N A:GLU694 3.8 44.1 1.0 CB A:VAL693 3.8 43.4 1.0 N A:VAL693 3.8 44.6 1.0 CA A:GLU694 4.1 44.6 1.0 CE A:MET690 4.1 54.0 1.0 N A:GLY698 4.2 56.9 1.0 N A:VAL696 4.3 48.9 1.0 CA A:MET690 4.4 52.7 1.0 CA A:VAL696 4.4 50.0 1.0 C A:GLU697 4.4 56.2 1.0 SD A:MET690 4.4 52.9 1.0 C A:GLU694 4.5 45.4 1.0 N A:LYS691 4.5 52.2 1.0 CA A:GLY698 4.5 57.8 1.0 C A:LYS691 4.6 50.6 1.0 CG1 A:VAL693 4.6 42.8 1.0 CA A:LYS691 4.6 51.8 1.0 CB A:VAL696 4.6 49.9 1.0 CB A:MET690 4.6 52.8 1.0 N A:GLU697 4.6 53.8 1.0 O A:LYS691 4.7 50.8 1.0 CA A:GLU697 4.8 56.0 1.0 N A:ASP699 4.8 59.0 1.0 C A:ASN692 4.8 46.1 1.0 N A:ASN692 4.9 49.0 1.0 N A:MET695 4.9 46.3 1.0 O A:GLU697 4.9 56.3 1.0 O A:GLU694 4.9 45.7 1.0 CA A:ASP699 4.9 59.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 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 Mannose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1005 b:59.4 occ:1.00 O B:GLY250 2.8 60.7 1.0 O B:ILE245 3.1 52.1 1.0 O B:LEU242 3.1 59.7 1.0 O B:VAL248 3.4 50.5 1.0 C B:ILE245 3.8 52.0 1.0 O B:ARG243 3.9 60.8 1.0 C B:GLY250 3.9 60.5 1.0 C B:ARG243 4.1 60.3 1.0 CA B:ARG243 4.1 60.8 1.0 N B:GLY250 4.1 56.9 1.0 C B:LEU242 4.2 59.5 1.0 CA B:ASP246 4.3 50.2 1.0 N B:ASP246 4.4 51.0 1.0 C B:VAL248 4.4 50.6 1.0 N B:ILE245 4.5 54.5 1.0 O B:ASP246 4.6 49.4 1.0 CA B:GLY250 4.7 59.1 1.0 N B:ARG243 4.7 60.2 1.0 CA B:ILE245 4.7 52.8 1.0 C B:ASP246 4.8 49.4 1.0 C B:GLU249 4.8 55.2 1.0 N B:ASP251 4.8 62.0 1.0 CA B:GLU249 4.8 54.0 1.0 N B:HIS244 4.9 59.4 1.0 CA B:ASP251 4.9 63.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with Mannose 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 Mannose 6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:49.7 occ:1.00 O B:GLY698 2.3 59.8 1.0 O B:VAL696 2.5 52.7 1.0 O B:MET690 2.7 53.4 1.0 O B:VAL693 2.8 44.3 1.0 C B:GLY698 3.3 59.7 1.0 C B:VAL693 3.5 44.4 1.0 C B:MET690 3.6 53.3 1.0 N B:GLY698 3.6 58.2 1.0 C B:VAL696 3.6 52.7 1.0 CE B:MET690 3.9 52.3 1.0 CA B:GLY698 4.0 59.1 1.0 C B:GLU697 4.1 57.5 1.0 CB B:MET690 4.2 53.2 1.0 N B:GLU694 4.2 44.5 1.0 CA B:MET690 4.2 53.5 1.0 CA B:VAL693 4.3 44.2 1.0 CA B:GLU694 4.3 45.1 1.0 CB B:VAL693 4.4 43.9 1.0 N B:ASP699 4.4 60.2 1.0 N B:VAL693 4.4 45.4 1.0 CA B:GLU697 4.4 57.1 1.0 N B:GLU697 4.5 54.9 1.0 N B:LYS691 4.5 52.9 1.0 N B:VAL696 4.5 49.8 1.0 CA B:VAL696 4.6 51.0 1.0 CA B:ASP699 4.7 60.6 1.0 O B:GLU697 4.7 57.4 1.0 CA B:LYS691 4.7 52.4 1.0 C B:GLU694 4.8 45.9 1.0 C B:LYS691 4.8 51.4 1.0 SD B:MET690 4.9 53.4 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.