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Sodium in PDB 4foi: Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate

Enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate

All present enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate:
2.7.1.1;

Protein crystallography data

The structure of Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate, PDB code: 4foi 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) 35.41 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.380, 120.772, 120.591, 90.00, 92.80, 90.00
R / Rfree (%) 24.7 / 27.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate (pdb code 4foi). 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 Mutant D413N with Glucose 1,6-Bisphosphate, PDB code: 4foi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4foi

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Sodium binding site 1 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate


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 Mutant D413N with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:55.1
occ:1.00
 O A:VAL248 2.2 56.6 1.0
O A:LEU242 2.6 60.9 1.0
O A:ILE245 2.7 55.9 1.0
O A:GLY250 2.8 63.1 1.0
C A:VAL248 3.4 56.7 1.0
C A:ILE245 3.5 56.0 1.0
C A:LEU242 3.6 60.8 1.0
N A:GLY250 3.8 60.8 1.0
C A:GLY250 3.8 63.0 1.0
CD1 A:LEU242 3.9 61.5 1.0
CA A:ILE245 4.1 56.4 1.0
CA A:VAL248 4.2 56.0 1.0
N A:ILE245 4.2 57.7 1.0
CB A:ILE245 4.2 56.2 1.0
N A:VAL248 4.2 55.4 1.0
CB A:VAL248 4.3 55.8 1.0
N A:ASP246 4.3 55.5 1.0
CA A:GLY250 4.3 62.1 1.0
CA A:LEU242 4.3 60.2 1.0
C A:GLU249 4.4 59.7 1.0
N A:GLU249 4.4 57.8 1.0
CB A:LEU242 4.5 60.4 1.0
CA A:ASP246 4.6 55.1 1.0
CA A:GLU249 4.6 59.0 1.0
N A:ARG243 4.6 61.4 1.0
C A:ASP246 4.7 54.9 1.0
O A:ASP246 4.8 54.9 1.0
CG A:LEU242 4.8 60.9 1.0
CA A:ARG243 4.8 62.0 1.0
CG2 A:ILE245 4.9 55.8 1.0
CG1 A:VAL248 5.0 55.3 1.0
N A:HIS244 5.0 60.8 1.0
N A:ASP251 5.0 63.8 1.0

Sodium binding site 2 out of 4 in 4foi

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Sodium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate


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 Mutant D413N with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:54.6
occ:1.00
 O A:VAL696 2.2 55.6 1.0
O A:GLY698 2.3 59.9 1.0
O A:VAL693 2.5 47.0 1.0
O A:MET690 2.8 50.4 1.0
C A:VAL696 3.4 55.5 1.0
C A:VAL693 3.4 47.1 1.0
C A:GLY698 3.4 59.8 1.0
CE A:MET690 3.7 51.0 1.0
N A:GLY698 3.8 59.1 1.0
C A:MET690 3.9 50.3 1.0
C A:GLU697 4.1 58.7 1.0
CA A:GLY698 4.2 59.5 1.0
N A:GLU694 4.2 47.5 1.0
CA A:GLU694 4.2 48.0 1.0
CA A:VAL693 4.3 46.9 1.0
N A:VAL696 4.3 53.0 1.0
N A:GLU697 4.3 57.0 1.0
CB A:VAL693 4.3 46.6 1.0
CA A:VAL696 4.3 54.3 1.0
CA A:GLU697 4.3 58.4 1.0
N A:VAL693 4.4 47.5 1.0
N A:ASP699 4.4 60.1 1.0
C A:GLU694 4.6 48.8 1.0
CA A:ASP699 4.6 60.3 1.0
CA A:MET690 4.6 50.1 1.0
CB A:VAL696 4.6 54.3 1.0
SD A:MET690 4.6 50.5 1.0
O A:GLU697 4.7 58.6 1.0
CB A:MET690 4.7 50.2 1.0
N A:LYS691 4.8 50.4 1.0
CA A:LYS691 4.8 50.6 1.0
O A:GLU694 4.9 48.9 1.0
C A:LYS691 4.9 50.2 1.0
CG1 A:VAL693 5.0 46.1 1.0
N A:MET695 5.0 49.9 1.0

Sodium binding site 3 out of 4 in 4foi

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Sodium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate


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 Mutant D413N with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:53.2
occ:1.00
 O B:VAL248 1.9 56.1 1.0
O B:ILE245 2.5 54.9 1.0
O B:GLY250 2.6 62.5 1.0
O B:LEU242 2.8 59.8 1.0
C B:VAL248 3.1 56.3 1.0
N B:GLY250 3.4 60.3 1.0
C B:ILE245 3.6 55.0 1.0
C B:GLY250 3.6 62.5 1.0
C B:GLU249 3.7 59.3 1.0
N B:GLU249 3.9 57.4 1.0
CA B:GLU249 3.9 58.6 1.0
C B:LEU242 3.9 59.7 1.0
CA B:GLY250 3.9 61.6 1.0
CA B:VAL248 4.1 55.5 1.0
N B:VAL248 4.2 54.9 1.0
CB B:ILE245 4.3 55.3 1.0
CA B:ILE245 4.3 55.4 1.0
O B:GLU249 4.4 59.2 1.0
CG B:LEU242 4.4 59.7 1.0
CB B:VAL248 4.4 55.4 1.0
N B:ILE245 4.5 56.7 1.0
N B:ASP246 4.5 54.5 1.0
CA B:LEU242 4.7 59.2 1.0
CA B:ASP246 4.7 54.3 1.0
CB B:LEU242 4.7 59.4 1.0
C B:ASP246 4.7 54.2 1.0
O B:ASP246 4.8 54.1 1.0
CG1 B:VAL248 4.8 55.0 1.0
N B:ASP251 4.8 63.3 1.0
N B:ARG243 4.9 60.4 1.0
CD2 B:LEU242 4.9 60.3 1.0
CG2 B:ILE245 5.0 54.9 1.0

Sodium binding site 4 out of 4 in 4foi

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Sodium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N with Glucose 1,6-Bisphosphate


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 Mutant D413N with Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:53.6
occ:1.00
 O B:VAL696 2.4 56.0 1.0
O B:GLY698 2.4 60.4 1.0
O B:MET690 2.7 51.1 1.0
O B:VAL693 2.7 47.5 1.0
C B:VAL693 3.3 47.6 1.0
C B:VAL696 3.6 55.9 1.0
C B:GLY698 3.6 60.3 1.0
C B:MET690 3.8 51.0 1.0
CE B:MET690 3.9 51.4 1.0
N B:GLU694 4.0 47.8 1.0
N B:GLY698 4.0 59.6 1.0
CA B:GLU694 4.1 48.3 1.0
CA B:VAL693 4.1 47.4 1.0
CB B:VAL693 4.1 47.2 1.0
C B:GLU697 4.2 59.2 1.0
N B:VAL693 4.3 48.0 1.0
N B:VAL696 4.3 53.3 1.0
CA B:GLY698 4.4 60.0 1.0
C B:GLU694 4.4 49.0 1.0
CA B:MET690 4.4 50.9 1.0
CA B:VAL696 4.5 54.7 1.0
N B:GLU697 4.5 57.4 1.0
CB B:MET690 4.6 50.8 1.0
CA B:GLU697 4.6 59.0 1.0
N B:ASP699 4.7 60.5 1.0
CG1 B:VAL693 4.7 46.8 1.0
O B:GLU697 4.7 59.3 1.0
O B:GLU694 4.7 48.9 1.0
N B:LYS691 4.8 51.2 1.0
CA B:ASP699 4.8 60.6 1.0
N B:MET695 4.9 50.0 1.0
CB B:VAL696 4.9 54.6 1.0
SD B:MET690 4.9 51.7 1.0
C B:LYS691 4.9 50.9 1.0
CA B:LYS691 5.0 51.4 1.0

Reference:

L.Shen, Y.Gao, R.B.Honzatko. Determination of Site Affinity Constants For Product Inhibition of Wild-Type and Mutant Forms of Recombinant Human Hexokinase Type I To Be Published.
Page generated: Mon Oct 7 15:25:34 2024

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