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Sodium in PDB 4fpa: Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N Glucose 6-Phosphate

Enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N Glucose 6-Phosphate

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

Protein crystallography data

The structure of Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N Glucose 6-Phosphate, PDB code: 4fpa 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) 44.15 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.607, 121.140, 119.888, 90.00, 92.69, 90.00
R / Rfree (%) 23.8 / 25.6

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 4fpa

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Sodium binding site 1 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N 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 Mutant D413N Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:63.0
occ:1.00
O A:VAL248 2.4 65.2 1.0
O A:LEU242 2.5 67.4 1.0
O A:ILE245 2.7 62.2 1.0
O A:GLY250 2.7 71.2 1.0
C A:ILE245 3.4 62.4 1.0
C A:LEU242 3.6 67.3 1.0
C A:VAL248 3.6 65.2 1.0
C A:GLY250 3.8 71.1 1.0
N A:GLY250 3.9 69.1 1.0
CA A:ILE245 4.2 62.8 1.0
N A:ASP246 4.2 61.9 1.0
N A:ILE245 4.2 64.1 1.0
N A:VAL248 4.3 63.5 1.0
CB A:ILE245 4.3 62.5 1.0
CA A:GLY250 4.3 70.3 1.0
CA A:VAL248 4.3 64.3 1.0
CA A:ASP246 4.4 61.6 1.0
CA A:LEU242 4.4 66.9 1.0
CB A:LEU242 4.5 67.1 1.0
N A:ARG243 4.5 67.7 1.0
CB A:VAL248 4.6 64.2 1.0
C A:GLU249 4.6 68.2 1.0
C A:ASP246 4.6 61.6 1.0
N A:GLU249 4.6 66.3 1.0
CA A:ARG243 4.7 68.2 1.0
N A:HIS244 4.7 67.3 1.0
O A:ASP246 4.8 61.5 1.0
CA A:GLU249 4.8 67.5 1.0
CG A:LEU242 4.8 67.7 1.0
CG2 A:ILE245 4.8 62.0 1.0
N A:ASP251 4.9 71.9 1.0
C A:ARG243 5.0 67.8 1.0

Sodium binding site 2 out of 4 in 4fpa

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Sodium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N 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 Mutant D413N Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:53.8
occ:1.00
O A:VAL696 2.3 63.8 1.0
O A:GLY698 2.5 69.0 1.0
O A:MET690 2.5 57.7 1.0
O A:VAL693 2.6 53.9 1.0
C A:VAL693 3.4 53.9 1.0
C A:VAL696 3.5 63.7 1.0
C A:GLY698 3.6 68.9 1.0
C A:MET690 3.6 57.7 1.0
CE A:MET690 3.9 60.1 1.0
N A:GLY698 4.0 68.1 1.0
C A:GLU697 4.1 67.6 1.0
N A:GLU694 4.2 54.3 1.0
CA A:VAL693 4.3 53.6 1.0
CA A:GLU694 4.3 54.8 1.0
CB A:VAL693 4.3 53.4 1.0
CA A:GLY698 4.4 68.6 1.0
N A:VAL696 4.4 60.6 1.0
N A:GLU697 4.4 65.5 1.0
N A:VAL693 4.4 54.2 1.0
CA A:VAL696 4.4 62.3 1.0
CA A:MET690 4.4 57.6 1.0
CA A:GLU697 4.4 67.2 1.0
N A:ASP699 4.5 69.2 1.0
CB A:MET690 4.6 57.7 1.0
N A:LYS691 4.6 57.7 1.0
O A:GLU697 4.6 67.6 1.0
CA A:ASP699 4.6 69.3 1.0
CA A:LYS691 4.6 57.8 1.0
SD A:MET690 4.7 59.2 1.0
C A:GLU694 4.7 55.6 1.0
CB A:VAL696 4.7 62.2 1.0
C A:LYS691 4.8 57.2 1.0
O A:LYS691 5.0 57.3 1.0
CG1 A:VAL693 5.0 52.8 1.0

Sodium binding site 3 out of 4 in 4fpa

Go back to Sodium Binding Sites List in 4fpa
Sodium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N 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 Mutant D413N Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:65.3
occ:1.00
O B:VAL248 2.1 64.6 1.0
O B:GLY250 2.5 70.5 1.0
O B:ILE245 2.5 61.0 1.0
O B:LEU242 2.5 66.3 1.0
C B:VAL248 3.3 64.6 1.0
C B:ILE245 3.5 61.3 1.0
C B:GLY250 3.6 70.5 1.0
N B:GLY250 3.6 68.5 1.0
C B:LEU242 3.7 66.3 1.0
C B:GLU249 4.0 67.6 1.0
CG B:LEU242 4.0 66.4 1.0
CA B:GLY250 4.1 69.7 1.0
N B:GLU249 4.2 65.7 1.0
CA B:VAL248 4.2 63.8 1.0
CA B:GLU249 4.3 66.9 1.0
CA B:ILE245 4.3 61.8 1.0
CD1 B:LEU242 4.3 66.4 1.0
CB B:ILE245 4.3 61.6 1.0
N B:VAL248 4.3 63.0 1.0
N B:ILE245 4.4 63.1 1.0
CB B:VAL248 4.4 63.7 1.0
N B:ASP246 4.5 61.0 1.0
CA B:LEU242 4.6 65.9 1.0
N B:ARG243 4.6 66.7 1.0
CA B:ARG243 4.6 67.1 1.0
CA B:ASP246 4.6 60.8 1.0
O B:ASP246 4.6 60.9 1.0
C B:ASP246 4.7 61.0 1.0
N B:ASP251 4.7 71.2 1.0
CB B:LEU242 4.7 66.0 1.0
C B:ARG243 4.8 66.8 1.0
O B:GLU249 4.8 67.6 1.0
O B:ARG243 4.8 66.9 1.0
CG2 B:ILE245 4.9 61.1 1.0
CG1 B:VAL248 5.0 63.7 1.0

Sodium binding site 4 out of 4 in 4fpa

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Sodium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I Mutant D413N 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 Mutant D413N Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:52.1
occ:1.00
O B:GLY698 2.3 69.5 1.0
O B:VAL696 2.4 64.2 1.0
O B:MET690 2.6 58.2 1.0
O B:VAL693 2.8 54.1 1.0
C B:VAL693 3.4 54.2 1.0
C B:GLY698 3.5 69.3 1.0
C B:VAL696 3.6 64.1 1.0
C B:MET690 3.7 58.1 1.0
N B:GLY698 3.8 68.5 1.0
CE B:MET690 3.8 60.2 1.0
N B:GLU694 4.0 54.5 1.0
CA B:GLU694 4.1 55.1 1.0
C B:GLU697 4.1 68.0 1.0
CA B:GLY698 4.2 69.0 1.0
CA B:VAL693 4.3 54.0 1.0
CB B:VAL693 4.3 53.8 1.0
N B:VAL696 4.3 61.0 1.0
O B:LYS691 4.3 57.6 1.0
C B:GLU694 4.4 55.9 1.0
N B:VAL693 4.4 54.5 1.0
CA B:VAL696 4.4 62.6 1.0
N B:GLU697 4.5 65.8 1.0
N B:ASP699 4.5 69.5 1.0
CA B:GLU697 4.5 67.7 1.0
CA B:MET690 4.6 58.1 1.0
C B:LYS691 4.6 57.5 1.0
O B:GLU697 4.6 68.1 1.0
N B:LYS691 4.6 58.0 1.0
CA B:LYS691 4.7 58.0 1.0
O B:GLU694 4.7 56.0 1.0
CB B:MET690 4.7 58.1 1.0
CA B:ASP699 4.7 69.6 1.0
CG1 B:VAL693 4.8 53.2 1.0
N B:MET695 4.9 57.1 1.0
CB B:VAL696 4.9 62.5 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: Tue Dec 15 06:40:51 2020

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