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Sodium in PDB 4fpb: Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 6-Phosphate

Enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 6-Phosphate

All present enzymatic activity of Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 6-Phosphate:
2.7.1.1;

Protein crystallography data

The structure of Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 6-Phosphate, PDB code: 4fpb 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) 46.24 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.723, 121.211, 120.790, 90.00, 93.12, 90.00
R / Rfree (%) 22.9 / 25.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 6-Phosphate (pdb code 4fpb). 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 1,5- Anhydroglucitol 6-Phosphate, PDB code: 4fpb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4fpb

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Sodium binding site 1 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 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 1,5- Anhydroglucitol 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:74.4
occ:1.00
 O A:VAL248 2.4 76.3 1.0
O A:LEU242 2.5 85.7 1.0
O A:ILE245 2.6 80.0 1.0
O A:GLY250 3.3 84.3 1.0
C A:LEU242 3.5 85.6 1.0
C A:ILE245 3.6 80.1 1.0
C A:VAL248 3.6 76.4 1.0
C A:GLY250 3.7 84.2 1.0
CG A:LEU242 3.8 85.5 1.0
N A:GLY250 3.9 81.4 1.0
CA A:GLY250 4.2 83.0 1.0
CA A:ILE245 4.2 81.0 1.0
N A:ILE245 4.2 82.7 1.0
CB A:ILE245 4.3 81.0 1.0
CA A:VAL248 4.3 75.5 1.0
CA A:LEU242 4.3 85.0 1.0
N A:VAL248 4.3 75.0 1.0
N A:ARG243 4.4 86.4 1.0
CB A:VAL248 4.4 75.2 1.0
CD1 A:LEU242 4.4 85.8 1.0
N A:ASP251 4.4 85.2 1.0
CB A:LEU242 4.5 85.0 1.0
CA A:ARG243 4.5 87.2 1.0
N A:ASP246 4.6 78.8 1.0
C A:GLU249 4.6 80.1 1.0
CG1 A:VAL248 4.6 74.6 1.0
N A:GLU249 4.7 77.6 1.0
CD2 A:LEU242 4.7 86.1 1.0
CG2 A:ILE245 4.8 80.5 1.0
CA A:ASP246 4.8 77.6 1.0
CA A:ASP251 4.8 86.2 1.0
C A:ARG243 4.9 86.8 1.0
N A:HIS244 4.9 86.2 1.0
C A:ASP246 4.9 76.6 1.0
CA A:GLU249 4.9 79.1 1.0

Sodium binding site 2 out of 4 in 4fpb

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Sodium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 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 1,5- Anhydroglucitol 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:55.9
occ:1.00
 O A:VAL696 2.2 76.2 1.0
O A:GLY698 2.6 81.2 1.0
O A:VAL693 2.7 68.9 1.0
O A:MET690 3.2 72.5 1.0
C A:VAL696 3.2 76.1 1.0
C A:VAL693 3.4 69.0 1.0
C A:GLY698 3.8 81.2 1.0
N A:VAL696 3.9 73.3 1.0
N A:GLY698 4.0 79.9 1.0
CA A:VAL696 4.1 74.8 1.0
N A:GLU694 4.1 69.0 1.0
CA A:GLU694 4.1 69.2 1.0
C A:GLU697 4.1 79.2 1.0
N A:GLU697 4.2 77.5 1.0
CA A:GLU697 4.3 78.9 1.0
CA A:VAL693 4.3 69.2 1.0
C A:GLU694 4.4 69.8 1.0
C A:MET690 4.4 72.6 1.0
CB A:VAL693 4.4 69.1 1.0
CE A:MET690 4.4 75.3 1.0
N A:VAL693 4.5 69.9 1.0
CA A:GLY698 4.5 80.6 1.0
N A:MET695 4.5 70.6 1.0
CB A:VAL696 4.6 74.7 1.0
O A:GLU697 4.6 79.3 1.0
N A:ASP699 4.8 81.8 1.0
CA A:ASP699 4.9 82.5 1.0
CG1 A:VAL693 4.9 68.8 1.0
SD A:MET690 5.0 74.6 1.0
CB A:ASP699 5.0 82.7 1.0
O A:GLU694 5.0 70.0 1.0

Sodium binding site 3 out of 4 in 4fpb

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Sodium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 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 1,5- Anhydroglucitol 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1005

b:77.6
occ:1.00
 O B:GLY250 2.4 83.5 1.0
O B:ILE245 2.5 79.5 1.0
O B:LEU242 2.5 85.2 1.0
O B:VAL248 2.7 75.7 1.0
C B:ILE245 3.5 79.5 1.0
C B:GLY250 3.5 83.3 1.0
N B:GLY250 3.6 80.5 1.0
C B:LEU242 3.6 85.0 1.0
C B:VAL248 3.8 75.6 1.0
CA B:GLY250 4.1 82.1 1.0
N B:ILE245 4.3 82.1 1.0
CA B:ILE245 4.3 80.4 1.0
CG B:LEU242 4.3 84.5 1.0
N B:ASP246 4.3 78.3 1.0
CA B:ASP246 4.4 77.0 1.0
CA B:ARG243 4.5 86.7 1.0
N B:ARG243 4.5 85.9 1.0
C B:ARG243 4.5 86.3 1.0
CB B:ILE245 4.5 80.4 1.0
C B:GLU249 4.5 79.2 1.0
N B:ASP251 4.5 84.3 1.0
O B:ARG243 4.6 86.3 1.0
N B:VAL248 4.6 74.4 1.0
CA B:LEU242 4.6 84.3 1.0
O B:ASP246 4.6 76.1 1.0
CA B:VAL248 4.6 74.7 1.0
C B:ASP246 4.7 76.2 1.0
N B:GLU249 4.7 76.8 1.0
CA B:GLU249 4.7 78.2 1.0
CB B:LEU242 4.8 84.3 1.0
CD1 B:LEU242 4.8 84.5 1.0
CA B:ASP251 4.9 85.2 1.0
CB B:VAL248 4.9 74.5 1.0

Sodium binding site 4 out of 4 in 4fpb

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Sodium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Hexokinase Type I with 1,5- Anhydroglucitol 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 1,5- Anhydroglucitol 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1006

b:54.7
occ:1.00
 O B:VAL696 2.2 76.8 1.0
O B:GLY698 2.6 82.0 1.0
O B:MET690 2.7 73.0 1.0
O B:VAL693 3.0 69.6 1.0
C B:VAL696 3.4 76.6 1.0
C B:VAL693 3.6 69.8 1.0
C B:GLY698 3.7 81.9 1.0
CE B:MET690 3.8 75.5 1.0
C B:MET690 3.8 73.1 1.0
N B:GLY698 3.9 80.5 1.0
C B:GLU697 3.9 79.9 1.0
N B:GLU694 4.1 69.7 1.0
CA B:GLU694 4.2 69.8 1.0
N B:GLU697 4.3 78.1 1.0
CA B:GLU697 4.3 79.6 1.0
N B:VAL696 4.3 74.0 1.0
O B:GLU697 4.3 80.0 1.0
CA B:VAL693 4.3 69.9 1.0
CA B:GLY698 4.3 81.3 1.0
CB B:VAL693 4.4 69.8 1.0
CA B:VAL696 4.4 75.3 1.0
C B:GLU694 4.5 70.3 1.0
N B:VAL693 4.5 70.6 1.0
CA B:MET690 4.6 73.0 1.0
O B:GLU694 4.6 70.4 1.0
CB B:MET690 4.6 73.1 1.0
SD B:MET690 4.7 75.0 1.0
N B:LYS691 4.8 73.4 1.0
N B:ASP699 4.8 82.5 1.0
CB B:VAL696 4.8 75.1 1.0
CA B:LYS691 4.9 73.6 1.0
C B:LYS691 4.9 73.3 1.0
O B:LYS691 4.9 73.4 1.0

Reference:

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.
Page generated: Mon Oct 7 15:27:30 2024

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