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Sodium in PDB 6jku: Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida

Protein crystallography data

The structure of Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida, PDB code: 6jku was solved by L.Manjunath, S.Bose, R.Subramanian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.13 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.162, 139.549, 166.556, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20

Other elements in 6jku:

The structure of Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida (pdb code 6jku). 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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida, PDB code: 6jku:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6jku

Go back to Sodium Binding Sites List in 6jku
Sodium binding site 1 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na415

b:20.0
occ:1.00
 O A:ILE163 2.6 25.0 1.0
O A:ALA160 2.6 31.6 1.0
O A:HOH713 2.8 34.8 1.0
O A:HOH687 2.8 39.6 1.0
O A:HOH553 3.1 27.2 1.0
O A:GLY185 3.2 38.8 1.0
C A:ILE163 3.6 25.4 1.0
C A:ALA160 3.8 31.4 1.0
C A:GLY185 4.0 34.2 1.0
CA A:THR164 4.1 25.6 1.0
N A:THR164 4.2 21.7 1.0
N A:ILE163 4.4 24.2 1.0
CA A:ASP161 4.6 33.5 1.0
CA A:ILE163 4.6 24.1 1.0
C A:ASP161 4.6 23.9 1.0
N A:ILE186 4.6 27.2 1.0
CA A:ILE186 4.6 25.9 1.0
O A:HOH625 4.7 25.1 1.0
N A:ASP161 4.7 35.5 1.0
CA A:ALA160 4.7 31.2 1.0
CG1 A:ILE186 4.7 29.4 1.0
O A:THR164 4.8 25.3 1.0
C A:THR164 4.8 22.0 1.0
O A:ASP161 4.8 32.2 1.0
CA A:GLY185 4.8 31.9 1.0
CB A:ALA160 4.8 31.5 1.0
O A:HOH761 4.9 38.4 1.0
N A:VAL162 5.0 25.6 1.0
OG1 A:THR164 5.0 26.8 1.0

Sodium binding site 2 out of 4 in 6jku

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Sodium binding site 2 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na412

b:21.7
occ:1.00
 O B:HOH712 2.4 42.1 1.0
O B:ALA160 2.6 33.5 1.0
O B:HOH715 2.6 33.0 1.0
O B:ILE163 2.6 23.8 1.0
O B:HOH530 3.1 25.4 1.0
O B:GLY185 3.1 41.2 1.0
C B:ILE163 3.6 26.1 1.0
C B:ALA160 3.8 32.9 1.0
C B:GLY185 4.0 38.1 1.0
CA B:THR164 4.1 19.2 1.0
N B:THR164 4.2 21.8 1.0
N B:ILE163 4.4 23.9 1.0
CA B:ASP161 4.5 31.5 1.0
C B:ASP161 4.6 36.0 1.0
CA B:ILE163 4.6 20.6 1.0
N B:ILE186 4.6 31.0 1.0
CA B:ILE186 4.6 30.0 1.0
N B:ASP161 4.6 32.4 1.0
CA B:ALA160 4.7 33.2 1.0
O B:ASP161 4.7 34.7 1.0
O B:HOH592 4.7 25.9 1.0
O B:THR164 4.7 21.7 1.0
CG1 B:ILE186 4.7 26.6 1.0
CB B:ALA160 4.8 28.6 1.0
C B:THR164 4.8 16.9 1.0
O B:HOH539 4.8 38.0 1.0
CA B:GLY185 4.9 35.0 1.0
OG1 B:THR164 5.0 21.5 1.0

Sodium binding site 3 out of 4 in 6jku

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Sodium binding site 3 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:21.2
occ:1.00
 O C:HOH765 2.5 43.3 1.0
O C:ALA160 2.6 32.0 1.0
O C:ILE163 2.6 20.7 1.0
O C:HOH683 2.7 33.0 1.0
O C:HOH595 3.0 27.1 1.0
O C:GLY185 3.2 34.7 1.0
C C:ILE163 3.6 22.7 1.0
C C:ALA160 3.8 28.1 1.0
O C:HOH678 4.0 41.1 1.0
CA C:THR164 4.1 19.6 1.0
C C:GLY185 4.1 29.4 1.0
N C:THR164 4.2 18.7 1.0
N C:ILE163 4.3 23.8 1.0
CA C:ILE163 4.6 22.9 1.0
C C:ASP161 4.6 25.4 1.0
CA C:ALA160 4.6 27.8 1.0
CG1 C:ILE186 4.7 25.4 1.0
CA C:ASP161 4.7 31.2 1.0
N C:ASP161 4.7 24.5 1.0
O C:ASP161 4.7 23.4 1.0
CB C:ALA160 4.8 25.9 1.0
CA C:ILE186 4.8 24.1 1.0
O C:THR164 4.8 20.9 1.0
N C:ILE186 4.8 24.5 1.0
C C:THR164 4.8 20.0 1.0
O C:HOH582 4.9 26.3 1.0
N C:VAL162 4.9 24.1 1.0
OG1 C:THR164 5.0 21.2 1.0
O C:HOH717 5.0 31.9 1.0

Sodium binding site 4 out of 4 in 6jku

Go back to Sodium Binding Sites List in 6jku
Sodium binding site 4 out of 4 in the Crystal Structure of N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida


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 N-Acetylglucosamine-6-Phosphate Deacetylase From Pasteurella Multocida within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na411

b:20.8
occ:1.00
 O D:ALA160 2.6 31.3 1.0
O D:ILE163 2.7 23.2 1.0
O D:HOH752 2.7 51.6 1.0
O D:HOH731 2.9 47.2 1.0
O D:HOH701 3.0 36.4 1.0
O D:GLY185 3.0 35.2 1.0
O D:HOH550 3.1 28.1 1.0
C D:ILE163 3.6 27.2 1.0
C D:ALA160 3.8 31.6 1.0
C D:GLY185 3.8 27.4 1.0
O D:HOH727 3.9 44.2 1.0
CA D:THR164 4.2 22.8 1.0
N D:THR164 4.3 24.8 1.0
N D:ILE163 4.4 24.7 1.0
N D:ILE186 4.5 28.9 1.0
C D:ASP161 4.6 34.5 1.0
CA D:ILE186 4.6 28.3 1.0
CA D:ILE163 4.6 25.1 1.0
CA D:GLY185 4.7 30.0 1.0
CA D:ASP161 4.7 29.2 1.0
CA D:ALA160 4.7 30.9 1.0
N D:ASP161 4.7 30.7 1.0
CG1 D:ILE186 4.8 28.0 1.0
O D:ASP161 4.8 30.6 1.0
CB D:ALA160 4.8 30.1 1.0
O D:THR164 4.8 20.2 1.0
O D:HOH597 4.9 31.0 1.0
C D:THR164 4.9 20.8 1.0
N D:VAL162 4.9 28.4 1.0
O D:HOH601 5.0 41.8 1.0

Reference:

L.Manjunath, S.Bose, R.Subramanian. Crystal Structure of Pasteurella Multocida N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase To Be Published.
Page generated: Tue Oct 8 11:27:16 2024

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