Atomistry » Sodium » PDB 6jbu-6kcb » 6jku
Atomistry »
  Sodium »
    PDB 6jbu-6kcb »
      6jku »

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

Go back to Sodium Binding Sites List in 6jku
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

Go back to Sodium Binding Sites List in 6jku
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy