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Sodium in PDB 4nyy: Structure of Vibrio Cholerae Chitin De-N-Acetylase

Enzymatic activity of Structure of Vibrio Cholerae Chitin De-N-Acetylase

All present enzymatic activity of Structure of Vibrio Cholerae Chitin De-N-Acetylase:
3.5.1.41;

Protein crystallography data

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase, PDB code: 4nyy was solved by D.Albesa-Jove, E.Andres, X.Biarnes, A.Planas, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.170, 165.010, 203.360, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 4nyy:

The structure of Structure of Vibrio Cholerae Chitin De-N-Acetylase also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Vibrio Cholerae Chitin De-N-Acetylase (pdb code 4nyy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Vibrio Cholerae Chitin De-N-Acetylase, PDB code: 4nyy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4nyy

Go back to Sodium Binding Sites List in 4nyy
Sodium binding site 1 out of 4 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:16.1
occ:1.00
O A:GLY355 2.1 13.4 1.0
O A:HOH672 2.3 22.2 1.0
O A:GLY223 2.3 6.1 1.0
O A:HOH671 2.5 2.6 1.0
O A:HOH651 2.5 20.3 1.0
O A:HOH678 3.0 27.1 1.0
C A:GLY355 3.2 13.4 1.0
C A:GLY223 3.3 6.1 1.0
CA A:GLY223 3.7 6.1 1.0
CA A:GLY355 3.8 13.4 1.0
O A:HOH675 4.1 15.5 1.0
N A:VAL356 4.3 10.3 1.0
O A:HOH676 4.5 4.1 1.0
N A:TYR224 4.5 4.7 1.0
CG A:GLU163 4.5 17.0 1.0
CA A:VAL356 4.7 10.3 1.0
OD1 A:ASP383 4.8 11.3 1.0
CA A:TYR224 5.0 4.7 1.0

Sodium binding site 2 out of 4 in 4nyy

Go back to Sodium Binding Sites List in 4nyy
Sodium binding site 2 out of 4 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:24.1
occ:1.00
O B:GLY355 2.1 21.6 1.0
O B:GLY223 2.2 3.0 1.0
O B:HOH659 2.4 29.8 1.0
O B:HOH660 2.5 20.9 1.0
O B:HOH661 2.5 30.4 1.0
O B:HOH658 2.5 21.8 1.0
C B:GLY223 3.2 3.0 1.0
C B:GLY355 3.3 21.6 1.0
CA B:GLY223 3.6 3.0 1.0
CA B:GLY355 4.0 21.6 1.0
O B:HOH663 4.2 26.7 1.0
N B:VAL356 4.4 7.5 1.0
N B:TYR224 4.4 7.0 1.0
CG B:GLU163 4.6 25.9 1.0
O B:HOH608 4.6 4.7 1.0
CA B:VAL356 4.6 7.5 1.0
OD1 B:ASP383 4.6 14.8 1.0
O B:HOH662 4.8 20.7 1.0
CA B:TYR224 4.8 7.0 1.0
C B:TYR224 4.9 7.0 1.0
OD2 B:ASP383 5.0 14.8 1.0

Sodium binding site 3 out of 4 in 4nyy

Go back to Sodium Binding Sites List in 4nyy
Sodium binding site 3 out of 4 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:17.5
occ:1.00
O C:GLY355 2.1 28.7 1.0
O C:GLY223 2.2 9.3 1.0
O C:HOH644 2.3 28.9 1.0
O C:HOH645 2.4 37.9 1.0
O C:HOH643 2.5 5.9 1.0
O C:HOH647 3.2 19.0 1.0
C C:GLY355 3.2 28.7 1.0
C C:GLY223 3.3 9.3 1.0
CA C:GLY223 3.8 9.3 1.0
CA C:GLY355 3.9 28.7 1.0
N C:VAL356 4.3 13.2 1.0
CG C:GLU163 4.4 23.6 1.0
N C:TYR224 4.4 11.0 1.0
O C:HOH646 4.5 11.4 1.0
CA C:VAL356 4.6 13.2 1.0
OD1 C:ASP383 4.7 14.9 1.0
O C:HOH698 4.7 12.7 1.0
CA C:TYR224 4.8 11.0 1.0
C C:TYR224 4.9 11.0 1.0
CD C:GLU163 5.0 23.6 1.0

Sodium binding site 4 out of 4 in 4nyy

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Sodium binding site 4 out of 4 in the Structure of Vibrio Cholerae Chitin De-N-Acetylase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Vibrio Cholerae Chitin De-N-Acetylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:27.0
occ:1.00
O D:GLY355 2.2 19.3 1.0
O D:GLY223 2.3 12.3 1.0
O D:HOH635 2.5 19.4 1.0
O D:HOH612 2.5 12.6 1.0
O D:HOH651 2.6 33.8 1.0
O D:HOH649 2.7 43.5 1.0
C D:GLY355 3.3 19.3 1.0
C D:GLY223 3.3 12.3 1.0
CA D:GLY223 3.6 12.3 1.0
CA D:GLY355 3.9 19.3 1.0
O D:HOH690 4.3 30.3 1.0
N D:VAL356 4.4 10.6 1.0
CG D:GLU163 4.5 21.3 1.0
N D:TYR224 4.5 8.9 1.0
O D:HOH696 4.5 32.5 1.0
O D:HOH613 4.5 10.1 1.0
CA D:VAL356 4.7 10.6 1.0
OD1 D:ASP383 4.9 14.0 1.0
CA D:TYR224 5.0 8.9 1.0

Reference:

E.Andres, D.Albesa-Jove, X.Biarnes, B.M.Moerschbacher, M.E.Guerin, A.Planas. Structural Basis of Chitin Oligosaccharide Deacetylation. Angew.Chem.Int.Ed.Engl. V. 53 6882 2014.
ISSN: ISSN 1433-7851
PubMed: 24810719
DOI: 10.1002/ANIE.201400220
Page generated: Tue Dec 15 06:56:11 2020

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