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Sodium in PDB 8yh4: Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2

Protein crystallography data

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2, PDB code: 8yh4 was solved by P.Sirikan, F.Tamo, R.C.Robinson, S.Wipa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 2.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.894, 118.458, 252.574, 90, 90, 90
R / Rfree (%) 15.1 / 18.2

Other elements in 8yh4:

The structure of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 (pdb code 8yh4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2, PDB code: 8yh4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 8yh4

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Sodium binding site 1 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:26.5
occ:1.00
 O A:GLY329 2.2 22.2 1.0
O A:GLY197 2.2 13.3 1.0
O A:HOH810 2.4 20.1 1.0
O A:HOH761 2.5 28.8 1.0
O A:HOH884 2.5 27.3 1.0
C A:GLY329 3.3 21.6 1.0
O A:HOH648 3.4 24.2 1.0
C A:GLY197 3.4 15.2 1.0
CA A:GLY197 4.0 9.4 1.0
CA A:GLY329 4.1 22.5 1.0
N A:THR330 4.3 16.8 1.0
N A:TYR198 4.4 14.7 1.0
O A:HOH686 4.5 20.8 1.0
CG A:GLU137 4.5 38.1 1.0
CA A:THR330 4.5 12.8 1.0
C A:TYR198 4.7 13.3 1.0
CA A:TYR198 4.7 12.7 1.0
OD1 A:ASP357 4.7 19.6 1.0
CB A:GLU137 4.7 28.9 1.0
O A:GLU137 4.7 14.7 1.0
N A:GLN199 4.8 10.8 1.0
OD2 A:ASP357 4.9 21.7 1.0
O A:HOH641 4.9 28.2 1.0
O A:HOH605 4.9 54.9 1.0

Sodium binding site 2 out of 7 in 8yh4

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Sodium binding site 2 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:25.0
occ:1.00
 O B:GLY329 2.3 19.7 1.0
O B:GLY197 2.3 12.6 1.0
O B:HOH759 2.4 21.9 1.0
O B:HOH869 2.4 26.4 1.0
O B:HOH783 2.5 19.5 1.0
C B:GLY329 3.4 18.0 1.0
C B:GLY197 3.4 15.7 1.0
O B:HOH777 3.5 30.2 1.0
CA B:GLY197 4.1 12.6 1.0
CA B:GLY329 4.2 19.8 1.0
O B:HOH628 4.3 28.8 1.0
N B:THR330 4.4 14.4 1.0
CG B:GLU137 4.5 35.2 1.0
N B:TYR198 4.5 14.9 1.0
CA B:THR330 4.5 15.4 1.0
O B:HOH792 4.5 22.1 1.0
O B:GLU137 4.6 11.8 1.0
CB B:GLU137 4.6 27.6 1.0
OD1 B:ASP357 4.7 23.5 1.0
C B:TYR198 4.7 14.9 1.0
N B:GLN199 4.7 12.8 1.0
CA B:TYR198 4.7 14.6 1.0
O B:HOH776 4.8 33.9 1.0
CG B:GLN199 5.0 11.6 1.0
CD B:GLU137 5.0 39.1 1.0
CA B:GLU137 5.0 18.6 1.0

Sodium binding site 3 out of 7 in 8yh4

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Sodium binding site 3 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:22.1
occ:1.00
 O B:THR310 2.4 13.5 1.0
O B:ASP307 2.5 18.5 1.0
OG1 B:THR326 2.5 17.8 1.0
O B:HOH692 2.6 20.9 1.0
O B:HOH735 2.7 20.6 1.0
CG2 B:THR326 3.4 12.6 1.0
CB B:THR326 3.5 15.2 1.0
C B:THR310 3.6 14.9 1.0
C B:ASP307 3.6 16.0 1.0
O B:HOH922 3.6 28.4 1.0
CG2 B:VAL312 3.9 21.5 1.0
CB B:THR310 4.0 15.6 1.0
O B:HOH788 4.1 19.7 1.0
CA B:THR310 4.2 12.2 1.0
N B:THR310 4.3 11.2 1.0
N B:VAL312 4.3 14.0 1.0
C B:PRO311 4.3 14.2 1.0
N B:ASN308 4.5 10.9 1.0
CA B:ASN308 4.5 12.3 1.0
CA B:ASP307 4.5 15.9 1.0
O B:PRO311 4.5 11.3 1.0
O B:HOH666 4.6 28.0 1.0
N B:PRO311 4.6 14.7 1.0
CA B:THR326 4.7 15.2 1.0
CA B:VAL312 4.7 16.5 1.0
O B:HOH846 4.7 17.8 1.0
N B:THR326 4.8 12.5 1.0
CA B:PRO311 4.8 16.1 1.0
O B:HOH953 4.8 22.6 1.0
C B:ASN308 4.8 15.1 1.0
CG2 B:THR310 4.9 11.8 1.0
CB B:VAL312 5.0 21.3 1.0
OG1 B:THR310 5.0 16.3 1.0

Sodium binding site 4 out of 7 in 8yh4

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Sodium binding site 4 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:28.5
occ:1.00
 O C:GLY329 2.3 25.6 1.0
O C:GLY197 2.3 19.7 1.0
O C:HOH792 2.4 37.8 1.0
O C:HOH643 2.4 31.4 1.0
O C:HOH716 2.5 18.6 1.0
C C:GLY197 3.4 21.5 1.0
C C:GLY329 3.5 20.4 1.0
O C:HOH707 3.7 30.6 1.0
CA C:GLY197 4.0 17.6 1.0
CA C:GLY329 4.3 21.2 1.0
CG C:GLU137 4.4 38.4 1.0
N C:THR330 4.4 17.1 1.0
O C:HOH648 4.4 32.0 1.0
N C:TYR198 4.4 18.1 1.0
CA C:THR330 4.5 14.8 1.0
O C:GLU137 4.5 17.2 1.0
O C:HOH759 4.5 15.0 1.0
CB C:GLU137 4.5 30.1 1.0
C C:TYR198 4.6 16.5 1.0
OD1 C:ASP357 4.6 26.9 1.0
CA C:TYR198 4.6 17.5 1.0
O C:HOH791 4.6 32.2 1.0
N C:GLN199 4.7 15.7 1.0
CA C:GLU137 4.9 24.8 1.0
O C:TYR198 4.9 14.9 1.0
CG C:GLN199 5.0 17.3 1.0

Sodium binding site 5 out of 7 in 8yh4

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Sodium binding site 5 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:22.1
occ:1.00
 O C:ASP307 2.4 19.3 1.0
O C:HOH730 2.4 20.2 1.0
OG1 C:THR326 2.4 18.4 1.0
O C:HOH647 2.4 22.4 1.0
O C:THR310 2.5 15.5 1.0
CG2 C:THR326 3.4 12.3 1.0
O C:HOH878 3.4 27.4 1.0
CB C:THR326 3.4 16.1 1.0
C C:ASP307 3.6 19.6 1.0
C C:THR310 3.7 15.8 1.0
CG2 C:VAL312 3.9 23.1 1.0
CB C:THR310 4.1 15.2 1.0
O C:HOH749 4.2 18.2 1.0
CA C:THR310 4.3 14.6 1.0
CA C:ASP307 4.4 19.0 1.0
N C:VAL312 4.4 16.0 1.0
C C:PRO311 4.4 15.9 1.0
N C:THR310 4.4 13.7 1.0
N C:ASN308 4.5 15.1 1.0
CA C:ASN308 4.5 14.6 1.0
O C:HOH826 4.6 21.4 1.0
O C:PRO311 4.6 15.8 1.0
O C:HOH907 4.6 31.4 1.0
CA C:THR326 4.6 17.2 1.0
N C:PRO311 4.7 15.2 1.0
CA C:VAL312 4.7 18.6 1.0
N C:THR326 4.7 10.7 1.0
O C:HOH616 4.8 31.4 1.0
O C:HOH648 4.8 32.0 1.0
CA C:PRO311 4.9 16.3 1.0
C C:ASN308 4.9 14.9 1.0
CG2 C:THR310 4.9 15.3 1.0
OE1 C:GLN199 5.0 23.0 1.0
CB C:VAL312 5.0 23.2 1.0

Sodium binding site 6 out of 7 in 8yh4

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Sodium binding site 6 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:34.2
occ:1.00
 O D:GLY197 2.3 16.5 1.0
O D:GLY329 2.3 26.7 1.0
O D:HOH671 2.4 34.9 1.0
O D:HOH694 2.4 23.4 1.0
O D:HOH830 2.5 33.3 1.0
C D:GLY197 3.5 18.4 1.0
C D:GLY329 3.5 25.0 1.0
O D:HOH665 3.7 36.7 1.0
CA D:GLY197 4.2 17.8 1.0
CA D:GLY329 4.3 26.7 1.0
CG D:GLU137 4.3 35.7 1.0
O D:HOH703 4.5 39.2 1.0
N D:TYR198 4.5 19.4 1.0
N D:THR330 4.5 22.3 1.0
CB D:GLU137 4.6 25.7 1.0
O D:GLU137 4.6 19.3 1.0
C D:TYR198 4.6 17.5 1.0
N D:GLN199 4.6 18.4 1.0
O D:HOH768 4.6 37.9 1.0
OD1 D:ASP357 4.7 28.7 1.0
CA D:THR330 4.7 18.5 1.0
O D:HOH717 4.7 23.3 1.0
CA D:TYR198 4.7 17.1 1.0
CG D:GLN199 4.9 21.2 1.0
CA D:GLU137 5.0 22.5 1.0
CD D:GLU137 5.0 41.4 1.0

Sodium binding site 7 out of 7 in 8yh4

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Sodium binding site 7 out of 7 in the Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:28.0
occ:1.00
 O D:THR310 2.4 18.8 1.0
OG1 D:THR326 2.4 23.7 1.0
O D:HOH680 2.5 25.3 1.0
O D:HOH713 2.5 45.5 1.0
O D:ASP307 2.6 28.2 1.0
CG2 D:THR326 3.2 23.3 1.0
CB D:THR326 3.3 21.0 1.0
C D:THR310 3.6 21.4 1.0
O D:HOH857 3.6 38.7 1.0
C D:ASP307 3.7 25.2 1.0
CB D:THR310 4.0 21.5 1.0
CG2 D:VAL312 4.0 24.4 1.0
O D:HOH811 4.2 35.0 1.0
CA D:THR310 4.2 21.9 1.0
N D:VAL312 4.4 24.1 1.0
C D:PRO311 4.4 24.9 1.0
N D:THR310 4.4 21.7 1.0
CA D:THR326 4.6 21.2 1.0
O D:HOH788 4.6 30.7 1.0
O D:HOH703 4.6 39.2 1.0
CA D:ASP307 4.6 23.1 1.0
O D:PRO311 4.6 23.9 1.0
N D:PRO311 4.6 22.2 1.0
N D:ASN308 4.6 20.3 1.0
O D:HOH872 4.6 23.8 1.0
N D:THR326 4.6 20.8 1.0
CA D:ASN308 4.6 20.1 1.0
O D:HOH725 4.7 30.5 1.0
CA D:VAL312 4.7 22.6 1.0
CG2 D:THR310 4.8 21.9 1.0
CA D:PRO311 4.8 22.6 1.0
OG1 D:THR310 5.0 24.8 1.0

Reference:

P.Sirikan, S.Wipa, F.Tamo, R.C.Robinson. Chito Oligosaccharide Deacetylase From Vibrio Campbellii (Vhcod) in Complex with Chitosanbiose (Glcn)2 To Be Published.
Page generated: Mon Aug 18 16:28:45 2025

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