Zinc in PDB 8hfa: The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae

Enzymatic activity of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae

All present enzymatic activity of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae:
3.5.1.41;

Protein crystallography data

The structure of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae, PDB code: 8hfa was solved by L.Liu, Y.Zhou, Q.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.36 / 2.64
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 138.617, 125.899, 127.007, 90, 90, 90
R / Rfree (%) 19.2 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae (pdb code 8hfa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae, PDB code: 8hfa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8hfa

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Zinc binding site 1 out of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:57.2
occ:1.00
 OD1 A:ASP56 2.3 24.1 1.0
NE2 A:HIS112 2.3 42.5 1.0
NE2 A:HIS108 2.3 29.6 1.0
O A:HOH463 2.5 31.1 1.0
CG A:ASP56 3.1 25.1 1.0
OD2 A:ASP56 3.2 31.2 1.0
CE1 A:HIS112 3.2 39.9 1.0
CD2 A:HIS108 3.3 31.1 1.0
CD2 A:HIS112 3.3 43.1 1.0
CE1 A:HIS108 3.3 31.1 1.0
OD2 A:ASP55 4.1 28.5 1.0
CB A:ASP55 4.1 19.3 1.0
ND1 A:HIS112 4.4 45.8 1.0
N A:TYR149 4.4 30.8 1.0
CA A:PRO148 4.4 36.1 1.0
NE2 A:HIS201 4.4 17.5 1.0
CG A:HIS112 4.4 46.7 1.0
ND1 A:HIS108 4.5 28.5 1.0
CG A:HIS108 4.5 29.7 1.0
CD2 A:HIS201 4.5 20.9 1.0
CB A:ASP56 4.5 21.3 1.0
CG A:ASP55 4.6 28.0 1.0
CB A:PRO148 4.7 33.8 1.0
N A:ASP56 4.9 31.9 1.0
C A:PRO148 5.0 38.8 1.0

Zinc binding site 2 out of 5 in 8hfa

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Zinc binding site 2 out of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:49.1
occ:1.00
 OD1 B:ASP56 2.2 27.2 1.0
NE2 B:HIS108 2.3 32.1 1.0
NE2 B:HIS112 2.3 26.3 1.0
O B:HOH459 2.5 16.7 1.0
O B:HOH454 2.7 33.1 1.0
CG B:ASP56 3.0 28.9 1.0
OD2 B:ASP56 3.0 29.7 1.0
CE1 B:HIS112 3.2 24.1 1.0
CD2 B:HIS108 3.2 27.4 1.0
CE1 B:HIS108 3.4 24.9 1.0
CD2 B:HIS112 3.4 28.2 1.0
CB B:ASP55 4.0 23.9 1.0
OD2 B:ASP55 4.0 24.3 1.0
ND1 B:HIS112 4.3 28.6 1.0
CG B:HIS108 4.4 25.2 1.0
N B:TYR149 4.4 27.9 1.0
CB B:ASP56 4.4 21.0 1.0
ND1 B:HIS108 4.4 26.6 1.0
CG B:ASP55 4.5 25.7 1.0
O B:HOH450 4.5 34.5 1.0
CG B:HIS112 4.5 31.1 1.0
CA B:PRO148 4.5 26.2 1.0
O B:HOH498 4.6 21.9 1.0
CD2 B:HIS201 4.6 20.8 1.0
NE2 B:HIS201 4.8 22.8 1.0
N B:ASP56 4.8 29.8 1.0
CB B:PRO148 4.9 29.2 1.0
CA B:ASP56 4.9 24.5 1.0

Zinc binding site 3 out of 5 in 8hfa

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Zinc binding site 3 out of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:46.4
occ:1.00
 OD1 C:ASP56 2.0 22.4 1.0
O C:HOH427 2.2 23.5 1.0
NE2 C:HIS112 2.3 24.5 1.0
NE2 C:HIS108 2.4 21.2 1.0
O C:HOH441 2.4 16.9 1.0
CG C:ASP56 2.9 20.3 1.0
OD2 C:ASP56 3.1 25.6 1.0
CE1 C:HIS112 3.2 24.4 1.0
CD2 C:HIS108 3.3 19.6 1.0
CD2 C:HIS112 3.3 20.9 1.0
CE1 C:HIS108 3.5 17.6 1.0
OD2 C:ASP55 3.9 21.6 1.0
CB C:ASP55 4.0 20.7 1.0
O C:HOH542 4.3 31.5 1.0
CB C:ASP56 4.4 15.7 1.0
ND1 C:HIS112 4.4 20.6 1.0
CG C:ASP55 4.4 20.0 1.0
CG C:HIS112 4.4 22.7 1.0
N C:TYR149 4.5 20.8 1.0
CD2 C:HIS201 4.5 19.6 1.0
CG C:HIS108 4.5 21.6 1.0
O C:HOH509 4.5 20.9 1.0
NE2 C:HIS201 4.5 20.7 1.0
CA C:PRO148 4.5 19.7 1.0
ND1 C:HIS108 4.6 19.7 1.0
N C:ASP56 4.7 23.7 1.0
CA C:ASP56 4.8 17.9 1.0
CB C:PRO148 4.9 18.9 1.0

Zinc binding site 4 out of 5 in 8hfa

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Zinc binding site 4 out of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:46.5
occ:1.00
 NE2 D:HIS112 2.3 24.7 1.0
O D:HOH465 2.4 23.9 1.0
OD1 D:ASP56 2.4 21.6 1.0
NE2 D:HIS108 2.4 19.8 1.0
CE1 D:HIS112 3.1 19.0 1.0
CG D:ASP56 3.2 23.9 1.0
OD2 D:ASP56 3.4 21.4 1.0
CD2 D:HIS108 3.4 20.8 1.0
CD2 D:HIS112 3.4 21.9 1.0
CE1 D:HIS108 3.4 19.8 1.0
OD2 D:ASP55 4.1 22.7 1.0
CB D:ASP55 4.1 19.9 1.0
O D:HOH516 4.1 27.5 1.0
ND1 D:HIS112 4.3 23.1 1.0
N D:TYR149 4.3 22.6 1.0
NE2 D:HIS201 4.4 18.8 1.0
CD2 D:HIS201 4.4 17.9 1.0
CG D:HIS112 4.5 20.2 1.0
ND1 D:HIS108 4.5 17.1 1.0
CA D:PRO148 4.5 18.3 1.0
CG D:HIS108 4.5 18.0 1.0
CG D:ASP55 4.5 20.6 1.0
CB D:ASP56 4.7 21.3 1.0
O D:HOH480 4.8 28.5 1.0
CB D:PRO148 4.9 17.4 1.0
N D:ASP56 5.0 16.4 1.0
C D:PRO148 5.0 21.9 1.0

Zinc binding site 5 out of 5 in 8hfa

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Zinc binding site 5 out of 5 in the The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:55.8
occ:1.00
 NE2 E:HIS112 2.3 22.1 1.0
OD1 E:ASP56 2.4 20.2 1.0
NE2 E:HIS108 2.4 19.8 1.0
O E:HOH446 2.5 22.9 1.0
O E:HOH507 2.8 31.6 1.0
CE1 E:HIS112 3.1 18.9 1.0
CG E:ASP56 3.2 18.0 1.0
OD2 E:ASP56 3.3 20.4 1.0
CD2 E:HIS108 3.4 19.9 1.0
CE1 E:HIS108 3.4 18.5 1.0
CD2 E:HIS112 3.4 21.5 1.0
CB E:ASP55 4.1 19.1 1.0
OD2 E:ASP55 4.2 23.4 1.0
N E:TYR149 4.3 23.8 1.0
ND1 E:HIS112 4.3 17.1 1.0
O E:HOH529 4.3 28.9 1.0
CA E:PRO148 4.4 18.1 1.0
NE2 E:HIS201 4.4 22.9 1.0
CG E:HIS112 4.5 18.1 1.0
ND1 E:HIS108 4.5 21.1 1.0
CG E:HIS108 4.5 22.7 1.0
CD2 E:HIS201 4.5 23.1 1.0
CG E:ASP55 4.7 22.9 1.0
CB E:ASP56 4.7 14.6 1.0
CB E:PRO148 4.9 18.9 1.0
C E:PRO148 4.9 19.8 1.0

Reference:

L.Liu, Y.Zhou, Q.Yang. The Structure of Chitin Deacetylase VDPDA1 From Verticillium Dahliae To Be Published.
Page generated: Thu Oct 31 07:11:40 2024

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