Zinc in PDB 4cxv: Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.

Enzymatic activity of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.

All present enzymatic activity of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.:
3.1.30.1;

Protein crystallography data

The structure of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate., PDB code: 4cxv was solved by T.-F.Yu, M.Maestre-Reyna, C.-Y.Ko, T.-P.Ko, Y.-J.Sun, T.-Y.Lin, J.-F.Shaw, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.43 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.524, 52.870, 60.841, 71.34, 78.63, 76.62
R / Rfree (%) 20.184 / 24.942

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. (pdb code 4cxv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate., PDB code: 4cxv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4cxv

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Zinc binding site 1 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn431

b:23.4
occ:1.00
 O3 A:PO4401 2.1 13.9 0.8
NE2 A:HIS120 2.2 17.8 1.0
O2 A:PO4401 2.2 13.0 0.8
OD2 A:ASP124 2.2 13.9 1.0
ND1 A:HIS58 2.3 20.2 1.0
OD1 A:ASP45 2.5 21.3 1.0
P A:PO4401 2.7 16.2 0.8
CE1 A:HIS120 3.1 18.5 1.0
CG A:ASP124 3.1 15.1 1.0
CE1 A:HIS58 3.1 19.7 1.0
CD2 A:HIS120 3.2 17.7 1.0
CG A:HIS58 3.3 19.9 1.0
OD1 A:ASP124 3.4 16.7 1.0
CG A:ASP45 3.5 24.6 1.0
ZN A:ZN433 3.5 18.7 1.0
CB A:HIS58 3.7 20.1 1.0
O1 A:PO4401 3.7 14.6 0.8
OD2 A:ASP45 3.8 22.1 1.0
O4 A:PO4401 4.0 13.2 0.8
ND1 A:HIS120 4.2 19.2 1.0
NE2 A:HIS58 4.3 19.7 1.0
CG A:HIS120 4.3 18.3 1.0
NE2 A:HIS6 4.3 22.5 1.0
CE1 A:HIS130 4.3 20.4 1.0
CE A:LYS48 4.4 20.6 1.0
CD2 A:HIS58 4.4 20.3 1.0
CB A:ASP124 4.4 17.8 1.0
O A:HOH2054 4.4 29.7 1.0
NZ A:LYS48 4.5 21.4 1.0
CA A:HIS58 4.7 19.9 1.0
CE1 A:HIS6 4.7 22.7 1.0
CB A:ASP45 4.9 23.8 1.0

Zinc binding site 2 out of 6 in 4cxv

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Zinc binding site 2 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn432

b:24.1
occ:1.00
 O A:HOH2117 1.8 20.3 1.0
OD2 A:ASP158 2.1 24.8 1.0
O4 A:PO4401 2.1 13.2 0.8
NE2 A:HIS130 2.2 20.3 1.0
NE2 A:HIS154 2.3 21.1 1.0
OD1 A:ASP158 2.6 24.7 1.0
CG A:ASP158 2.7 23.5 1.0
CE1 A:HIS130 3.0 20.4 1.0
CD2 A:HIS154 3.2 21.3 1.0
CD2 A:HIS130 3.2 21.0 1.0
CE1 A:HIS154 3.3 22.2 1.0
P A:PO4401 3.5 16.2 0.8
ND1 A:HIS130 4.2 19.5 1.0
CB A:ASP158 4.2 22.7 1.0
O3 A:PO4401 4.2 13.9 0.8
N A:TRP1 4.2 20.0 1.0
O1 A:PO4401 4.2 14.6 0.8
CG A:HIS130 4.3 19.9 1.0
O A:HOH2057 4.3 32.0 1.0
CG A:HIS154 4.3 21.4 1.0
ND1 A:HIS154 4.4 21.3 1.0
O A:HOH2054 4.4 29.7 1.0
NE2 A:GLN127 4.4 19.8 1.0
O2 A:PO4401 4.4 13.0 0.8
O A:HOH2133 4.8 36.8 1.0
ZN A:ZN433 4.9 18.7 1.0
CA A:TRP1 4.9 20.0 1.0

Zinc binding site 3 out of 6 in 4cxv

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Zinc binding site 3 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn433

b:18.7
occ:1.00
 O2 A:PO4401 1.8 13.0 0.8
NE2 A:HIS6 2.0 22.5 1.0
OD1 A:ASP124 2.0 16.7 1.0
O A:TRP1 2.2 19.8 1.0
N A:TRP1 2.2 20.0 1.0
C A:TRP1 2.9 21.1 1.0
CD2 A:HIS6 2.9 21.9 1.0
CA A:TRP1 2.9 20.0 1.0
CE1 A:HIS6 3.0 22.7 1.0
P A:PO4401 3.1 16.2 0.8
CG A:ASP124 3.1 15.1 1.0
O4 A:PO4401 3.3 13.2 0.8
OD2 A:ASP124 3.5 13.9 1.0
ZN A:ZN431 3.5 23.4 1.0
CB A:TRP1 3.6 21.0 1.0
CE1 A:HIS120 3.8 18.5 1.0
NE2 A:HIS120 3.9 17.8 1.0
O1 A:PO4401 3.9 14.6 0.8
O3 A:PO4401 4.0 13.9 0.8
ND1 A:HIS6 4.1 22.0 1.0
CG A:HIS6 4.1 23.1 1.0
N A:GLY2 4.2 21.8 1.0
CG A:TRP1 4.3 20.2 1.0
CD1 A:TRP1 4.3 19.8 1.0
OD2 A:ASP45 4.4 22.1 1.0
CB A:ASP124 4.4 17.8 1.0
CE1 A:HIS130 4.5 20.4 1.0
NE2 A:HIS130 4.6 20.3 1.0
CA A:ASP124 4.6 19.2 1.0
ND1 A:HIS120 4.7 19.2 1.0
OD1 A:ASP158 4.8 24.7 1.0
OD1 A:ASP45 4.8 21.3 1.0
CD2 A:HIS120 4.9 17.7 1.0
O A:GLY2 4.9 21.9 1.0
ZN A:ZN432 4.9 24.1 1.0
CA A:GLY2 4.9 23.0 1.0
N A:ASP124 5.0 19.1 1.0

Zinc binding site 4 out of 6 in 4cxv

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Zinc binding site 4 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn431

b:21.7
occ:1.00
 NE2 B:HIS120 2.1 19.2 1.0
O3 B:PO4401 2.2 16.3 0.8
OD2 B:ASP124 2.2 16.7 1.0
ND1 B:HIS58 2.2 18.9 1.0
OD1 B:ASP45 2.4 17.6 1.0
O2 B:PO4401 2.4 17.3 0.8
P B:PO4401 2.9 17.6 0.8
CE1 B:HIS120 3.1 18.6 1.0
CE1 B:HIS58 3.1 19.0 1.0
CG B:ASP124 3.1 18.9 1.0
CD2 B:HIS120 3.2 19.1 1.0
CG B:HIS58 3.3 17.9 1.0
CG B:ASP45 3.4 19.7 1.0
OD1 B:ASP124 3.4 19.1 1.0
ZN B:ZN433 3.6 18.5 1.0
CB B:HIS58 3.7 18.8 1.0
OD2 B:ASP45 3.8 18.2 1.0
O4 B:PO4401 3.8 15.8 0.8
O1 B:PO4401 4.2 16.9 0.8
ND1 B:HIS120 4.2 18.5 1.0
NE2 B:HIS58 4.3 18.7 1.0
CG B:HIS120 4.3 19.6 1.0
NE2 B:HIS6 4.3 21.8 1.0
CE B:LYS48 4.3 20.4 1.0
O B:HOH2041 4.3 31.9 1.0
CE1 B:HIS130 4.4 23.9 1.0
CD2 B:HIS58 4.4 18.1 1.0
NZ B:LYS48 4.4 21.1 1.0
CB B:ASP124 4.5 20.2 1.0
CA B:HIS58 4.7 18.6 1.0
CE1 B:HIS6 4.7 22.5 1.0
CB B:ASP45 4.8 20.3 1.0
CA B:ASP45 5.0 21.3 1.0

Zinc binding site 5 out of 6 in 4cxv

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Zinc binding site 5 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn432

b:25.1
occ:1.00
 O1 B:PO4401 2.0 16.9 0.8
O B:HOH2102 2.0 20.5 1.0
OD2 B:ASP158 2.1 19.7 1.0
NE2 B:HIS130 2.1 24.1 1.0
NE2 B:HIS154 2.3 19.5 1.0
OD1 B:ASP158 2.6 19.0 1.0
CG B:ASP158 2.7 20.4 1.0
CE1 B:HIS130 3.0 23.9 1.0
CD2 B:HIS130 3.2 24.4 1.0
CD2 B:HIS154 3.2 18.4 1.0
CE1 B:HIS154 3.3 19.2 1.0
P B:PO4401 3.4 17.6 0.8
O2 B:PO4401 3.9 17.3 0.8
N B:TRP1 4.1 20.1 1.0
CB B:ASP158 4.1 19.6 1.0
ND1 B:HIS130 4.2 22.2 1.0
O4 B:PO4401 4.2 15.8 0.8
CG B:HIS130 4.3 23.0 1.0
O B:HOH2040 4.3 21.5 1.0
O3 B:PO4401 4.4 16.3 0.8
CG B:HIS154 4.4 18.7 1.0
ND1 B:HIS154 4.4 19.9 1.0
NE2 B:GLN127 4.4 21.2 1.0
O B:HOH2041 4.4 31.9 1.0
ZN B:ZN433 4.9 18.5 1.0
CA B:TRP1 4.9 20.7 1.0
O B:HOH2114 4.9 30.0 1.0

Zinc binding site 6 out of 6 in 4cxv

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Zinc binding site 6 out of 6 in the Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Bifunctional Endonuclease (ATBFN2) in Complex with Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn433

b:18.5
occ:1.00
 O3 B:PO4401 1.9 16.3 0.8
NE2 B:HIS6 2.0 21.8 1.0
OD1 B:ASP124 2.1 19.1 1.0
O B:TRP1 2.2 21.0 1.0
N B:TRP1 2.2 20.1 1.0
C B:TRP1 2.9 21.8 1.0
CD2 B:HIS6 2.9 22.8 1.0
CA B:TRP1 2.9 20.7 1.0
CE1 B:HIS6 3.0 22.5 1.0
P B:PO4401 3.1 17.6 0.8
CG B:ASP124 3.1 18.9 1.0
O1 B:PO4401 3.3 16.9 0.8
OD2 B:ASP124 3.5 16.7 1.0
ZN B:ZN431 3.6 21.7 1.0
CB B:TRP1 3.6 21.7 1.0
CE1 B:HIS120 3.8 18.6 1.0
NE2 B:HIS120 3.9 19.2 1.0
O4 B:PO4401 4.0 15.8 0.8
CG B:HIS6 4.1 20.6 1.0
ND1 B:HIS6 4.1 20.9 1.0
O2 B:PO4401 4.1 17.3 0.8
N B:GLY2 4.2 21.0 1.0
CG B:TRP1 4.3 21.4 1.0
CD1 B:TRP1 4.3 20.2 1.0
OD2 B:ASP45 4.3 18.2 1.0
CB B:ASP124 4.5 20.2 1.0
CE1 B:HIS130 4.5 23.9 1.0
NE2 B:HIS130 4.5 24.1 1.0
CA B:ASP124 4.7 20.1 1.0
ND1 B:HIS120 4.7 18.5 1.0
OD1 B:ASP45 4.8 17.6 1.0
OD1 B:ASP158 4.8 19.0 1.0
ZN B:ZN432 4.9 25.1 1.0
CD2 B:HIS120 4.9 19.1 1.0
O B:GLY2 4.9 21.5 1.0
CA B:GLY2 4.9 23.0 1.0
CG B:ASP45 5.0 19.7 1.0
N B:ASP124 5.0 20.2 1.0

Reference:

T.-F.Yu, M.Maestre-Reyna, C.-Y.Ko, T.-P.Ko, Y.-J.Sun, T.-Y.Lin, J.-F.Shaw, A.H.-J.Wang. Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease ATBFN2 From Arabidopsis Thaliana To Be Published.
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