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Zinc in PDB 4cwm: High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana

Enzymatic activity of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana

All present enzymatic activity of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana:
3.1.30.1;

Protein crystallography data

The structure of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana, PDB code: 4cwm 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) 23.28 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.375, 52.706, 61.105, 71.34, 78.57, 76.74
R / Rfree (%) 19.749 / 26.802

Zinc Binding Sites:

The binding sites of Zinc atom in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana (pdb code 4cwm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana, PDB code: 4cwm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4cwm

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Zinc binding site 1 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn431

b:22.9
occ:1.00
 O A:HOH2002 2.1 8.8 1.0
OD2 A:ASP124 2.3 15.1 1.0
ND1 A:HIS58 2.3 17.8 1.0
NE2 A:HIS120 2.4 16.0 1.0
OD1 A:ASP45 2.4 16.7 1.0
O A:HOH2058 2.4 11.8 1.0
CE1 A:HIS58 3.1 17.4 1.0
CG A:ASP124 3.2 14.3 1.0
CE1 A:HIS120 3.3 16.6 1.0
CG A:ASP45 3.3 17.3 1.0
CG A:HIS58 3.3 17.3 1.0
CD2 A:HIS120 3.4 16.1 1.0
ZN A:ZN433 3.5 16.0 1.0
OD1 A:ASP124 3.5 14.2 1.0
OD2 A:ASP45 3.5 14.7 1.0
CB A:HIS58 3.7 16.6 1.0
CE1 A:HIS130 4.2 18.5 1.0
O A:HOH2001 4.2 14.7 1.0
NE2 A:HIS58 4.3 17.2 1.0
CD2 A:HIS58 4.4 17.4 1.0
ND1 A:HIS120 4.4 17.4 1.0
NE2 A:HIS6 4.5 19.4 1.0
CE A:LYS48 4.5 28.7 1.0
CG A:HIS120 4.5 16.8 1.0
CB A:ASP124 4.6 15.1 1.0
NZ A:LYS48 4.6 30.9 1.0
CB A:ASP45 4.7 18.1 1.0
CA A:HIS58 4.7 16.4 1.0
O A:HOH2027 4.8 31.3 1.0
ND1 A:HIS130 4.9 18.3 1.0
NE2 A:HIS130 5.0 18.0 1.0
O A:HIS58 5.0 17.4 1.0

Zinc binding site 2 out of 6 in 4cwm

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Zinc binding site 2 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn432

b:18.9
occ:1.00
 O A:HOH2132 2.0 17.8 1.0
NE2 A:HIS154 2.1 20.5 1.0
O A:HOH2001 2.1 14.7 1.0
OD2 A:ASP158 2.2 18.6 1.0
NE2 A:HIS130 2.2 18.0 1.0
OD1 A:ASP158 2.6 19.3 1.0
CG A:ASP158 2.7 19.4 1.0
CE1 A:HIS154 3.1 20.9 1.0
CD2 A:HIS154 3.1 19.8 1.0
CE1 A:HIS130 3.1 18.5 1.0
CD2 A:HIS130 3.1 19.8 1.0
O A:HOH2149 4.0 39.8 1.0
O A:HOH2003 4.1 23.4 1.0
ND1 A:HIS154 4.2 20.9 1.0
ND1 A:HIS130 4.2 18.3 1.0
CG A:HIS154 4.2 19.2 1.0
CB A:ASP158 4.2 18.6 1.0
CG A:HIS130 4.2 19.0 1.0
N A:TRP1 4.3 14.8 1.0
NE2 A:GLN127 4.3 18.4 1.0
O A:HOH2027 4.4 31.3 1.0
O A:HOH2058 4.5 11.8 1.0
O A:HOH2002 4.5 8.8 1.0
CA A:TRP1 4.9 15.1 1.0
ZN A:ZN433 5.0 16.0 1.0

Zinc binding site 3 out of 6 in 4cwm

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Zinc binding site 3 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn433

b:16.0
occ:1.00
 O A:HOH2002 2.0 8.8 1.0
NE2 A:HIS6 2.1 19.4 1.0
N A:TRP1 2.1 14.8 1.0
OD1 A:ASP124 2.1 14.2 1.0
O A:TRP1 2.3 14.6 1.0
C A:TRP1 3.0 15.5 1.0
CA A:TRP1 3.0 15.1 1.0
CD2 A:HIS6 3.0 18.5 1.0
CE1 A:HIS6 3.1 19.6 1.0
CG A:ASP124 3.2 14.3 1.0
O A:HOH2001 3.3 14.7 1.0
ZN A:ZN431 3.5 22.9 1.0
OD2 A:ASP124 3.5 15.1 1.0
CB A:TRP1 3.8 14.7 1.0
CE1 A:HIS120 3.8 16.6 1.0
NE2 A:HIS120 3.9 16.0 1.0
OD2 A:ASP45 4.0 14.7 1.0
ND1 A:HIS6 4.2 19.2 1.0
CG A:HIS6 4.2 18.9 1.0
N A:GLY2 4.3 16.6 1.0
NE2 A:HIS130 4.4 18.0 1.0
CD1 A:TRP1 4.4 15.1 1.0
CG A:TRP1 4.4 14.8 1.0
CE1 A:HIS130 4.5 18.5 1.0
CB A:ASP124 4.5 15.1 1.0
OD1 A:ASP45 4.7 16.7 1.0
CA A:ASP124 4.7 15.5 1.0
O A:HOH2058 4.7 11.8 1.0
CG A:ASP45 4.8 17.3 1.0
ND1 A:HIS120 4.8 17.4 1.0
O A:GLY2 4.9 19.7 1.0
CD2 A:HIS120 4.9 16.1 1.0
O A:HOH2003 4.9 23.4 1.0
ZN A:ZN432 5.0 18.9 1.0
OD1 A:ASP158 5.0 19.3 1.0

Zinc binding site 4 out of 6 in 4cwm

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Zinc binding site 4 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn431

b:22.5
occ:1.00
 O B:HOH2043 2.2 11.3 1.0
OD2 B:ASP124 2.2 13.7 1.0
OD1 B:ASP45 2.3 17.1 1.0
ND1 B:HIS58 2.4 17.4 1.0
NE2 B:HIS120 2.4 18.0 1.0
CE1 B:HIS120 3.2 18.4 1.0
CE1 B:HIS58 3.2 17.2 1.0
CG B:ASP124 3.3 13.8 1.0
CG B:ASP45 3.3 18.9 1.0
CG B:HIS58 3.4 16.8 1.0
CD2 B:HIS120 3.4 17.6 1.0
ZN B:ZN433 3.5 17.6 1.0
OD1 B:ASP124 3.6 13.1 1.0
OD2 B:ASP45 3.6 17.3 1.0
CB B:HIS58 3.7 16.6 1.0
CE1 B:HIS130 4.2 13.9 1.0
O B:HOH2001 4.4 12.4 1.0
ND1 B:HIS120 4.4 18.9 1.0
NE2 B:HIS58 4.4 17.3 1.0
CE B:LYS48 4.4 31.7 1.0
CD2 B:HIS58 4.5 17.5 1.0
CG B:HIS120 4.5 18.5 1.0
O B:HOH2054 4.5 37.1 1.0
NE2 B:HIS6 4.5 23.6 1.0
CB B:ASP124 4.6 14.6 1.0
CB B:ASP45 4.6 19.2 1.0
NZ B:LYS48 4.7 32.3 1.0
CA B:HIS58 4.8 16.3 1.0
CE1 B:HIS6 4.9 24.0 1.0
CA B:ASP45 4.9 20.3 1.0
ND1 B:HIS130 5.0 13.7 1.0
NE2 B:HIS130 5.0 13.9 1.0

Zinc binding site 5 out of 6 in 4cwm

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Zinc binding site 5 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn432

b:20.0
occ:1.00
 O B:HOH2118 2.0 21.0 1.0
O B:HOH2001 2.1 12.4 1.0
OD2 B:ASP158 2.1 13.9 1.0
NE2 B:HIS130 2.2 13.9 1.0
NE2 B:HIS154 2.2 18.5 1.0
OD1 B:ASP158 2.6 15.3 1.0
CG B:ASP158 2.7 15.8 1.0
CD2 B:HIS154 3.1 17.8 1.0
CD2 B:HIS130 3.1 15.4 1.0
CE1 B:HIS130 3.2 13.9 1.0
CE1 B:HIS154 3.2 18.8 1.0
O B:HOH2117 3.6 41.1 1.0
CB B:ASP158 4.1 15.4 1.0
N B:TRP1 4.2 15.8 1.0
CG B:HIS130 4.2 14.6 1.0
CG B:HIS154 4.2 17.5 1.0
ND1 B:HIS130 4.2 13.7 1.0
ND1 B:HIS154 4.3 19.1 1.0
NE2 B:GLN127 4.4 15.9 1.0
O B:HOH2002 4.4 20.4 1.0
O B:HOH2137 4.4 28.6 1.0
O B:HOH2043 4.6 11.3 1.0
CA B:TRP1 4.9 15.0 1.0
ZN B:ZN433 5.0 17.6 1.0

Zinc binding site 6 out of 6 in 4cwm

Go back to Zinc Binding Sites List in 4cwm
Zinc binding site 6 out of 6 in the High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High-Glycosylation Crystal Structure of the Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn433

b:17.6
occ:1.00
 NE2 B:HIS6 2.1 23.6 1.0
OD1 B:ASP124 2.2 13.1 1.0
N B:TRP1 2.3 15.8 1.0
O B:TRP1 2.3 16.1 1.0
CE1 B:HIS6 2.9 24.0 1.0
C B:TRP1 3.0 15.8 1.0
CA B:TRP1 3.1 15.0 1.0
CD2 B:HIS6 3.1 22.8 1.0
CG B:ASP124 3.1 13.8 1.0
O B:HOH2001 3.4 12.4 1.0
OD2 B:ASP124 3.4 13.7 1.0
ZN B:ZN431 3.5 22.5 1.0
CB B:TRP1 3.6 14.7 1.0
CE1 B:HIS120 3.7 18.4 1.0
NE2 B:HIS120 3.9 18.0 1.0
OD2 B:ASP45 4.0 17.3 1.0
ND1 B:HIS6 4.1 22.0 1.0
CG B:HIS6 4.2 21.7 1.0
CG B:TRP1 4.3 14.9 1.0
N B:GLY2 4.3 15.3 1.0
CD1 B:TRP1 4.4 14.3 1.0
CB B:ASP124 4.5 14.6 1.0
NE2 B:HIS130 4.6 13.9 1.0
CE1 B:HIS130 4.6 13.9 1.0
ND1 B:HIS120 4.6 18.9 1.0
OD1 B:ASP45 4.7 17.1 1.0
O B:HOH2043 4.7 11.3 1.0
CG B:ASP45 4.8 18.9 1.0
CA B:ASP124 4.8 14.8 1.0
OD1 B:ASP158 4.9 15.3 1.0
CD2 B:HIS120 4.9 17.6 1.0
O B:HOH2002 4.9 20.4 1.0
ZN B:ZN432 5.0 20.0 1.0
O B:GLY2 5.0 16.6 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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