Atomistry » Zinc » PDB 4csh-4cxp » 4cwm
Atomistry »
  Zinc »
    PDB 4csh-4cxp »
      4cwm »

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

Go back to Zinc Binding Sites List in 4cwm
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

Go back to Zinc Binding Sites List in 4cwm
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

Go back to Zinc Binding Sites List in 4cwm
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

Go back to Zinc Binding Sites List in 4cwm
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

Go back to Zinc Binding Sites List in 4cwm
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.
Page generated: Sat Oct 26 21:07:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy