Zinc in PDB 4cxp: Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
Enzymatic activity of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
All present enzymatic activity of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate:
3.1.30.1;
Protein crystallography data
The structure of Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate, PDB code: 4cxp
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)
|
24.34 /
1.22
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.140,
66.819,
99.556,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
11.868 /
13.444
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
(pdb code 4cxp). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate, PDB code: 4cxp:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 4cxp
Go back to
Zinc Binding Sites List in 4cxp
Zinc binding site 1 out
of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
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) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn931
b:10.0
occ:1.00
|
OD2
|
A:ASP124
|
2.2
|
8.7
|
1.0
|
O4
|
A:SO4961
|
2.2
|
6.0
|
0.7
|
NE2
|
A:HIS120
|
2.2
|
8.3
|
1.0
|
ND1
|
A:HIS58
|
2.2
|
8.4
|
1.0
|
O2
|
A:SO4961
|
2.4
|
9.8
|
0.7
|
OD1
|
A:ASP45
|
2.4
|
9.8
|
1.0
|
S
|
A:SO4961
|
2.8
|
9.3
|
0.7
|
CE1
|
A:HIS58
|
3.0
|
8.5
|
1.0
|
CG
|
A:ASP124
|
3.1
|
7.8
|
1.0
|
CE1
|
A:HIS120
|
3.2
|
8.4
|
1.0
|
CD2
|
A:HIS120
|
3.2
|
8.5
|
1.0
|
CG
|
A:HIS58
|
3.3
|
8.6
|
1.0
|
CG
|
A:ASP45
|
3.4
|
10.1
|
1.0
|
OD1
|
A:ASP124
|
3.5
|
8.5
|
1.0
|
ZN
|
A:ZN933
|
3.5
|
8.1
|
1.0
|
O1
|
A:SO4961
|
3.7
|
10.1
|
0.7
|
OD2
|
A:ASP45
|
3.7
|
14.8
|
1.0
|
CB
|
A:HIS58
|
3.7
|
8.7
|
1.0
|
O3
|
A:SO4961
|
4.1
|
8.5
|
0.7
|
NZ
|
A:LYS48
|
4.2
|
13.7
|
1.0
|
CE
|
A:LYS48
|
4.2
|
11.8
|
1.0
|
NE2
|
A:HIS58
|
4.2
|
9.3
|
1.0
|
ND1
|
A:HIS120
|
4.3
|
8.5
|
1.0
|
CG
|
A:HIS120
|
4.3
|
8.1
|
1.0
|
CE1
|
A:HIS130
|
4.3
|
8.6
|
1.0
|
CD2
|
A:HIS58
|
4.4
|
9.2
|
1.0
|
CB
|
A:ASP124
|
4.5
|
7.9
|
1.0
|
NE2
|
A:HIS6
|
4.5
|
8.2
|
1.0
|
O
|
A:HOH2121
|
4.6
|
16.7
|
1.0
|
CB
|
A:ASP45
|
4.7
|
11.1
|
1.0
|
CA
|
A:HIS58
|
4.8
|
8.7
|
1.0
|
CE1
|
A:HIS6
|
5.0
|
8.5
|
1.0
|
|
Zinc binding site 2 out
of 3 in 4cxp
Go back to
Zinc Binding Sites List in 4cxp
Zinc binding site 2 out
of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
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) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn932
b:9.7
occ:1.00
|
O
|
A:HOH2260
|
2.1
|
14.1
|
1.0
|
O3
|
A:SO4961
|
2.1
|
8.5
|
0.7
|
NE2
|
A:HIS130
|
2.1
|
8.8
|
1.0
|
NE2
|
A:HIS154
|
2.2
|
9.4
|
1.0
|
OD2
|
A:ASP158
|
2.2
|
9.2
|
1.0
|
OD1
|
A:ASP158
|
2.5
|
8.2
|
1.0
|
CG
|
A:ASP158
|
2.7
|
7.9
|
1.0
|
CE1
|
A:HIS130
|
3.0
|
8.6
|
1.0
|
CD2
|
A:HIS154
|
3.1
|
9.1
|
1.0
|
CD2
|
A:HIS130
|
3.2
|
8.3
|
1.0
|
CE1
|
A:HIS154
|
3.2
|
9.3
|
1.0
|
S
|
A:SO4961
|
3.4
|
9.3
|
0.7
|
O2
|
A:SO4961
|
4.0
|
9.8
|
0.7
|
O
|
A:HOH2123
|
4.1
|
27.1
|
1.0
|
O
|
A:HOH2269
|
4.1
|
33.2
|
1.0
|
CB
|
A:ASP158
|
4.2
|
7.8
|
1.0
|
N
|
A:TRP1
|
4.2
|
7.6
|
1.0
|
ND1
|
A:HIS130
|
4.2
|
8.6
|
1.0
|
O
|
A:HOH2001
|
4.2
|
16.7
|
1.0
|
O1
|
A:SO4961
|
4.2
|
10.1
|
0.7
|
CG
|
A:HIS130
|
4.3
|
8.2
|
1.0
|
ND1
|
A:HIS154
|
4.3
|
9.2
|
1.0
|
CG
|
A:HIS154
|
4.3
|
9.1
|
1.0
|
NE2
|
A:GLN127
|
4.3
|
8.0
|
1.0
|
O
|
A:HOH2050
|
4.4
|
32.0
|
1.0
|
O4
|
A:SO4961
|
4.5
|
6.0
|
0.7
|
O
|
A:HOH2299
|
4.5
|
16.3
|
1.0
|
O
|
A:HOH2121
|
4.6
|
16.7
|
1.0
|
CA
|
A:TRP1
|
4.9
|
7.8
|
1.0
|
ZN
|
A:ZN933
|
4.9
|
8.1
|
1.0
|
|
Zinc binding site 3 out
of 3 in 4cxp
Go back to
Zinc Binding Sites List in 4cxp
Zinc binding site 3 out
of 3 in the Structure of Bifunctional Endonuclease (ATBFN2) From Arabidopsis Thaliana in Complex with Sulfate
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) From Arabidopsis Thaliana in Complex with Sulfate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn933
b:8.1
occ:1.00
|
O4
|
A:SO4961
|
1.9
|
6.0
|
0.7
|
NE2
|
A:HIS6
|
2.0
|
8.2
|
1.0
|
OD1
|
A:ASP124
|
2.1
|
8.5
|
1.0
|
N
|
A:TRP1
|
2.1
|
7.6
|
1.0
|
O
|
A:TRP1
|
2.3
|
8.3
|
1.0
|
C
|
A:TRP1
|
3.0
|
8.0
|
1.0
|
CA
|
A:TRP1
|
3.0
|
7.8
|
1.0
|
CE1
|
A:HIS6
|
3.0
|
8.5
|
1.0
|
CD2
|
A:HIS6
|
3.0
|
8.2
|
1.0
|
CG
|
A:ASP124
|
3.1
|
7.8
|
1.0
|
S
|
A:SO4961
|
3.1
|
9.3
|
0.7
|
O3
|
A:SO4961
|
3.2
|
8.5
|
0.7
|
OD2
|
A:ASP124
|
3.5
|
8.7
|
1.0
|
ZN
|
A:ZN931
|
3.5
|
10.0
|
1.0
|
CB
|
A:TRP1
|
3.6
|
7.5
|
1.0
|
CE1
|
A:HIS120
|
3.8
|
8.4
|
1.0
|
NE2
|
A:HIS120
|
3.8
|
8.3
|
1.0
|
O1
|
A:SO4961
|
4.0
|
10.1
|
0.7
|
ND1
|
A:HIS6
|
4.1
|
9.0
|
1.0
|
CG
|
A:HIS6
|
4.2
|
8.5
|
1.0
|
O2
|
A:SO4961
|
4.2
|
9.8
|
0.7
|
N
|
A:GLY2
|
4.3
|
8.7
|
1.0
|
CG
|
A:TRP1
|
4.3
|
7.6
|
1.0
|
CD1
|
A:TRP1
|
4.4
|
7.7
|
1.0
|
OD2
|
A:ASP45
|
4.4
|
14.8
|
1.0
|
CB
|
A:ASP124
|
4.4
|
7.9
|
1.0
|
CE1
|
A:HIS130
|
4.5
|
8.6
|
1.0
|
NE2
|
A:HIS130
|
4.6
|
8.8
|
1.0
|
CA
|
A:ASP124
|
4.7
|
7.3
|
1.0
|
ND1
|
A:HIS120
|
4.7
|
8.5
|
1.0
|
OD1
|
A:ASP158
|
4.8
|
8.2
|
1.0
|
CD2
|
A:HIS120
|
4.8
|
8.5
|
1.0
|
OD1
|
A:ASP45
|
4.8
|
9.8
|
1.0
|
ZN
|
A:ZN932
|
4.9
|
9.7
|
1.0
|
O
|
A:HOH2001
|
5.0
|
16.7
|
1.0
|
O
|
A:GLY2
|
5.0
|
9.0
|
1.0
|
N
|
A:ASP124
|
5.0
|
7.3
|
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: Wed Dec 16 05:09:59 2020
|