Zinc in PDB 8e2p: Crystal Structure of Tada*8.20 in A Complex with Ssdna
Enzymatic activity of Crystal Structure of Tada*8.20 in A Complex with Ssdna
All present enzymatic activity of Crystal Structure of Tada*8.20 in A Complex with Ssdna:
3.5.4.33;
Protein crystallography data
The structure of Crystal Structure of Tada*8.20 in A Complex with Ssdna, PDB code: 8e2p
was solved by
P.R.Feliciano,
S.J.Lee,
G.Ciaramella,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.34 /
2.72
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.67,
84.67,
214.93,
90,
90,
120
|
R / Rfree (%)
|
19 /
21.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Tada*8.20 in A Complex with Ssdna
(pdb code 8e2p). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Tada*8.20 in A Complex with Ssdna, PDB code: 8e2p:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8e2p
Go back to
Zinc Binding Sites List in 8e2p
Zinc binding site 1 out
of 4 in the Crystal Structure of Tada*8.20 in A Complex with Ssdna
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Tada*8.20 in A Complex with Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:52.2
occ:1.00
|
O6
|
E:UEL9
|
2.2
|
57.6
|
1.0
|
SG
|
A:CYS90
|
2.3
|
50.1
|
1.0
|
SG
|
A:CYS87
|
2.3
|
45.6
|
1.0
|
ND1
|
A:HIS57
|
2.3
|
50.6
|
1.0
|
CE1
|
A:HIS57
|
2.9
|
51.2
|
1.0
|
CB
|
A:CYS90
|
3.2
|
51.6
|
1.0
|
C6
|
E:UEL9
|
3.2
|
54.3
|
1.0
|
CB
|
A:CYS87
|
3.3
|
49.5
|
1.0
|
C5
|
E:UEL9
|
3.4
|
53.0
|
1.0
|
N
|
A:CYS87
|
3.5
|
53.3
|
1.0
|
CG
|
A:HIS57
|
3.5
|
52.3
|
1.0
|
OE2
|
A:GLU59
|
3.8
|
64.7
|
1.0
|
C4
|
E:UEL9
|
3.9
|
53.4
|
1.0
|
CA
|
A:CYS87
|
3.9
|
51.6
|
1.0
|
N1
|
E:UEL9
|
4.0
|
55.8
|
1.0
|
C2
|
E:UEL9
|
4.0
|
54.5
|
1.0
|
N3
|
E:UEL9
|
4.0
|
53.7
|
1.0
|
N
|
A:CYS90
|
4.1
|
48.9
|
1.0
|
N7
|
E:UEL9
|
4.1
|
54.6
|
1.0
|
NE2
|
A:HIS57
|
4.1
|
52.5
|
1.0
|
CB
|
A:HIS57
|
4.1
|
53.2
|
1.0
|
CA
|
A:CYS90
|
4.2
|
49.4
|
1.0
|
CE
|
A:MET89
|
4.3
|
51.3
|
1.0
|
CD2
|
A:HIS57
|
4.5
|
52.6
|
1.0
|
CD
|
A:GLU59
|
4.5
|
64.3
|
1.0
|
C
|
A:PRO86
|
4.6
|
53.2
|
1.0
|
OE1
|
A:GLU59
|
4.6
|
64.4
|
1.0
|
N9
|
E:UEL9
|
4.6
|
54.3
|
1.0
|
NE2
|
B:HIS96
|
4.6
|
48.2
|
1.0
|
N8
|
E:UEL9
|
4.7
|
55.5
|
1.0
|
C
|
A:CYS87
|
4.7
|
51.2
|
1.0
|
CA
|
A:PRO86
|
4.7
|
55.0
|
1.0
|
CE1
|
B:HIS96
|
4.9
|
50.1
|
1.0
|
O
|
A:CYS87
|
4.9
|
51.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8e2p
Go back to
Zinc Binding Sites List in 8e2p
Zinc binding site 2 out
of 4 in the Crystal Structure of Tada*8.20 in A Complex with Ssdna
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Tada*8.20 in A Complex with Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn201
b:61.3
occ:1.00
|
O6
|
F:UEL9
|
2.0
|
52.2
|
1.0
|
SG
|
B:CYS87
|
2.3
|
49.5
|
1.0
|
ND1
|
B:HIS57
|
2.3
|
52.2
|
1.0
|
SG
|
B:CYS90
|
2.3
|
47.2
|
1.0
|
CE1
|
B:HIS57
|
2.9
|
52.9
|
1.0
|
C6
|
F:UEL9
|
3.1
|
53.1
|
1.0
|
CB
|
B:CYS87
|
3.1
|
53.5
|
1.0
|
CB
|
B:CYS90
|
3.4
|
53.6
|
1.0
|
C5
|
F:UEL9
|
3.4
|
51.5
|
1.0
|
N
|
B:CYS87
|
3.5
|
55.7
|
1.0
|
CG
|
B:HIS57
|
3.5
|
52.8
|
1.0
|
CA
|
B:CYS87
|
3.9
|
55.5
|
1.0
|
N1
|
F:UEL9
|
3.9
|
52.8
|
1.0
|
OE2
|
B:GLU59
|
3.9
|
57.7
|
1.0
|
CB
|
B:HIS57
|
4.1
|
53.4
|
1.0
|
N7
|
F:UEL9
|
4.1
|
52.3
|
1.0
|
N
|
B:CYS90
|
4.1
|
53.8
|
1.0
|
C4
|
F:UEL9
|
4.1
|
52.1
|
1.0
|
C2
|
F:UEL9
|
4.1
|
50.4
|
1.0
|
NE2
|
B:HIS57
|
4.2
|
53.2
|
1.0
|
N3
|
F:UEL9
|
4.3
|
49.5
|
1.0
|
CA
|
B:CYS90
|
4.4
|
53.3
|
1.0
|
NE2
|
A:HIS96
|
4.4
|
54.9
|
1.0
|
CD2
|
B:HIS57
|
4.5
|
53.6
|
1.0
|
C
|
B:CYS87
|
4.6
|
57.2
|
1.0
|
CD
|
B:GLU59
|
4.6
|
55.4
|
1.0
|
OE1
|
B:GLU59
|
4.6
|
54.0
|
1.0
|
C
|
B:PRO86
|
4.6
|
54.0
|
1.0
|
N8
|
F:UEL9
|
4.8
|
53.6
|
1.0
|
CE
|
B:MET89
|
4.8
|
50.6
|
1.0
|
N9
|
F:UEL9
|
4.8
|
54.2
|
1.0
|
CA
|
B:PRO86
|
4.9
|
55.9
|
1.0
|
O
|
B:CYS87
|
4.9
|
58.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8e2p
Go back to
Zinc Binding Sites List in 8e2p
Zinc binding site 3 out
of 4 in the Crystal Structure of Tada*8.20 in A Complex with Ssdna
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Tada*8.20 in A Complex with Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:58.4
occ:1.00
|
O6
|
G:UEL9
|
1.9
|
56.5
|
1.0
|
ND1
|
C:HIS57
|
2.3
|
55.1
|
1.0
|
SG
|
C:CYS90
|
2.3
|
51.4
|
1.0
|
SG
|
C:CYS87
|
2.3
|
56.6
|
1.0
|
C6
|
G:UEL9
|
3.0
|
56.7
|
1.0
|
CE1
|
C:HIS57
|
3.1
|
55.1
|
1.0
|
CB
|
C:CYS90
|
3.2
|
57.5
|
1.0
|
CG
|
C:HIS57
|
3.4
|
60.0
|
1.0
|
C5
|
G:UEL9
|
3.4
|
55.9
|
1.0
|
CB
|
C:CYS87
|
3.6
|
59.4
|
1.0
|
N
|
C:CYS87
|
3.7
|
61.2
|
1.0
|
N1
|
G:UEL9
|
3.7
|
54.8
|
1.0
|
CB
|
C:HIS57
|
3.8
|
61.3
|
1.0
|
OE1
|
C:GLU59
|
3.8
|
59.1
|
1.0
|
C2
|
G:UEL9
|
3.9
|
53.9
|
1.0
|
C4
|
G:UEL9
|
4.1
|
54.9
|
1.0
|
CE
|
C:MET89
|
4.1
|
55.8
|
1.0
|
N
|
C:CYS90
|
4.1
|
62.1
|
1.0
|
N7
|
G:UEL9
|
4.1
|
53.8
|
1.0
|
N3
|
G:UEL9
|
4.2
|
52.6
|
1.0
|
CA
|
C:CYS90
|
4.2
|
59.0
|
1.0
|
CA
|
C:CYS87
|
4.2
|
61.3
|
1.0
|
NE2
|
C:HIS57
|
4.3
|
53.3
|
1.0
|
CD
|
C:GLU59
|
4.4
|
60.5
|
1.0
|
OE2
|
C:GLU59
|
4.4
|
63.6
|
1.0
|
CD2
|
C:HIS57
|
4.5
|
60.5
|
1.0
|
C
|
C:PRO86
|
4.8
|
61.0
|
1.0
|
N8
|
G:UEL9
|
4.8
|
55.8
|
1.0
|
N9
|
G:UEL9
|
4.8
|
55.8
|
1.0
|
CA
|
C:PRO86
|
4.9
|
58.8
|
1.0
|
C
|
C:CYS87
|
4.9
|
64.1
|
1.0
|
NE2
|
D:HIS96
|
5.0
|
56.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8e2p
Go back to
Zinc Binding Sites List in 8e2p
Zinc binding site 4 out
of 4 in the Crystal Structure of Tada*8.20 in A Complex with Ssdna
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/e2/8e2p-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Tada*8.20 in A Complex with Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:61.6
occ:1.00
|
O6
|
H:UEL9
|
2.0
|
69.7
|
1.0
|
SG
|
D:CYS87
|
2.3
|
68.1
|
1.0
|
SG
|
D:CYS90
|
2.3
|
61.6
|
1.0
|
ND1
|
D:HIS57
|
2.3
|
62.1
|
1.0
|
CB
|
D:CYS90
|
3.1
|
63.0
|
1.0
|
CE1
|
D:HIS57
|
3.1
|
60.7
|
1.0
|
C6
|
H:UEL9
|
3.2
|
68.3
|
1.0
|
CG
|
D:HIS57
|
3.3
|
64.9
|
1.0
|
C5
|
H:UEL9
|
3.6
|
65.4
|
1.0
|
CB
|
D:HIS57
|
3.6
|
64.1
|
1.0
|
CB
|
D:CYS87
|
3.7
|
72.2
|
1.0
|
OE2
|
D:GLU59
|
3.9
|
65.1
|
1.0
|
N
|
D:CYS87
|
3.9
|
65.0
|
1.0
|
N1
|
H:UEL9
|
3.9
|
68.2
|
1.0
|
N
|
D:CYS90
|
3.9
|
67.9
|
1.0
|
CE
|
D:MET89
|
4.0
|
62.7
|
1.0
|
CA
|
D:CYS90
|
4.0
|
63.9
|
1.0
|
C2
|
H:UEL9
|
4.1
|
65.7
|
1.0
|
OE1
|
D:GLU59
|
4.2
|
60.3
|
1.0
|
NE2
|
D:HIS57
|
4.2
|
62.4
|
1.0
|
C4
|
H:UEL9
|
4.3
|
63.1
|
1.0
|
CD
|
D:GLU59
|
4.3
|
63.1
|
1.0
|
CD2
|
D:HIS57
|
4.3
|
63.5
|
1.0
|
N7
|
H:UEL9
|
4.4
|
64.4
|
1.0
|
CA
|
D:CYS87
|
4.4
|
73.7
|
1.0
|
N3
|
H:UEL9
|
4.4
|
63.5
|
1.0
|
NE2
|
C:HIS96
|
4.7
|
58.9
|
1.0
|
C
|
D:PRO86
|
5.0
|
65.1
|
1.0
|
C
|
D:CYS87
|
5.0
|
80.1
|
1.0
|
|
Reference:
D.K.Lam,
P.R.Feliciano,
A.Arif,
T.Bohnuud,
T.P.Fernandez,
J.M.Gehrke,
P.Grayson,
K.D.Lee,
M.A.Ortega,
C.Sawyer,
N.Schwaegerle,
L.Peraro,
L.Young,
S.J.Lee,
G.Ciaramella,
N.M.Gaudelli.
Improved Cytosine Base Editors Generated From Tada Variants Nat.Biotechnol. 2023.
ISSN: ISSN 1087-0156
Page generated: Sat Apr 8 08:22:08 2023
|