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


Mono view


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


Mono view


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


Mono view


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


Mono view


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

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