Zinc in PDB 8e2s: Crystal Structure of Tadac-1.19

Enzymatic activity of Crystal Structure of Tadac-1.19

All present enzymatic activity of Crystal Structure of Tadac-1.19:
3.5.4.33;

Protein crystallography data

The structure of Crystal Structure of Tadac-1.19, PDB code: 8e2s 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) 51.49 / 2.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.495, 63.396, 95.169, 87.89, 82.82, 77.14
R / Rfree (%) 21.9 / 26.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tadac-1.19 (pdb code 8e2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Tadac-1.19, PDB code: 8e2s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8e2s

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Zinc binding site 1 out of 8 in the Crystal Structure of Tadac-1.19


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 Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:31.9
occ:1.00
 ND1 A:HIS57 2.0 23.9 1.0
O A:HOH303 2.2 27.2 1.0
SG A:CYS90 2.3 22.5 1.0
SG A:CYS87 2.3 22.6 1.0
CE1 A:HIS57 2.9 21.6 1.0
CG A:HIS57 3.2 21.5 1.0
CB A:CYS90 3.2 22.4 1.0
CB A:CYS87 3.6 22.9 1.0
CB A:HIS57 3.6 18.0 1.0
N A:CYS87 3.8 29.1 1.0
N A:CYS90 4.0 29.0 1.0
NE2 A:HIS57 4.0 24.8 1.0
OE1 A:GLU59 4.1 19.2 1.0
CD2 A:HIS57 4.2 18.8 1.0
CA A:CYS90 4.2 26.1 1.0
CE A:MET89 4.3 24.1 1.0
CA A:CYS87 4.3 26.9 1.0
OE2 A:GLU59 4.5 33.4 1.0
CD A:GLU59 4.5 25.4 1.0
NE2 B:HIS96 4.9 23.1 1.0
C A:PRO86 4.9 25.4 1.0
C A:CYS87 4.9 26.9 1.0

Zinc binding site 2 out of 8 in 8e2s

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Zinc binding site 2 out of 8 in the Crystal Structure of Tadac-1.19


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 Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:26.9
occ:1.00
 ND1 B:HIS57 2.0 17.9 1.0
O B:HOH303 2.1 28.4 1.0
SG B:CYS90 2.3 21.6 1.0
SG B:CYS87 2.3 24.1 1.0
CE1 B:HIS57 2.8 20.4 1.0
CG B:HIS57 3.2 22.9 1.0
CB B:CYS90 3.2 28.8 1.0
CB B:CYS87 3.3 26.1 1.0
N B:CYS87 3.6 23.9 1.0
CB B:HIS57 3.7 23.9 1.0
N B:CYS90 3.9 29.0 1.0
OE2 B:GLU59 3.9 28.9 1.0
NE2 B:HIS57 4.0 18.0 1.0
CA B:CYS87 4.0 24.2 1.0
CE B:MET89 4.1 28.9 1.0
O B:HOH312 4.1 18.2 1.0
CA B:CYS90 4.2 27.8 1.0
CD2 B:HIS57 4.2 21.0 1.0
OE1 B:GLU59 4.2 22.1 1.0
CD B:GLU59 4.4 23.1 1.0
C B:CYS87 4.7 26.9 1.0
C B:PRO86 4.8 24.8 1.0
O B:CYS87 4.9 31.6 1.0
CA B:PRO86 5.0 25.0 1.0

Zinc binding site 3 out of 8 in 8e2s

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Zinc binding site 3 out of 8 in the Crystal Structure of Tadac-1.19


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 Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:31.6
occ:1.00
 ND1 C:HIS57 2.0 18.2 1.0
SG C:CYS87 2.3 30.9 1.0
SG C:CYS90 2.3 20.1 1.0
O C:HOH301 2.4 21.3 1.0
CE1 C:HIS57 2.9 17.5 1.0
CG C:HIS57 3.2 20.1 1.0
CB C:CYS90 3.4 23.1 1.0
CB C:CYS87 3.4 32.7 1.0
CB C:HIS57 3.6 22.4 1.0
N C:CYS87 3.7 26.3 1.0
OE2 C:GLU59 3.9 30.6 1.0
OE1 C:GLU59 4.0 23.3 1.0
NE2 C:HIS57 4.1 19.8 1.0
O C:HOH304 4.1 17.7 1.0
N C:CYS90 4.1 29.0 1.0
CA C:CYS87 4.1 32.8 1.0
CD2 C:HIS57 4.2 17.4 1.0
CD C:GLU59 4.2 25.5 1.0
CA C:CYS90 4.3 21.4 1.0
C C:CYS87 4.7 31.8 1.0
CE1 D:HIS96 4.7 55.0 1.0
C C:PRO86 4.8 28.8 1.0
CA C:PRO86 4.9 33.0 1.0
O C:CYS87 5.0 20.8 1.0

Zinc binding site 4 out of 8 in 8e2s

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Zinc binding site 4 out of 8 in the Crystal Structure of Tadac-1.19


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 Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:26.0
occ:1.00
 ND1 D:HIS57 2.0 28.3 1.0
O D:HOH303 2.2 26.9 1.0
SG D:CYS90 2.3 25.9 1.0
SG D:CYS87 2.3 26.9 1.0
CE1 D:HIS57 2.8 25.1 1.0
CG D:HIS57 3.2 27.7 1.0
CB D:CYS87 3.3 20.5 1.0
CB D:CYS90 3.5 31.9 1.0
CB D:HIS57 3.7 22.5 1.0
N D:CYS87 3.8 24.6 1.0
NE2 D:HIS57 4.0 29.6 1.0
N D:CYS90 4.1 20.8 1.0
CA D:CYS87 4.1 23.3 1.0
CD2 D:HIS57 4.2 24.9 1.0
OE1 D:GLU59 4.3 19.9 1.0
CA D:CYS90 4.4 19.8 1.0
O D:HOH306 4.4 16.8 1.0
CE D:MET89 4.7 31.2 1.0
CD D:GLU59 4.7 24.0 1.0
OE2 D:GLU59 4.7 27.1 1.0
CE1 C:HIS96 4.8 33.0 1.0
C D:CYS87 4.8 26.5 1.0
C D:PRO86 5.0 26.1 1.0

Zinc binding site 5 out of 8 in 8e2s

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Zinc binding site 5 out of 8 in the Crystal Structure of Tadac-1.19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:26.4
occ:1.00
 ND1 E:HIS57 2.0 26.9 1.0
SG E:CYS87 2.3 27.6 1.0
SG E:CYS90 2.3 22.9 1.0
O E:HOH301 2.4 30.6 1.0
CE1 E:HIS57 2.9 28.2 1.0
CG E:HIS57 3.1 27.3 1.0
CB E:CYS90 3.3 25.1 1.0
CB E:HIS57 3.5 27.1 1.0
CB E:CYS87 3.6 33.0 1.0
OE2 E:GLU59 3.6 21.9 1.0
N E:CYS87 3.8 23.1 1.0
NE2 E:HIS57 4.0 29.5 1.0
OE1 E:GLU59 4.1 23.1 1.0
CD E:GLU59 4.1 22.9 1.0
CD2 E:HIS57 4.2 26.6 1.0
N E:CYS90 4.2 30.6 1.0
CE E:MET89 4.2 29.7 1.0
CA E:CYS87 4.3 29.9 1.0
CA E:CYS90 4.3 26.2 1.0
C E:PRO86 4.9 23.1 1.0
NE2 F:HIS96 4.9 40.3 1.0
CA E:PRO86 5.0 28.5 1.0

Zinc binding site 6 out of 8 in 8e2s

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Zinc binding site 6 out of 8 in the Crystal Structure of Tadac-1.19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:34.0
occ:1.00
 ND1 F:HIS57 2.0 38.5 1.0
O F:HOH302 2.2 37.1 1.0
SG F:CYS90 2.3 31.4 1.0
SG F:CYS87 2.3 42.8 1.0
CE1 F:HIS57 2.9 28.6 1.0
CG F:HIS57 3.1 27.2 1.0
CB F:CYS90 3.3 32.5 1.0
CB F:HIS57 3.5 28.9 1.0
CB F:CYS87 3.6 40.9 1.0
N F:CYS87 3.9 40.7 1.0
OE1 F:GLU59 4.0 31.6 1.0
N F:CYS90 4.1 38.6 1.0
NE2 F:HIS57 4.1 27.3 1.0
CD2 F:HIS57 4.2 22.4 1.0
CA F:CYS90 4.3 32.3 1.0
CA F:CYS87 4.3 40.8 1.0
OE2 F:GLU59 4.4 35.9 1.0
CD F:GLU59 4.4 29.8 1.0
C F:CYS87 5.0 39.4 1.0
CA F:HIS57 5.0 25.0 1.0

Zinc binding site 7 out of 8 in 8e2s

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Zinc binding site 7 out of 8 in the Crystal Structure of Tadac-1.19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:23.0
occ:1.00
 ND1 G:HIS57 2.0 25.2 1.0
O G:HOH301 2.2 32.5 1.0
SG G:CYS90 2.3 30.9 1.0
SG G:CYS87 2.3 22.5 1.0
CE1 G:HIS57 2.8 24.0 1.0
CG G:HIS57 3.2 23.6 1.0
CB G:CYS90 3.3 22.0 1.0
CB G:CYS87 3.4 20.1 1.0
CB G:HIS57 3.7 21.6 1.0
N G:CYS87 3.8 20.4 1.0
N G:CYS90 4.0 21.6 1.0
NE2 G:HIS57 4.0 27.4 1.0
OE2 G:GLU59 4.1 25.6 1.0
CE G:MET89 4.2 27.5 1.0
CA G:CYS87 4.2 22.7 1.0
OE1 G:GLU59 4.2 26.3 1.0
CD2 G:HIS57 4.2 26.5 1.0
CA G:CYS90 4.2 20.5 1.0
CD G:GLU59 4.4 28.7 1.0
C G:CYS87 4.8 25.2 1.0
C G:PRO86 4.9 20.7 1.0
NE2 H:HIS96 5.0 26.5 1.0

Zinc binding site 8 out of 8 in 8e2s

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Zinc binding site 8 out of 8 in the Crystal Structure of Tadac-1.19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Tadac-1.19 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:21.8
occ:1.00
 ND1 H:HIS57 2.0 27.9 1.0
O H:HOH302 2.2 21.5 1.0
SG H:CYS90 2.3 29.5 1.0
SG H:CYS87 2.3 19.7 1.0
CE1 H:HIS57 2.8 21.0 1.0
CG H:HIS57 3.2 20.9 1.0
CB H:CYS90 3.3 20.1 1.0
CB H:CYS87 3.4 20.4 1.0
CB H:HIS57 3.7 21.2 1.0
N H:CYS87 3.8 25.5 1.0
N H:CYS90 3.9 29.2 1.0
NE2 H:HIS57 4.0 20.1 1.0
CA H:CYS87 4.1 28.2 1.0
CA H:CYS90 4.2 26.1 1.0
CD2 H:HIS57 4.2 20.0 1.0
OE1 H:GLU59 4.4 28.1 1.0
OE2 H:GLU59 4.5 26.9 1.0
CD H:GLU59 4.7 26.0 1.0
C H:CYS87 4.7 26.7 1.0
C H:PRO86 4.9 21.9 1.0
O H:CYS87 5.0 20.7 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: Wed Oct 30 19:26:06 2024

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