Zinc in PDB 4p3n: Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
Enzymatic activity of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
All present enzymatic activity of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1:
6.1.1.3;
Protein crystallography data
The structure of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1, PDB code: 4p3n
was solved by
P.Fang,
X.Yu,
K.Chen,
X.Chen,
M.Guo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.71 /
2.60
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.870,
78.000,
118.050,
86.99,
83.32,
84.39
|
R / Rfree (%)
|
22.8 /
25.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
(pdb code 4p3n). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1, PDB code: 4p3n:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4p3n
Go back to
Zinc Binding Sites List in 4p3n
Zinc binding site 1 out
of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:44.2
occ:1.00
|
NE2
|
A:HIS464
|
2.1
|
39.9
|
1.0
|
SG
|
A:CYS413
|
2.4
|
36.5
|
1.0
|
ND1
|
A:HIS590
|
2.4
|
47.6
|
1.0
|
CE1
|
A:HIS464
|
2.9
|
40.0
|
1.0
|
O
|
A:HOH907
|
3.0
|
31.5
|
1.0
|
CD2
|
A:HIS464
|
3.2
|
39.9
|
1.0
|
CG
|
A:HIS590
|
3.3
|
47.2
|
1.0
|
CE1
|
A:HIS590
|
3.3
|
48.5
|
1.0
|
CB
|
A:HIS590
|
3.5
|
45.5
|
1.0
|
CB
|
A:CYS413
|
3.8
|
49.2
|
1.0
|
OD1
|
A:ASP462
|
3.9
|
44.1
|
1.0
|
C9
|
A:2CR800
|
4.0
|
42.6
|
1.0
|
ND1
|
A:HIS464
|
4.1
|
39.5
|
1.0
|
CG
|
A:HIS464
|
4.2
|
39.5
|
1.0
|
CA
|
A:HIS590
|
4.2
|
44.4
|
1.0
|
OD2
|
A:ASP462
|
4.3
|
43.1
|
1.0
|
C7
|
A:2CR800
|
4.3
|
41.5
|
1.0
|
NE2
|
A:HIS590
|
4.4
|
49.2
|
1.0
|
CD2
|
A:HIS590
|
4.4
|
48.7
|
1.0
|
C5
|
A:2CR800
|
4.5
|
42.0
|
1.0
|
CG
|
A:ASP462
|
4.5
|
43.5
|
1.0
|
C8
|
A:2CR800
|
4.5
|
42.2
|
1.0
|
CA
|
A:CYS413
|
4.5
|
48.0
|
1.0
|
N
|
A:CYS413
|
4.7
|
47.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4p3n
Go back to
Zinc Binding Sites List in 4p3n
Zinc binding site 2 out
of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn801
b:50.5
occ:1.00
|
NE2
|
B:HIS464
|
2.1
|
39.2
|
1.0
|
ND1
|
B:HIS590
|
2.3
|
50.8
|
1.0
|
SG
|
B:CYS413
|
2.4
|
34.1
|
1.0
|
CE1
|
B:HIS464
|
2.9
|
39.4
|
1.0
|
CG
|
B:HIS590
|
3.1
|
50.2
|
1.0
|
CD2
|
B:HIS464
|
3.2
|
40.0
|
1.0
|
CE1
|
B:HIS590
|
3.3
|
51.5
|
1.0
|
O
|
B:HOH917
|
3.3
|
53.5
|
1.0
|
CB
|
B:HIS590
|
3.3
|
48.7
|
1.0
|
CB
|
B:CYS413
|
3.8
|
47.2
|
1.0
|
OD1
|
B:ASP462
|
3.8
|
51.2
|
1.0
|
ND1
|
B:HIS464
|
4.0
|
39.3
|
1.0
|
CA
|
B:HIS590
|
4.1
|
47.5
|
1.0
|
C9
|
B:2CR800
|
4.2
|
46.1
|
1.0
|
CG
|
B:HIS464
|
4.2
|
39.9
|
1.0
|
OD2
|
B:ASP462
|
4.3
|
51.2
|
1.0
|
C7
|
B:2CR800
|
4.3
|
46.4
|
1.0
|
CD2
|
B:HIS590
|
4.3
|
51.5
|
1.0
|
NE2
|
B:HIS590
|
4.4
|
51.9
|
1.0
|
C5
|
B:2CR800
|
4.5
|
46.8
|
1.0
|
CG
|
B:ASP462
|
4.5
|
50.5
|
1.0
|
CE
|
B:MET411
|
4.6
|
54.0
|
1.0
|
CA
|
B:CYS413
|
4.6
|
46.5
|
1.0
|
C8
|
B:2CR800
|
4.6
|
46.3
|
1.0
|
N
|
B:CYS413
|
4.7
|
47.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4p3n
Go back to
Zinc Binding Sites List in 4p3n
Zinc binding site 3 out
of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn801
b:58.1
occ:1.00
|
ND1
|
C:HIS590
|
2.1
|
46.8
|
1.0
|
NE2
|
C:HIS464
|
2.1
|
51.3
|
1.0
|
SG
|
C:CYS413
|
2.3
|
46.5
|
1.0
|
CG
|
C:HIS590
|
3.0
|
47.1
|
1.0
|
CD2
|
C:HIS464
|
3.1
|
51.1
|
1.0
|
CE1
|
C:HIS464
|
3.1
|
51.0
|
1.0
|
CE1
|
C:HIS590
|
3.2
|
47.6
|
1.0
|
O
|
C:HOH906
|
3.2
|
39.1
|
1.0
|
CB
|
C:HIS590
|
3.2
|
46.9
|
1.0
|
CB
|
C:CYS413
|
3.7
|
57.1
|
1.0
|
OD1
|
C:ASP462
|
4.0
|
56.5
|
1.0
|
CA
|
C:HIS590
|
4.0
|
47.3
|
1.0
|
OD2
|
C:ASP462
|
4.1
|
55.5
|
1.0
|
C7
|
C:2CR800
|
4.1
|
52.5
|
1.0
|
ND1
|
C:HIS464
|
4.2
|
50.5
|
1.0
|
C9
|
C:2CR800
|
4.2
|
53.2
|
1.0
|
CG
|
C:HIS464
|
4.2
|
50.3
|
1.0
|
CD2
|
C:HIS590
|
4.2
|
47.6
|
1.0
|
NE2
|
C:HIS590
|
4.2
|
47.9
|
1.0
|
CG
|
C:ASP462
|
4.5
|
55.7
|
1.0
|
CA
|
C:CYS413
|
4.6
|
56.0
|
1.0
|
C8
|
C:2CR800
|
4.6
|
53.0
|
1.0
|
C5
|
C:2CR800
|
4.7
|
52.5
|
1.0
|
N
|
C:CYS413
|
4.7
|
55.2
|
1.0
|
C1
|
C:2CR800
|
5.0
|
52.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4p3n
Go back to
Zinc Binding Sites List in 4p3n
Zinc binding site 4 out
of 4 in the Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structural Basis For Full-Spectrum Inhibition of Threonyl-Trna Synthetase By Borrelidin 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn801
b:52.8
occ:1.00
|
NE2
|
D:HIS464
|
2.2
|
41.9
|
1.0
|
ND1
|
D:HIS590
|
2.2
|
49.4
|
1.0
|
SG
|
D:CYS413
|
2.3
|
42.8
|
1.0
|
CE1
|
D:HIS464
|
3.1
|
42.1
|
1.0
|
CD2
|
D:HIS464
|
3.1
|
42.0
|
1.0
|
CG
|
D:HIS590
|
3.1
|
48.6
|
1.0
|
CE1
|
D:HIS590
|
3.2
|
50.2
|
1.0
|
O
|
D:HOH925
|
3.3
|
51.1
|
1.0
|
CB
|
D:HIS590
|
3.4
|
47.9
|
1.0
|
CB
|
D:CYS413
|
3.8
|
54.8
|
1.0
|
OD1
|
D:ASP462
|
4.0
|
45.4
|
1.0
|
OD2
|
D:ASP462
|
4.0
|
46.4
|
1.0
|
C9
|
D:2CR800
|
4.0
|
52.9
|
1.0
|
CA
|
D:HIS590
|
4.1
|
47.4
|
1.0
|
C7
|
D:2CR800
|
4.1
|
52.1
|
1.0
|
ND1
|
D:HIS464
|
4.1
|
41.5
|
1.0
|
CG
|
D:HIS464
|
4.2
|
41.8
|
1.0
|
NE2
|
D:HIS590
|
4.3
|
50.1
|
1.0
|
CD2
|
D:HIS590
|
4.3
|
49.2
|
1.0
|
C5
|
D:2CR800
|
4.3
|
52.3
|
1.0
|
CG
|
D:ASP462
|
4.4
|
46.0
|
1.0
|
C8
|
D:2CR800
|
4.5
|
52.8
|
1.0
|
CA
|
D:CYS413
|
4.6
|
54.1
|
1.0
|
N
|
D:CYS413
|
4.7
|
53.9
|
1.0
|
CE
|
D:MET411
|
4.9
|
32.4
|
1.0
|
C1
|
D:2CR800
|
4.9
|
52.6
|
1.0
|
|
Reference:
P.Fang,
X.Yu,
S.Jeong,
A.Mirando,
K.Chen,
X.Chen,
S.Kim,
C.S.Francklyn,
M.Guo.
Structural Basis For Full-Spectrum Inhibition of Translational and Nontranslational Functions on A Human Trna Synthetase To Be Published.
Page generated: Sun Oct 27 04:10:58 2024
|