Zinc in PDB 6se2: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions
Protein crystallography data
The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions, PDB code: 6se2
was solved by
F.Magari,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.78 /
1.45
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.935,
57.935,
397.468,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17 /
18.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions
(pdb code 6se2). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions, PDB code: 6se2:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6se2
Go back to
Zinc Binding Sites List in 6se2
Zinc binding site 1 out
of 2 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:22.6
occ:0.69
|
O
|
A:HOH571
|
1.9
|
35.1
|
1.0
|
O
|
A:HOH515
|
2.0
|
37.6
|
1.0
|
OD1
|
A:ASP98
|
2.0
|
21.4
|
0.7
|
OD2
|
A:ASP102
|
2.1
|
24.5
|
1.0
|
O
|
A:HOH542
|
2.2
|
30.9
|
1.0
|
OD2
|
A:ASP98
|
2.6
|
25.2
|
0.7
|
CG
|
A:ASP98
|
2.7
|
20.2
|
0.7
|
CG
|
A:ASP102
|
3.0
|
21.5
|
1.0
|
OD1
|
A:ASP102
|
3.2
|
24.3
|
1.0
|
HB3
|
A:ASP98
|
3.3
|
20.1
|
0.3
|
HE22
|
A:GLN167
|
3.5
|
35.0
|
1.0
|
HZ2
|
A:LYS273
|
4.0
|
50.3
|
1.0
|
OD2
|
A:ASP170
|
4.1
|
29.9
|
1.0
|
CB
|
A:ASP98
|
4.2
|
16.2
|
0.7
|
CB
|
A:ASP98
|
4.2
|
16.8
|
0.3
|
O
|
A:HOH562
|
4.2
|
30.2
|
1.0
|
HZ1
|
A:LYS273
|
4.3
|
50.3
|
1.0
|
HG12
|
A:VAL171
|
4.3
|
40.6
|
1.0
|
NE2
|
A:GLN167
|
4.3
|
29.2
|
1.0
|
CB
|
A:ASP102
|
4.4
|
19.4
|
1.0
|
HE2
|
A:MET101
|
4.4
|
26.3
|
1.0
|
OE1
|
A:GLN167
|
4.4
|
29.4
|
1.0
|
O
|
A:ASP98
|
4.5
|
14.9
|
0.3
|
HB2
|
A:ASP98
|
4.5
|
19.4
|
0.7
|
CG
|
A:ASP98
|
4.5
|
15.5
|
0.3
|
O
|
A:ASP98
|
4.5
|
15.3
|
0.7
|
HB2
|
A:ASP102
|
4.6
|
23.3
|
1.0
|
NZ
|
A:LYS273
|
4.6
|
42.0
|
1.0
|
HA
|
A:ASP98
|
4.6
|
15.9
|
0.7
|
HA
|
A:ASP98
|
4.6
|
15.8
|
0.3
|
HB3
|
A:ASP98
|
4.7
|
19.4
|
0.7
|
HB3
|
A:ASP102
|
4.7
|
23.3
|
1.0
|
HB2
|
A:ASP98
|
4.8
|
20.1
|
0.3
|
OD2
|
A:ASP98
|
4.8
|
19.7
|
0.3
|
CD
|
A:GLN167
|
4.8
|
31.0
|
1.0
|
CA
|
A:ASP98
|
4.8
|
13.2
|
0.7
|
CA
|
A:ASP98
|
4.8
|
13.1
|
0.3
|
HE21
|
A:GLN167
|
4.9
|
35.0
|
1.0
|
HG13
|
A:VAL171
|
5.0
|
40.6
|
1.0
|
C
|
A:ASP98
|
5.0
|
13.8
|
0.3
|
C
|
A:ASP98
|
5.0
|
13.4
|
0.7
|
|
Zinc binding site 2 out
of 2 in 6se2
Go back to
Zinc Binding Sites List in 6se2
Zinc binding site 2 out
of 2 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:23.6
occ:0.43
|
O
|
A:HOH597
|
2.0
|
39.7
|
1.0
|
O
|
A:HOH522
|
2.0
|
28.8
|
1.0
|
OD2
|
A:ASP250
|
2.1
|
45.9
|
1.0
|
O
|
A:HOH513
|
2.2
|
35.1
|
1.0
|
O
|
A:HOH660
|
2.2
|
33.0
|
1.0
|
O
|
A:HOH505
|
2.5
|
32.5
|
0.5
|
CG
|
A:ASP250
|
3.1
|
50.9
|
1.0
|
HE22
|
A:GLN247
|
3.4
|
30.4
|
1.0
|
OD1
|
A:ASP250
|
3.5
|
56.9
|
1.0
|
HB2
|
A:ASP254
|
3.8
|
34.5
|
1.0
|
O
|
A:HOH505
|
3.9
|
27.4
|
0.5
|
OD1
|
A:ASP254
|
4.0
|
30.4
|
1.0
|
OD2
|
A:ASP268
|
4.1
|
26.6
|
1.0
|
NE2
|
A:GLN247
|
4.1
|
25.4
|
1.0
|
HE21
|
A:GLN247
|
4.1
|
30.4
|
1.0
|
HA
|
A:ASP251
|
4.4
|
31.4
|
1.0
|
OD1
|
A:ASP251
|
4.4
|
25.2
|
1.0
|
OD1
|
A:ASP268
|
4.4
|
27.8
|
1.0
|
O
|
A:ASP250
|
4.4
|
27.4
|
1.0
|
CB
|
A:ASP250
|
4.5
|
25.8
|
1.0
|
HB3
|
A:ASP250
|
4.5
|
30.9
|
1.0
|
CB
|
A:ASP254
|
4.6
|
28.8
|
1.0
|
CG
|
A:ASP254
|
4.6
|
30.8
|
1.0
|
C
|
A:ASP250
|
4.6
|
26.7
|
1.0
|
CG
|
A:ASP268
|
4.7
|
26.8
|
1.0
|
N
|
A:ASP251
|
5.0
|
26.0
|
1.0
|
|
Reference:
F.Magari,
A.Heine,
G.Klebe.
Trypanosoma Cruzi Farnesyl Diphosphate Synthase Apo Structure with Zinc Ions To Be Published.
Page generated: Wed Dec 16 12:47:26 2020
|