Fluorine in PDB 1qz0: Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Enzymatic activity of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
All present enzymatic activity of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide:
3.1.3.48;
Protein crystallography data
The structure of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide, PDB code: 1qz0
was solved by
J.Phan,
K.Lee,
S.Cherry,
J.E.Tropea,
T.R.Burke Jr,
D.S.Waugh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.292,
53.450,
69.066,
109.61,
104.75,
89.98
|
R / Rfree (%)
|
18.8 /
20.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
(pdb code 1qz0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide, PDB code: 1qz0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 1 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F505
b:22.6
occ:1.00
|
F1
|
C:FTY505
|
0.0
|
22.6
|
1.0
|
C1
|
C:FTY505
|
1.4
|
19.6
|
1.0
|
CZ
|
C:FTY505
|
2.2
|
20.8
|
1.0
|
F2
|
C:FTY505
|
2.3
|
22.0
|
1.0
|
CE2
|
C:FTY505
|
2.6
|
19.7
|
1.0
|
P
|
C:FTY505
|
2.7
|
18.2
|
1.0
|
NE2
|
A:GLN357
|
3.0
|
35.3
|
1.0
|
O1P
|
C:FTY505
|
3.1
|
16.8
|
1.0
|
O2P
|
C:FTY505
|
3.1
|
17.1
|
1.0
|
CB
|
A:ASP356
|
3.4
|
26.5
|
1.0
|
O
|
C:HOH61
|
3.4
|
18.4
|
1.0
|
CE1
|
C:FTY505
|
3.5
|
21.4
|
1.0
|
N
|
A:GLN357
|
3.8
|
26.1
|
1.0
|
O3P
|
C:FTY505
|
3.9
|
16.9
|
1.0
|
CD2
|
C:FTY505
|
4.0
|
20.7
|
1.0
|
NH2
|
A:ARG409
|
4.0
|
13.5
|
1.0
|
CD
|
A:GLN357
|
4.1
|
34.0
|
1.0
|
CA
|
A:ASP356
|
4.1
|
24.1
|
1.0
|
OD2
|
A:ASP356
|
4.3
|
31.7
|
1.0
|
CG
|
A:GLN357
|
4.3
|
32.0
|
1.0
|
CG
|
A:ASP356
|
4.4
|
29.7
|
1.0
|
C
|
A:ASP356
|
4.4
|
25.1
|
1.0
|
CD1
|
C:FTY505
|
4.6
|
22.1
|
1.0
|
NE
|
A:ARG409
|
4.6
|
11.4
|
1.0
|
CA
|
A:GLN357
|
4.6
|
26.8
|
1.0
|
CZ
|
A:ARG409
|
4.6
|
11.7
|
1.0
|
NE2
|
A:GLN446
|
4.7
|
28.6
|
1.0
|
CG
|
C:FTY505
|
4.8
|
21.5
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 1qz0
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Fluorine Binding Sites List in 1qz0
Fluorine binding site 2 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F505
b:22.0
occ:1.00
|
F2
|
C:FTY505
|
0.0
|
22.0
|
1.0
|
C1
|
C:FTY505
|
1.4
|
19.6
|
1.0
|
CZ
|
C:FTY505
|
2.2
|
20.8
|
1.0
|
F1
|
C:FTY505
|
2.3
|
22.6
|
1.0
|
CE1
|
C:FTY505
|
2.6
|
21.4
|
1.0
|
P
|
C:FTY505
|
2.7
|
18.2
|
1.0
|
O
|
C:HOH61
|
3.0
|
18.4
|
1.0
|
NE2
|
A:GLN446
|
3.0
|
28.6
|
1.0
|
O2P
|
C:FTY505
|
3.1
|
17.1
|
1.0
|
O3P
|
C:FTY505
|
3.2
|
16.9
|
1.0
|
NE2
|
A:GLN357
|
3.3
|
35.3
|
1.0
|
CE2
|
C:FTY505
|
3.5
|
19.7
|
1.0
|
CD
|
A:GLN446
|
3.9
|
28.8
|
1.0
|
O1P
|
C:FTY505
|
3.9
|
16.8
|
1.0
|
CA
|
A:GLY408
|
3.9
|
11.0
|
1.0
|
CD1
|
C:FTY505
|
4.0
|
22.1
|
1.0
|
N
|
A:GLY408
|
4.0
|
10.4
|
1.0
|
CG2
|
A:VAL407
|
4.3
|
13.2
|
1.0
|
CB
|
A:GLN446
|
4.3
|
22.2
|
1.0
|
CD
|
A:GLN357
|
4.4
|
34.0
|
1.0
|
CG
|
A:GLN446
|
4.5
|
25.3
|
1.0
|
OE1
|
A:GLN446
|
4.6
|
32.3
|
1.0
|
N
|
A:GLN357
|
4.6
|
26.1
|
1.0
|
CD2
|
C:FTY505
|
4.6
|
20.7
|
1.0
|
CG
|
C:FTY505
|
4.8
|
21.5
|
1.0
|
CA
|
A:GLN357
|
4.9
|
26.8
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 1qz0
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Fluorine Binding Sites List in 1qz0
Fluorine binding site 3 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F605
b:23.0
occ:1.00
|
F1
|
D:FTY605
|
0.0
|
23.0
|
1.0
|
C1
|
D:FTY605
|
1.4
|
18.6
|
1.0
|
CZ
|
D:FTY605
|
2.2
|
17.4
|
1.0
|
F2
|
D:FTY605
|
2.3
|
18.8
|
1.0
|
P
|
D:FTY605
|
2.7
|
16.2
|
1.0
|
CE2
|
D:FTY605
|
2.7
|
16.6
|
1.0
|
O1P
|
D:FTY605
|
2.9
|
17.4
|
1.0
|
OE1
|
D:GLU604
|
3.0
|
23.4
|
1.0
|
O
|
A:HOH524
|
3.2
|
22.3
|
1.0
|
O2P
|
D:FTY605
|
3.3
|
16.1
|
1.0
|
NZ
|
A:LYS342
|
3.4
|
24.3
|
1.0
|
CE1
|
D:FTY605
|
3.4
|
15.8
|
1.0
|
O3P
|
D:FTY605
|
3.9
|
13.6
|
1.0
|
CD
|
D:GLU604
|
4.0
|
23.7
|
1.0
|
CD2
|
D:FTY605
|
4.0
|
16.9
|
1.0
|
O
|
D:HOH610
|
4.2
|
28.8
|
1.0
|
O
|
A:HOH690
|
4.3
|
29.7
|
1.0
|
CD1
|
D:FTY605
|
4.5
|
15.1
|
1.0
|
OE2
|
D:GLU604
|
4.7
|
23.4
|
1.0
|
CE
|
A:LYS342
|
4.8
|
23.4
|
1.0
|
CG
|
D:GLU604
|
4.8
|
20.7
|
1.0
|
CG
|
D:FTY605
|
4.8
|
13.4
|
1.0
|
NH2
|
A:ARG278
|
4.9
|
13.7
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 4 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F605
b:18.8
occ:1.00
|
F2
|
D:FTY605
|
0.0
|
18.8
|
1.0
|
C1
|
D:FTY605
|
1.4
|
18.6
|
1.0
|
CZ
|
D:FTY605
|
2.3
|
17.4
|
1.0
|
F1
|
D:FTY605
|
2.3
|
23.0
|
1.0
|
CE1
|
D:FTY605
|
2.6
|
15.8
|
1.0
|
P
|
D:FTY605
|
2.7
|
16.2
|
1.0
|
O2P
|
D:FTY605
|
3.0
|
16.1
|
1.0
|
CA
|
A:SER388
|
3.2
|
13.8
|
1.0
|
O3P
|
D:FTY605
|
3.4
|
13.6
|
1.0
|
CE2
|
D:FTY605
|
3.6
|
16.6
|
1.0
|
CB
|
A:SER388
|
3.6
|
13.0
|
1.0
|
N
|
A:SER388
|
3.8
|
13.4
|
1.0
|
O1P
|
D:FTY605
|
3.9
|
17.4
|
1.0
|
OG
|
A:SER388
|
4.0
|
13.4
|
1.0
|
CD1
|
D:FTY605
|
4.0
|
15.1
|
1.0
|
O
|
A:GLY387
|
4.1
|
14.1
|
1.0
|
C
|
A:GLY387
|
4.2
|
13.9
|
1.0
|
O
|
A:LYS386
|
4.3
|
15.0
|
1.0
|
N
|
A:SER389
|
4.3
|
15.3
|
1.0
|
C
|
A:SER388
|
4.3
|
15.0
|
1.0
|
OE1
|
D:GLU604
|
4.5
|
23.4
|
1.0
|
CD2
|
D:FTY605
|
4.7
|
16.9
|
1.0
|
O
|
D:HOH610
|
4.8
|
28.8
|
1.0
|
CG
|
D:FTY605
|
4.9
|
13.4
|
1.0
|
O
|
D:HOH615
|
4.9
|
33.5
|
1.0
|
C
|
A:LYS386
|
4.9
|
14.8
|
1.0
|
CD
|
D:GLU604
|
5.0
|
23.7
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 5 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F505
b:23.8
occ:1.00
|
F1
|
E:FTY505
|
0.0
|
23.8
|
1.0
|
C1
|
E:FTY505
|
1.4
|
20.4
|
1.0
|
CZ
|
E:FTY505
|
2.3
|
21.6
|
1.0
|
F2
|
E:FTY505
|
2.3
|
22.7
|
1.0
|
CE2
|
E:FTY505
|
2.7
|
20.6
|
1.0
|
P
|
E:FTY505
|
2.7
|
18.6
|
1.0
|
NE2
|
B:GLN357
|
3.0
|
36.5
|
1.0
|
O1P
|
E:FTY505
|
3.1
|
17.3
|
1.0
|
O2P
|
E:FTY505
|
3.1
|
16.1
|
1.0
|
CB
|
B:ASP356
|
3.4
|
27.1
|
1.0
|
O
|
E:HOH138
|
3.4
|
19.7
|
1.0
|
CE1
|
E:FTY505
|
3.5
|
21.9
|
1.0
|
N
|
B:GLN357
|
3.7
|
27.9
|
1.0
|
O3P
|
E:FTY505
|
3.9
|
16.4
|
1.0
|
NH2
|
B:ARG409
|
4.0
|
13.9
|
1.0
|
CD2
|
E:FTY505
|
4.0
|
21.6
|
1.0
|
CD
|
B:GLN357
|
4.1
|
34.7
|
1.0
|
CA
|
B:ASP356
|
4.1
|
25.3
|
1.0
|
OD2
|
B:ASP356
|
4.2
|
32.5
|
1.0
|
CG
|
B:GLN357
|
4.2
|
33.4
|
1.0
|
CG
|
B:ASP356
|
4.3
|
30.8
|
1.0
|
C
|
B:ASP356
|
4.3
|
26.6
|
1.0
|
CA
|
B:GLN357
|
4.6
|
28.0
|
1.0
|
NE
|
B:ARG409
|
4.6
|
11.5
|
1.0
|
CD1
|
E:FTY505
|
4.6
|
23.2
|
1.0
|
CZ
|
B:ARG409
|
4.6
|
12.8
|
1.0
|
NE2
|
B:GLN446
|
4.7
|
28.6
|
1.0
|
CG
|
E:FTY505
|
4.8
|
21.9
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 6 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F505
b:22.7
occ:1.00
|
F2
|
E:FTY505
|
0.0
|
22.7
|
1.0
|
C1
|
E:FTY505
|
1.4
|
20.4
|
1.0
|
CZ
|
E:FTY505
|
2.3
|
21.6
|
1.0
|
F1
|
E:FTY505
|
2.3
|
23.8
|
1.0
|
CE1
|
E:FTY505
|
2.6
|
21.9
|
1.0
|
P
|
E:FTY505
|
2.7
|
18.6
|
1.0
|
O
|
E:HOH138
|
2.9
|
19.7
|
1.0
|
NE2
|
B:GLN446
|
3.0
|
28.6
|
1.0
|
O2P
|
E:FTY505
|
3.1
|
16.1
|
1.0
|
O3P
|
E:FTY505
|
3.2
|
16.4
|
1.0
|
NE2
|
B:GLN357
|
3.3
|
36.5
|
1.0
|
CE2
|
E:FTY505
|
3.5
|
20.6
|
1.0
|
O1P
|
E:FTY505
|
3.9
|
17.3
|
1.0
|
CD
|
B:GLN446
|
3.9
|
29.1
|
1.0
|
CA
|
B:GLY408
|
3.9
|
12.1
|
1.0
|
CD1
|
E:FTY505
|
4.0
|
23.2
|
1.0
|
N
|
B:GLY408
|
4.1
|
11.4
|
1.0
|
CG2
|
B:VAL407
|
4.3
|
12.0
|
1.0
|
CB
|
B:GLN446
|
4.3
|
22.5
|
1.0
|
CD
|
B:GLN357
|
4.4
|
34.7
|
1.0
|
N
|
B:GLN357
|
4.5
|
27.9
|
1.0
|
CG
|
B:GLN446
|
4.6
|
26.4
|
1.0
|
OE1
|
B:GLN446
|
4.6
|
33.3
|
1.0
|
CD2
|
E:FTY505
|
4.7
|
21.6
|
1.0
|
CG
|
E:FTY505
|
4.8
|
21.9
|
1.0
|
CA
|
B:GLN357
|
4.9
|
28.0
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 7 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F605
b:22.8
occ:1.00
|
F1
|
F:FTY605
|
0.0
|
22.8
|
1.0
|
C1
|
F:FTY605
|
1.4
|
18.8
|
1.0
|
CZ
|
F:FTY605
|
2.2
|
16.6
|
1.0
|
F2
|
F:FTY605
|
2.3
|
19.7
|
1.0
|
P
|
F:FTY605
|
2.7
|
17.7
|
1.0
|
CE2
|
F:FTY605
|
2.7
|
16.4
|
1.0
|
O1P
|
F:FTY605
|
2.9
|
17.4
|
1.0
|
OE1
|
F:GLU604
|
3.0
|
24.2
|
1.0
|
O
|
B:HOH534
|
3.1
|
22.0
|
1.0
|
O2P
|
F:FTY605
|
3.3
|
17.8
|
1.0
|
NZ
|
B:LYS342
|
3.4
|
25.5
|
1.0
|
CE1
|
F:FTY605
|
3.4
|
14.8
|
1.0
|
O3P
|
F:FTY605
|
3.9
|
15.8
|
1.0
|
CD
|
F:GLU604
|
4.0
|
23.6
|
1.0
|
CD2
|
F:FTY605
|
4.0
|
16.5
|
1.0
|
O
|
F:HOH210
|
4.0
|
23.3
|
1.0
|
O
|
F:HOH519
|
4.4
|
28.2
|
1.0
|
CD1
|
F:FTY605
|
4.5
|
14.4
|
1.0
|
OE2
|
F:GLU604
|
4.7
|
23.8
|
1.0
|
CE
|
B:LYS342
|
4.7
|
22.0
|
1.0
|
CG
|
F:GLU604
|
4.8
|
21.6
|
1.0
|
CG
|
F:FTY605
|
4.8
|
14.2
|
1.0
|
NH2
|
B:ARG278
|
4.9
|
14.5
|
1.0
|
CG
|
B:LYS342
|
4.9
|
16.8
|
1.0
|
CD
|
B:LYS342
|
5.0
|
20.3
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 1qz0
Go back to
Fluorine Binding Sites List in 1qz0
Fluorine binding site 8 out
of 8 in the Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of the Yersinia Pestis Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F605
b:19.7
occ:1.00
|
F2
|
F:FTY605
|
0.0
|
19.7
|
1.0
|
C1
|
F:FTY605
|
1.4
|
18.8
|
1.0
|
CZ
|
F:FTY605
|
2.3
|
16.6
|
1.0
|
F1
|
F:FTY605
|
2.3
|
22.8
|
1.0
|
CE1
|
F:FTY605
|
2.6
|
14.8
|
1.0
|
P
|
F:FTY605
|
2.7
|
17.7
|
1.0
|
O2P
|
F:FTY605
|
3.0
|
17.8
|
1.0
|
CA
|
B:SER388
|
3.2
|
13.9
|
1.0
|
O3P
|
F:FTY605
|
3.4
|
15.8
|
1.0
|
CE2
|
F:FTY605
|
3.6
|
16.4
|
1.0
|
CB
|
B:SER388
|
3.6
|
13.2
|
1.0
|
O1P
|
F:FTY605
|
3.9
|
17.4
|
1.0
|
N
|
B:SER388
|
3.9
|
13.4
|
1.0
|
OG
|
B:SER388
|
4.0
|
13.3
|
1.0
|
CD1
|
F:FTY605
|
4.0
|
14.4
|
1.0
|
O
|
B:GLY387
|
4.2
|
14.5
|
1.0
|
C
|
B:GLY387
|
4.3
|
13.7
|
1.0
|
N
|
B:SER389
|
4.3
|
15.8
|
1.0
|
C
|
B:SER388
|
4.3
|
14.9
|
1.0
|
O
|
B:LYS386
|
4.4
|
15.4
|
1.0
|
OE1
|
F:GLU604
|
4.4
|
24.2
|
1.0
|
O
|
F:HOH210
|
4.5
|
23.3
|
1.0
|
CD2
|
F:FTY605
|
4.7
|
16.5
|
1.0
|
CG
|
F:FTY605
|
4.9
|
14.2
|
1.0
|
CD
|
F:GLU604
|
5.0
|
23.6
|
1.0
|
|
Reference:
J.Phan,
K.Lee,
S.Cherry,
J.E.Tropea,
T.R.Burke Jr,
D.S.Waugh.
High-Resolution Structure of the Yersinia Pestis Protein Tyrosine Phosphatase Yoph in Complex with A Phosphotyrosyl Mimetic-Containing Hexapeptide Biochemistry V. 42 13113 2003.
ISSN: ISSN 0006-2960
PubMed: 14609321
DOI: 10.1021/BI030156M
Page generated: Wed Jul 31 12:34:31 2024
|