Bromine in PDB 7tdl: M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
Enzymatic activity of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
All present enzymatic activity of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine:
4.1.99.2;
Protein crystallography data
The structure of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine, PDB code: 7tdl
was solved by
R.S.Phillips,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
58.41 /
1.60
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.25,
82.87,
94.33,
113.16,
96.54,
102.21
|
|
R / Rfree (%)
|
17.7 /
22.1
|
Other elements in 7tdl:
The structure of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
(pdb code 7tdl). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine, PDB code: 7tdl:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 7tdl
Go back to
Bromine Binding Sites List in 7tdl
Bromine binding site 1 out
of 4 in the M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
 Mono view
 Stereo pair view
|
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br501
b:58.8
occ:0.29
|
BR1
|
A:OY3501
|
0.0
|
58.8
|
0.3
|
|
H4
|
A:OY3501
|
0.7
|
54.7
|
0.7
|
|
C6
|
A:OY3501
|
1.5
|
45.6
|
0.7
|
|
C8
|
A:OY3501
|
1.9
|
45.4
|
0.3
|
|
C7
|
A:OY3501
|
2.2
|
46.7
|
0.7
|
|
H5
|
A:OY3501
|
2.2
|
56.0
|
0.7
|
|
C5
|
A:OY3501
|
2.7
|
42.1
|
0.7
|
|
HE2
|
A:PHE448
|
2.8
|
76.8
|
1.0
|
|
HE1
|
A:PHE36
|
2.8
|
47.3
|
1.0
|
|
C7
|
A:OY3501
|
2.8
|
46.5
|
0.3
|
|
C9
|
A:OY3501
|
2.8
|
42.0
|
0.3
|
|
HZ
|
A:PHE36
|
2.9
|
50.3
|
1.0
|
|
H6
|
A:OY3501
|
2.9
|
50.5
|
0.3
|
|
H5
|
A:OY3501
|
2.9
|
55.8
|
0.3
|
|
H3
|
A:OY3501
|
3.0
|
50.5
|
0.7
|
|
CE2
|
A:PHE448
|
3.2
|
64.0
|
1.0
|
|
CE1
|
A:PHE36
|
3.3
|
39.4
|
1.0
|
|
CZ
|
A:PHE36
|
3.3
|
41.9
|
1.0
|
|
HH22
|
A:ARG381
|
3.4
|
59.1
|
1.0
|
|
C8
|
A:OY3501
|
3.5
|
45.1
|
0.7
|
|
HE2
|
B:TYR71
|
3.6
|
39.7
|
1.0
|
|
HD2
|
A:PHE448
|
3.8
|
80.1
|
1.0
|
|
CD2
|
A:PHE448
|
3.8
|
66.8
|
1.0
|
|
C4
|
A:OY3501
|
3.9
|
40.5
|
0.7
|
|
NH2
|
A:ARG381
|
3.9
|
49.3
|
1.0
|
|
CZ
|
A:PHE448
|
3.9
|
66.6
|
1.0
|
|
HZ
|
A:PHE448
|
4.0
|
79.9
|
1.0
|
|
C6
|
A:OY3501
|
4.1
|
44.9
|
0.3
|
|
HH12
|
A:ARG381
|
4.1
|
54.9
|
1.0
|
|
C4
|
A:OY3501
|
4.1
|
40.3
|
0.3
|
|
C9
|
A:OY3501
|
4.2
|
41.0
|
0.7
|
|
HE3
|
B:MET288
|
4.2
|
59.6
|
1.0
|
|
HH21
|
A:ARG381
|
4.2
|
59.1
|
1.0
|
|
CE2
|
B:TYR71
|
4.3
|
33.1
|
1.0
|
|
HD2
|
B:TYR71
|
4.4
|
35.1
|
1.0
|
|
CD1
|
A:PHE36
|
4.5
|
39.3
|
1.0
|
|
CZ
|
A:ARG381
|
4.5
|
48.4
|
1.0
|
|
NH1
|
A:ARG381
|
4.5
|
45.8
|
1.0
|
|
CE2
|
A:PHE36
|
4.5
|
45.0
|
1.0
|
|
O
|
A:HOH857
|
4.6
|
49.0
|
1.0
|
|
C5
|
A:OY3501
|
4.6
|
40.7
|
0.3
|
|
CD2
|
B:TYR71
|
4.7
|
29.3
|
1.0
|
|
HH22
|
A:ARG404
|
4.8
|
40.0
|
1.0
|
|
HD1
|
A:PHE36
|
4.8
|
47.2
|
1.0
|
|
SD
|
B:MET288
|
4.8
|
55.4
|
1.0
|
|
CG
|
A:PHE448
|
4.8
|
68.2
|
1.0
|
|
H4
|
A:OY3501
|
4.8
|
53.9
|
0.3
|
|
HE2
|
A:PHE36
|
4.9
|
54.0
|
1.0
|
|
CE1
|
A:PHE448
|
4.9
|
77.1
|
1.0
|
|
HH
|
B:TYR71
|
4.9
|
43.6
|
1.0
|
|
CE
|
B:MET288
|
4.9
|
49.7
|
1.0
|
|
BR1
|
A:OY3501
|
5.0
|
56.4
|
0.7
|
|
Bromine binding site 2 out
of 4 in 7tdl
Go back to
Bromine Binding Sites List in 7tdl
Bromine binding site 2 out
of 4 in the M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
 Mono view
 Stereo pair view
|
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br501
b:56.4
occ:0.71
|
BR1
|
A:OY3501
|
0.0
|
56.4
|
0.7
|
|
H4
|
A:OY3501
|
0.8
|
53.9
|
0.3
|
|
C6
|
A:OY3501
|
1.6
|
44.9
|
0.3
|
|
C8
|
A:OY3501
|
1.9
|
45.1
|
0.7
|
|
H5
|
A:OY3501
|
2.2
|
55.8
|
0.3
|
|
C7
|
A:OY3501
|
2.2
|
46.5
|
0.3
|
|
C5
|
A:OY3501
|
2.8
|
40.7
|
0.3
|
|
C7
|
A:OY3501
|
2.8
|
46.7
|
0.7
|
|
C9
|
A:OY3501
|
2.9
|
41.0
|
0.7
|
|
H6
|
A:OY3501
|
2.9
|
49.2
|
0.7
|
|
H5
|
A:OY3501
|
2.9
|
56.0
|
0.7
|
|
HG23
|
A:THR125
|
3.0
|
40.5
|
1.0
|
|
H3
|
A:OY3501
|
3.1
|
48.8
|
0.3
|
|
HG13
|
B:VAL283
|
3.5
|
56.7
|
1.0
|
|
C8
|
A:OY3501
|
3.5
|
45.4
|
0.3
|
|
HG22
|
A:THR125
|
3.5
|
40.5
|
1.0
|
|
CG2
|
A:THR125
|
3.6
|
33.7
|
1.0
|
|
O
|
B:HOH635
|
3.6
|
41.1
|
1.0
|
|
HG21
|
A:THR125
|
3.7
|
40.5
|
1.0
|
|
HG11
|
B:VAL283
|
3.7
|
56.7
|
1.0
|
|
HG22
|
A:THR124
|
3.7
|
53.3
|
1.0
|
|
HB
|
A:THR124
|
3.8
|
48.9
|
1.0
|
|
HH22
|
A:ARG100
|
3.8
|
36.1
|
1.0
|
|
HH12
|
A:ARG100
|
3.8
|
38.4
|
1.0
|
|
HE3
|
B:MET288
|
3.9
|
59.6
|
1.0
|
|
HG12
|
B:VAL283
|
3.9
|
56.7
|
1.0
|
|
CG1
|
B:VAL283
|
3.9
|
47.2
|
1.0
|
|
HG21
|
A:THR124
|
3.9
|
53.3
|
1.0
|
|
HZ
|
A:PHE123
|
4.0
|
43.5
|
1.0
|
|
C4
|
A:OY3501
|
4.0
|
40.3
|
0.3
|
|
O
|
A:HOH857
|
4.1
|
49.0
|
1.0
|
|
HZ
|
A:PHE448
|
4.1
|
79.9
|
1.0
|
|
HE2
|
A:PHE123
|
4.1
|
43.1
|
1.0
|
|
C6
|
A:OY3501
|
4.1
|
45.6
|
0.7
|
|
NH2
|
A:ARG100
|
4.1
|
30.1
|
1.0
|
|
NH1
|
A:ARG100
|
4.1
|
32.0
|
1.0
|
|
C4
|
A:OY3501
|
4.2
|
40.5
|
0.7
|
|
CG2
|
A:THR124
|
4.2
|
44.4
|
1.0
|
|
C9
|
A:OY3501
|
4.2
|
42.0
|
0.3
|
|
CZ
|
A:ARG100
|
4.4
|
29.2
|
1.0
|
|
CZ
|
A:PHE123
|
4.5
|
36.2
|
1.0
|
|
CB
|
A:THR124
|
4.5
|
40.8
|
1.0
|
|
HH
|
B:TYR71
|
4.5
|
43.6
|
1.0
|
|
CE2
|
A:PHE123
|
4.6
|
35.9
|
1.0
|
|
HH21
|
A:ARG100
|
4.6
|
36.1
|
1.0
|
|
HH11
|
A:ARG100
|
4.6
|
38.4
|
1.0
|
|
CZ
|
A:PHE448
|
4.6
|
66.6
|
1.0
|
|
C5
|
A:OY3501
|
4.7
|
42.1
|
0.7
|
|
CE
|
B:MET288
|
4.7
|
49.7
|
1.0
|
|
H
|
A:THR125
|
4.7
|
38.5
|
1.0
|
|
HG1
|
A:THR124
|
4.8
|
54.3
|
1.0
|
|
HE1
|
A:PHE448
|
4.8
|
92.5
|
1.0
|
|
HE2
|
B:MET288
|
4.9
|
59.6
|
1.0
|
|
H4
|
A:OY3501
|
4.9
|
54.7
|
0.7
|
|
BR1
|
A:OY3501
|
5.0
|
58.8
|
0.3
|
|
HE1
|
B:MET288
|
5.0
|
59.6
|
1.0
|
|
CB
|
A:THR125
|
5.0
|
29.9
|
1.0
|
|
Bromine binding site 3 out
of 4 in 7tdl
Go back to
Bromine Binding Sites List in 7tdl
Bromine binding site 3 out
of 4 in the M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
 Mono view
 Stereo pair view
|
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br501
b:56.5
occ:0.33
|
BR1
|
B:OY3501
|
0.0
|
56.5
|
0.3
|
|
H4
|
B:OY3501
|
0.6
|
59.8
|
0.7
|
|
C6
|
B:OY3501
|
1.3
|
49.9
|
0.7
|
|
C8
|
B:OY3501
|
1.9
|
49.0
|
0.3
|
|
C7
|
B:OY3501
|
2.1
|
51.0
|
0.7
|
|
H5
|
B:OY3501
|
2.1
|
61.1
|
0.7
|
|
C5
|
B:OY3501
|
2.5
|
46.3
|
0.7
|
|
C7
|
B:OY3501
|
2.8
|
50.9
|
0.3
|
|
H3
|
B:OY3501
|
2.9
|
55.5
|
0.7
|
|
C9
|
B:OY3501
|
2.9
|
46.1
|
0.3
|
|
H5
|
B:OY3501
|
2.9
|
61.0
|
0.3
|
|
H6
|
B:OY3501
|
2.9
|
55.3
|
0.3
|
|
HG23
|
B:THR125
|
3.2
|
43.9
|
1.0
|
|
C8
|
B:OY3501
|
3.4
|
51.3
|
0.7
|
|
O
|
A:HOH681
|
3.4
|
40.2
|
1.0
|
|
H23
|
A:DMS504
|
3.5
|
73.6
|
1.0
|
|
HG13
|
A:VAL283
|
3.5
|
52.2
|
1.0
|
|
HH12
|
B:ARG100
|
3.5
|
35.8
|
1.0
|
|
HG11
|
A:VAL283
|
3.6
|
52.2
|
1.0
|
|
HG22
|
B:THR125
|
3.6
|
43.9
|
1.0
|
|
HE3
|
A:MET288
|
3.7
|
56.3
|
1.0
|
|
C4
|
B:OY3501
|
3.7
|
45.6
|
0.7
|
|
HB
|
B:THR124
|
3.7
|
60.9
|
1.0
|
|
CG2
|
B:THR125
|
3.7
|
36.6
|
1.0
|
|
HG21
|
B:THR125
|
3.8
|
43.9
|
1.0
|
|
HH22
|
B:ARG100
|
3.8
|
39.5
|
1.0
|
|
CG1
|
A:VAL283
|
3.9
|
43.5
|
1.0
|
|
HG12
|
A:VAL283
|
3.9
|
52.2
|
1.0
|
|
NH1
|
B:ARG100
|
4.0
|
29.8
|
1.0
|
|
C9
|
B:OY3501
|
4.0
|
47.5
|
0.7
|
|
HG22
|
B:THR124
|
4.1
|
70.2
|
1.0
|
|
HZ
|
B:PHE123
|
4.1
|
51.2
|
1.0
|
|
C6
|
B:OY3501
|
4.1
|
50.6
|
0.3
|
|
C4
|
B:OY3501
|
4.2
|
45.1
|
0.3
|
|
NH2
|
B:ARG100
|
4.2
|
32.9
|
1.0
|
|
O
|
B:HOH841
|
4.3
|
45.9
|
1.0
|
|
CE
|
A:MET288
|
4.3
|
46.9
|
1.0
|
|
HE2
|
A:MET288
|
4.4
|
56.3
|
1.0
|
|
HH11
|
B:ARG100
|
4.4
|
35.8
|
1.0
|
|
CZ
|
B:ARG100
|
4.4
|
31.4
|
1.0
|
|
HE1
|
A:MET288
|
4.4
|
56.3
|
1.0
|
|
HE2
|
B:PHE123
|
4.4
|
49.7
|
1.0
|
|
HH
|
A:TYR71
|
4.5
|
41.3
|
1.0
|
|
C2
|
A:DMS504
|
4.5
|
61.3
|
1.0
|
|
CB
|
B:THR124
|
4.5
|
50.7
|
1.0
|
|
C5
|
B:OY3501
|
4.7
|
46.5
|
0.3
|
|
HG1
|
B:THR124
|
4.7
|
66.3
|
1.0
|
|
CZ
|
B:PHE123
|
4.7
|
42.7
|
1.0
|
|
CG2
|
B:THR124
|
4.8
|
58.5
|
1.0
|
|
H
|
B:THR125
|
4.8
|
47.1
|
1.0
|
|
CE2
|
B:PHE123
|
4.8
|
41.4
|
1.0
|
|
HH21
|
B:ARG100
|
4.8
|
39.5
|
1.0
|
|
BR1
|
B:OY3501
|
4.8
|
77.5
|
0.7
|
|
H4
|
B:OY3501
|
4.9
|
60.8
|
0.3
|
|
OG1
|
B:THR124
|
4.9
|
55.3
|
1.0
|
|
H21
|
A:DMS504
|
4.9
|
73.6
|
1.0
|
|
H6
|
B:OY3501
|
4.9
|
57.0
|
0.7
|
|
HH12
|
B:ARG381
|
5.0
|
55.1
|
0.5
|
|
Bromine binding site 4 out
of 4 in 7tdl
Go back to
Bromine Binding Sites List in 7tdl
Bromine binding site 4 out
of 4 in the M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine
 Mono view
 Stereo pair view
|
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of M379A Mutant Tyrosine Phenol-Lyase Complexed with 3-Bromo-Dl- Phenylalanine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br501
b:77.5
occ:0.67
|
BR1
|
B:OY3501
|
0.0
|
77.5
|
0.7
|
|
H4
|
B:OY3501
|
1.1
|
60.8
|
0.3
|
|
C6
|
B:OY3501
|
1.7
|
50.6
|
0.3
|
|
C8
|
B:OY3501
|
1.9
|
51.3
|
0.7
|
|
H5
|
B:OY3501
|
2.1
|
61.0
|
0.3
|
|
C7
|
B:OY3501
|
2.1
|
50.9
|
0.3
|
|
HZ
|
B:PHE36
|
2.8
|
49.7
|
1.0
|
|
C7
|
B:OY3501
|
2.8
|
51.0
|
0.7
|
|
C9
|
B:OY3501
|
2.9
|
47.5
|
0.7
|
|
H5
|
B:OY3501
|
2.9
|
61.1
|
0.7
|
|
C5
|
B:OY3501
|
2.9
|
46.5
|
0.3
|
|
H6
|
B:OY3501
|
3.0
|
57.0
|
0.7
|
|
HH12
|
B:ARG381
|
3.2
|
55.1
|
0.5
|
|
H3
|
B:OY3501
|
3.3
|
55.8
|
0.3
|
|
C8
|
B:OY3501
|
3.5
|
49.0
|
0.3
|
|
O
|
B:HOH821
|
3.5
|
45.8
|
1.0
|
|
HE2
|
A:TYR71
|
3.6
|
43.6
|
1.0
|
|
NH1
|
B:ARG381
|
3.6
|
45.9
|
0.5
|
|
HH22
|
B:ARG381
|
3.6
|
55.4
|
0.5
|
|
CZ
|
B:PHE36
|
3.6
|
41.4
|
1.0
|
|
HE2
|
B:PHE36
|
3.7
|
45.4
|
1.0
|
|
HE3
|
A:MET288
|
3.9
|
56.3
|
1.0
|
|
NH2
|
B:ARG381
|
3.9
|
46.2
|
0.5
|
|
CZ
|
B:ARG381
|
4.0
|
46.9
|
0.5
|
|
HH11
|
B:ARG381
|
4.0
|
55.1
|
0.5
|
|
C4
|
B:OY3501
|
4.0
|
45.1
|
0.3
|
|
CE2
|
B:PHE36
|
4.1
|
37.8
|
1.0
|
|
C6
|
B:OY3501
|
4.1
|
49.9
|
0.7
|
|
HE1
|
B:PHE448
|
4.2
|
67.2
|
1.0
|
|
C4
|
B:OY3501
|
4.2
|
45.6
|
0.7
|
|
C9
|
B:OY3501
|
4.2
|
46.1
|
0.3
|
|
CE2
|
A:TYR71
|
4.2
|
36.4
|
1.0
|
|
HH22
|
B:ARG404
|
4.3
|
45.3
|
1.0
|
|
HD2
|
A:TYR71
|
4.3
|
37.7
|
1.0
|
|
CE1
|
B:PHE448
|
4.5
|
56.0
|
1.0
|
|
HH21
|
B:ARG381
|
4.5
|
55.4
|
0.5
|
|
HZ
|
B:PHE448
|
4.6
|
65.7
|
1.0
|
|
CD2
|
A:TYR71
|
4.6
|
31.4
|
1.0
|
|
C5
|
B:OY3501
|
4.7
|
46.3
|
0.7
|
|
CE1
|
B:PHE36
|
4.7
|
44.8
|
1.0
|
|
O
|
B:HOH841
|
4.8
|
45.9
|
1.0
|
|
CZ
|
B:PHE448
|
4.8
|
54.8
|
1.0
|
|
CE
|
A:MET288
|
4.8
|
46.9
|
1.0
|
|
HE1
|
B:PHE36
|
4.8
|
53.8
|
1.0
|
|
BR1
|
B:OY3501
|
4.8
|
56.5
|
0.3
|
|
H4
|
B:OY3501
|
4.9
|
59.8
|
0.7
|
|
O
|
A:HOH681
|
4.9
|
40.2
|
1.0
|
|
NH2
|
B:ARG404
|
4.9
|
37.8
|
1.0
|
|
O1
|
B:OY3501
|
5.0
|
43.1
|
0.7
|
|
NE
|
B:ARG381
|
5.0
|
47.3
|
0.5
|
|
Reference:
R.S.Phillips,
B.Jones,
S.Nash.
M379A Mutant Tyrosine Phenol-Lyase From Citrobacter Freundii Has Altered Conformational Dynamics. Chembiochem V. 23 00028 2022.
ISSN: ESSN 1439-7633
PubMed: 35577764
DOI: 10.1002/CBIC.202200028
Page generated: Thu Jul 11 04:36:13 2024
|
