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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:

Potassium (K) 4 atoms
Chlorine (Cl) 3 atoms

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

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