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Bromine in PDB 4r34: X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound

Protein crystallography data

The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound, PDB code: 4r34 was solved by Y.Nicolet, L.Zeppieri, P.Amara, J.-C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.97 / 1.80
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.150, 47.070, 113.920, 90.00, 108.99, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 4r34:

The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Iron (Fe) 8 atoms
Sodium (Na) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound (pdb code 4r34). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound, PDB code: 4r34:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 1 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br507

b:80.9
occ:0.70
O A:HOH868 3.3 48.0 1.0
NZ A:LYS290 3.5 46.7 1.0
C A:ARG286 3.7 36.3 1.0
N A:PRO287 3.8 32.1 1.0
O A:ARG286 3.9 34.8 1.0
CA A:ARG286 4.1 33.1 1.0
O A:HOH774 4.1 46.6 1.0
CG A:MET285 4.1 45.0 1.0
O A:MET285 4.1 29.6 1.0
CD A:PRO287 4.2 34.7 1.0
N A:ARG286 4.2 31.5 1.0
C A:MET285 4.2 33.6 1.0
CA A:PRO287 4.2 36.6 1.0
CB A:MET285 4.4 39.2 1.0
CE A:LYS290 4.4 54.1 1.0
CG A:PRO287 4.5 31.6 1.0
OG1 A:THR294 4.9 47.5 1.0
O A:HOH870 5.0 60.8 1.0
CB A:PRO287 5.0 35.5 1.0

Bromine binding site 2 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 2 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br508

b:55.3
occ:0.70
O A:HOH699 2.6 49.5 1.0
CA A:HIS388 3.6 25.8 1.0
N A:HIS388 3.7 27.2 1.0
OE2 A:GLU170 3.8 68.8 1.0
ND1 A:HIS388 3.8 31.7 1.0
CG A:ARG135 4.0 25.9 1.0
OD1 A:ASP387 4.0 36.6 1.0
CG A:GLU170 4.2 45.9 1.0
CB A:ARG135 4.3 23.7 1.0
C A:HIS388 4.3 26.3 1.0
O A:HOH751 4.4 52.2 1.0
CD A:GLU170 4.4 62.6 1.0
CG2 A:VAL390 4.5 28.5 1.0
N A:PHE389 4.6 21.2 1.0
CB A:HIS388 4.7 22.4 1.0
CG A:HIS388 4.7 23.2 1.0
CE1 A:HIS388 4.8 33.8 1.0
C A:ASP387 5.0 26.9 1.0

Bromine binding site 3 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 3 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br509

b:58.4
occ:0.66
O A:HOH627 3.0 33.2 1.0
CG A:ARG82 3.4 42.6 1.0
N A:ARG82 3.4 31.3 1.0
CD A:ARG82 3.7 47.2 1.0
CB A:ARG82 3.9 32.5 1.0
CD A:ARG80 4.0 44.0 1.0
O A:HOH736 4.0 40.6 1.0
CA A:PRO81 4.1 30.7 1.0
CG A:PRO385 4.2 30.7 1.0
C A:PRO81 4.2 30.5 1.0
CD A:PRO385 4.3 31.6 1.0
CA A:ARG82 4.3 27.9 1.0
NE A:ARG80 4.3 50.7 1.0
CB A:PRO81 4.4 33.5 1.0
CB A:PRO385 4.4 30.5 1.0
O A:PRO385 4.8 30.4 1.0
CZ A:ARG80 4.9 51.0 1.0

Bromine binding site 4 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 4 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br509

b:45.5
occ:0.66
O B:HOH697 3.1 24.5 1.0
N B:ARG82 3.4 23.8 1.0
CG B:ARG82 3.8 27.5 1.0
CD B:ARG80 3.9 36.0 1.0
CB B:ARG82 4.0 24.8 1.0
CA B:PRO81 4.1 31.4 1.0
CG B:PRO385 4.2 25.6 1.0
C B:PRO81 4.2 24.3 1.0
CA B:ARG82 4.3 23.9 1.0
NE B:ARG80 4.3 37.6 1.0
CD B:PRO385 4.4 25.2 1.0
CB B:PRO385 4.4 22.8 1.0
O B:HOH682 4.4 35.7 1.0
CB B:PRO81 4.5 30.9 1.0
NE B:ARG82 4.6 47.9 1.0
CD B:ARG82 4.8 38.6 1.0
O B:PRO385 4.9 21.4 1.0
CZ B:ARG80 5.0 38.5 1.0

Bromine binding site 5 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 5 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br510

b:50.5
occ:0.70
O B:HOH925 2.8 52.0 1.0
O B:HOH764 3.0 39.0 1.0
O B:HOH887 3.4 42.8 1.0
CA B:HIS388 3.4 21.9 1.0
N B:HIS388 3.6 21.6 1.0
CD2 B:HIS388 3.9 23.8 1.0
CG B:ARG135 4.0 17.3 1.0
OD1 B:ASP387 4.2 31.4 1.0
C B:HIS388 4.2 20.2 1.0
O B:HOH888 4.2 52.0 1.0
CG2 B:VAL390 4.3 28.5 1.0
CB B:ARG135 4.3 15.2 1.0
N B:PHE389 4.4 20.1 1.0
CB B:HIS388 4.5 16.3 1.0
CG B:HIS388 4.6 18.8 1.0
O B:HOH778 4.7 46.0 1.0
CG B:GLU170 4.8 38.3 1.0
C B:ASP387 4.9 23.9 1.0

Bromine binding site 6 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 6 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br511

b:80.3
occ:0.71
ZN B:ZN513 3.1 40.9 0.8
O B:HOH953 3.1 63.0 1.0
O B:LEU167 3.5 28.7 1.0
CD2 B:LEU167 3.7 26.4 1.0
NE2 B:HIS130 4.0 23.5 1.0
CE1 B:TYR129 4.1 23.3 1.0
CD1 B:TYR129 4.3 19.8 1.0
CZ B:TYR129 4.3 25.4 1.0
OE1 B:GLU126 4.4 42.2 1.0
C B:LEU167 4.4 23.8 1.0
CE1 B:HIS130 4.5 29.1 1.0
OE2 B:GLU126 4.5 38.2 1.0
O B:HOH839 4.6 51.0 1.0
CA B:LEU167 4.6 24.2 1.0
CG B:TYR129 4.6 16.3 1.0
CE2 B:TYR129 4.7 21.4 1.0
CB B:LEU167 4.7 20.9 1.0
CD2 B:TYR129 4.8 14.8 1.0
OH B:TYR129 4.8 29.9 1.0
CG B:LEU167 4.8 28.2 1.0
CD B:GLU126 4.8 37.9 1.0
CD2 B:HIS130 5.0 18.9 1.0

Bromine binding site 7 out of 7 in 4r34

Go back to Bromine Binding Sites List in 4r34
Bromine binding site 7 out of 7 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br514

b:39.4
occ:0.43
O B:HOH829 3.0 47.9 1.0
O B:HOH776 3.3 52.6 1.0
NZ B:LYS290 3.3 50.1 1.0
C B:ARG286 3.4 24.4 1.0
O B:HOH892 3.5 32.8 1.0
N B:PRO287 3.6 22.7 1.0
O B:ARG286 3.6 25.0 1.0
CA B:ARG286 3.9 22.1 1.0
O B:MET285 3.9 24.1 1.0
CA B:PRO287 4.0 25.8 1.0
C B:MET285 4.0 25.8 1.0
CD B:PRO287 4.1 23.6 1.0
N B:ARG286 4.1 22.4 1.0
CG B:MET285 4.1 25.3 0.4
CB B:MET285 4.4 25.9 0.4
CG B:PRO287 4.4 25.8 1.0
CE B:LYS290 4.4 47.3 1.0
CB B:MET285 4.4 25.7 0.6
O B:HOH675 4.4 31.3 1.0
O B:HOH957 4.4 61.0 1.0
CB B:PRO287 4.8 26.6 1.0
O B:HOH664 4.8 30.6 1.0
CA B:MET285 4.9 25.6 0.4
CA B:MET285 4.9 25.7 0.6
OG1 B:THR294 5.0 34.1 1.0

Reference:

Y.Nicolet, L.Zeppieri, P.Amara, J.C.Fontecilla-Camps. Crystal Structure of Tryptophan Lyase (Nosl): Evidence For Radical Formation at the Amino Group of Tryptophan. Angew.Chem.Int.Ed.Engl. V. 53 11840 2014.
ISSN: ISSN 1433-7851
PubMed: 25196319
DOI: 10.1002/ANIE.201407320
Page generated: Sat Dec 12 02:22:42 2020

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