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Bromine in PDB 6htm: X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin

Protein crystallography data

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin, PDB code: 6htm was solved by P.Amara, J.M.Mouesca, M.Bella, C.Saragaglia, S.Gambarelli, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.05 / 1.70
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.530, 47.140, 113.900, 90.00, 108.90, 90.00
R / Rfree (%) 16.2 / 18.9

Other elements in 6htm:

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Iron (Fe) 8 atoms
Chlorine (Cl) 7 atoms

Bromine Binding Sites:

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

Bromine binding site 1 out of 6 in 6htm

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Bromine binding site 1 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2507

b:51.6
occ:0.48
 O A:HOH2860 3.0 57.3 1.0
NZ A:LYS290 3.4 41.4 1.0
C A:ARG286 3.4 31.7 1.0
N A:PRO287 3.6 30.6 1.0
O A:ARG286 3.7 32.0 1.0
CA A:ARG286 3.9 29.1 1.0
O A:MET285 3.9 29.6 1.0
CD A:PRO287 4.0 30.4 1.0
CA A:PRO287 4.1 31.4 1.0
N A:ARG286 4.1 27.5 1.0
C A:MET285 4.1 30.4 1.0
CG A:MET285 4.2 35.5 1.0
CG A:PRO287 4.4 31.2 1.0
CB A:MET285 4.4 32.9 1.0
O A:HOH2731 4.5 43.0 1.0
O A:HOH2916 4.6 54.7 1.0
CE A:LYS290 4.8 39.8 1.0
OG1 A:THR294 4.8 42.3 1.0
CB A:PRO287 4.8 33.9 1.0
CA A:MET285 5.0 30.6 1.0

Bromine binding site 2 out of 6 in 6htm

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Bromine binding site 2 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2508

b:37.4
occ:0.56
 O A:HOH2855 3.0 46.7 1.0
CA A:HIS388 3.6 23.9 1.0
N A:HIS388 3.7 26.3 1.0
CD2 A:HIS388 3.8 26.4 1.0
CG A:ARG135 4.0 23.8 1.0
OD1 A:ASP387 4.0 36.4 1.0
O A:HOH2630 4.3 40.0 1.0
C A:HIS388 4.3 22.6 1.0
CG2 A:VAL390 4.3 29.5 1.0
CB A:ARG135 4.4 22.8 1.0
N A:PHE389 4.5 20.2 1.0
CG A:HIS388 4.6 22.7 1.0
CB A:HIS388 4.7 20.7 1.0
O A:HOH2828 4.8 53.5 1.0
CG A:GLU170 4.8 31.6 1.0
NE2 A:HIS388 4.9 31.5 1.0
C A:ASP387 5.0 25.4 1.0

Bromine binding site 3 out of 6 in 6htm

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Bromine binding site 3 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2509

b:41.9
occ:0.52
 O A:HOH2635 2.9 33.7 1.0
N A:ARG82 3.3 27.2 1.0
O A:HOH2924 3.5 48.0 1.0
CG A:ARG82 3.6 35.0 1.0
O A:HOH2892 3.8 46.0 1.0
CD A:ARG80 3.8 36.8 1.0
CD A:ARG82 4.0 37.7 1.0
CA A:PRO81 4.0 29.7 1.0
CB A:ARG82 4.0 30.5 1.0
C A:PRO81 4.1 26.5 1.0
CA A:ARG82 4.3 26.7 1.0
NE A:ARG80 4.3 39.9 1.0
CG A:PRO385 4.4 33.0 1.0
CB A:PRO385 4.4 29.8 1.0
CD A:PRO385 4.4 33.5 1.0
CB A:PRO81 4.4 31.4 1.0
O A:PRO385 4.9 26.6 1.0

Bromine binding site 4 out of 6 in 6htm

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Bromine binding site 4 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br509

b:35.8
occ:0.54
 O B:HOH658 3.2 29.8 1.0
N B:ARG82 3.4 24.8 1.0
O B:HOH999 3.4 40.5 1.0
CG B:ARG82 3.8 32.2 1.0
CD B:ARG80 4.0 33.0 1.0
CA B:PRO81 4.0 26.8 1.0
CB B:ARG82 4.0 26.2 1.0
C B:PRO81 4.2 23.2 1.0
O B:HOH893 4.2 50.1 1.0
CG B:PRO385 4.3 26.6 1.0
O B:HOH938 4.3 42.5 1.0
CD B:PRO385 4.3 26.4 1.0
CA B:ARG82 4.3 24.0 1.0
CB B:PRO385 4.5 25.9 1.0
NE B:ARG80 4.5 38.7 1.0
CB B:PRO81 4.5 25.7 1.0
NE B:ARG82 4.7 45.0 1.0
CD B:ARG82 4.9 40.0 1.0
O B:PRO385 4.9 25.4 1.0
CZ B:ARG80 5.0 39.6 1.0

Bromine binding site 5 out of 6 in 6htm

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Bromine binding site 5 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br510

b:38.8
occ:0.66
 O B:HOH926 2.8 37.1 1.0
O B:HOH786 3.4 44.6 1.0
CA B:HIS388 3.5 21.4 1.0
N B:HIS388 3.7 20.4 1.0
CD2 B:HIS388 3.8 23.4 1.0
CG B:ARG135 4.0 21.0 1.0
CG2 B:VAL390 4.2 27.6 1.0
OD1 B:ASP387 4.2 29.7 1.0
O B:HOH708 4.2 53.4 1.0
C B:HIS388 4.3 21.7 1.0
CB B:ARG135 4.4 18.4 1.0
O B:HOH751 4.4 39.8 1.0
N B:PHE389 4.5 20.2 1.0
CG B:HIS388 4.6 20.8 1.0
CB B:HIS388 4.6 19.4 1.0
CG B:GLU170 4.6 37.4 1.0
O B:HOH729 4.7 37.9 1.0
NE2 B:HIS388 4.9 24.8 1.0
C B:ASP387 5.0 22.2 1.0

Bromine binding site 6 out of 6 in 6htm

Go back to Bromine Binding Sites List in 6htm
Bromine binding site 6 out of 6 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


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 in Complex with Bound Tryptamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br511

b:39.4
occ:0.44
 O B:HOH982 3.0 61.1 1.0
O B:HOH890 3.2 46.3 1.0
NZ B:LYS290 3.2 45.2 1.0
C B:ARG286 3.4 24.2 1.0
O B:HOH912 3.4 37.7 1.0
N B:PRO287 3.5 22.3 1.0
O B:ARG286 3.7 22.9 1.0
CA B:ARG286 3.8 20.8 1.0
O B:MET285 3.9 22.9 1.0
CD B:PRO287 4.0 22.8 1.0
CG B:MET285 4.0 23.3 0.5
N B:ARG286 4.0 20.7 1.0
C B:MET285 4.1 23.7 1.0
CA B:PRO287 4.1 23.1 1.0
CB B:MET285 4.3 23.7 0.5
CG B:PRO287 4.3 25.7 1.0
CE B:LYS290 4.4 39.8 1.0
CB B:MET285 4.4 23.7 0.5
O B:HOH684 4.6 28.5 1.0
O B:HOH951 4.7 26.4 1.0
OG1 B:THR294 4.8 34.6 1.0
CA B:MET285 4.9 22.9 0.5
CB B:PRO287 4.9 25.5 1.0
CA B:MET285 4.9 22.9 0.5
CE B:MET285 5.0 23.3 0.5

Reference:

P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet. Radical S-Adenosyl-L-Methionine Tryptophan Lyase (Nosl): How the Protein Controls the Carboxyl Radical •CO2-Migration. J.Am.Chem.Soc. V. 140 16661 2018.
ISSN: ESSN 1520-5126
PubMed: 30418774
DOI: 10.1021/JACS.8B09142
Page generated: Thu Jul 11 02:08:28 2024

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