Bromine in PDB 7pd1: Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans

Protein crystallography data

The structure of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd1 was solved by P.Amara, C.Saragaglia, J.-M.Mouesca, L.Martin, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 1.27
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.09, 48.85, 85.41, 90, 97.02, 90
R / Rfree (%) 15 / 17

Other elements in 7pd1:

The structure of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans also contains other interesting chemical elements:

Potassium (K) 1 atom
Iron (Fe) 8 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans (pdb code 7pd1). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd1:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 7pd1

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Bromine binding site 1 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br409

b:38.3
occ:0.46
 O A:HOH962 2.6 42.4 1.0
N A:VAL345 3.4 13.9 1.0
O A:HOH794 3.4 18.3 1.0
CB A:THR344 3.6 15.7 1.0
CA A:THR344 3.8 15.2 1.0
CA A:GLY320 3.8 14.1 1.0
O A:HOH628 3.9 30.0 1.0
CG2 A:VAL345 3.9 15.8 1.0
CG2 A:THR120 3.9 22.8 1.0
CG2 A:THR344 4.1 17.2 1.0
C A:THR344 4.1 14.0 1.0
CB A:VAL345 4.2 14.6 1.0
CA A:VAL345 4.4 14.5 1.0
O A:HOH911 4.6 30.4 1.0
N A:GLY320 4.7 13.8 1.0
CB A:THR120 4.8 19.1 1.0
O A:HOH648 4.8 22.1 1.0
O A:GLY320 4.8 14.4 1.0
OG1 A:THR344 4.8 15.6 1.0
C A:GLY320 4.8 13.7 1.0

Bromine binding site 2 out of 12 in 7pd1

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Bromine binding site 2 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br410

b:22.7
occ:0.45
 O A:HOH853 1.8 66.5 1.0
NH1 A:ARG133 3.2 16.4 0.6
N A:ARG133 3.4 22.7 1.0
O A:HOH832 3.4 27.4 1.0
CG2 A:VAL86 3.8 20.8 1.0
CG A:ARG133 3.9 34.7 0.6
CB A:ARG133 3.9 32.4 0.6
CG A:GLU131 4.0 18.3 1.0
CA A:SER132 4.0 20.1 1.0
O A:GLU131 4.0 16.5 1.0
CB A:ARG133 4.0 35.9 0.4
CD A:ARG133 4.0 29.3 0.6
C A:SER132 4.2 22.9 1.0
CG A:ARG133 4.2 37.0 0.4
N A:SER132 4.3 18.0 1.0
CA A:ARG133 4.3 25.9 0.6
C A:GLU131 4.3 16.8 1.0
CA A:ARG133 4.3 26.9 0.4
CZ A:ARG133 4.4 24.1 0.6
CG1 A:VAL86 4.5 19.9 1.0
CD A:ARG133 4.5 44.3 0.4
OE2 A:GLU131 4.6 20.0 1.0
CG A:PRO198 4.6 22.6 1.0
NE A:ARG133 4.7 26.9 0.6
CD A:GLU131 4.7 21.6 1.0
CB A:VAL86 4.8 19.4 1.0
O A:HOH941 4.8 29.4 1.0

Bromine binding site 3 out of 12 in 7pd1

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Bromine binding site 3 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br411

b:33.4
occ:0.42
 O A:HOH544 2.8 32.0 1.0
O A:HOH923 2.8 38.1 1.0
O A:HOH921 2.9 46.8 1.0
N A:ARG292 3.1 13.9 1.0
C A:MET290 3.4 13.7 1.0
N A:PRO291 3.5 13.7 1.0
CA A:MET290 3.5 13.3 0.8
CB A:ARG292 3.5 17.6 1.0
CA A:MET290 3.6 17.5 0.2
CB A:MET290 3.7 13.1 0.8
CA A:ARG292 3.8 14.1 1.0
CD A:PRO291 3.8 15.4 1.0
CB A:MET290 3.9 13.0 0.2
O A:MET290 3.9 13.1 1.0
N A:SER293 4.0 14.7 1.0
C A:PRO291 4.1 14.5 1.0
C A:ARG292 4.2 15.8 1.0
CG A:ARG292 4.2 20.5 1.0
CA A:PRO291 4.3 13.6 1.0
CG A:MET290 4.4 13.5 0.8
CE A:MET290 4.4 14.0 0.2
OG A:SER293 4.4 21.8 1.0
SD A:MET290 4.5 19.5 0.2
CE A:MET290 4.7 17.0 0.8
CD A:ARG292 4.7 28.3 1.0
CG A:MET290 4.8 13.1 0.2
CB A:PRO291 4.8 15.3 1.0
CB A:SER293 4.9 15.1 1.0
N A:MET290 4.9 13.1 1.0

Bromine binding site 4 out of 12 in 7pd1

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Bromine binding site 4 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br412

b:40.9
occ:0.37
 OG A:SER26 2.8 25.0 0.5
N A:SER26 3.0 21.9 1.0
O A:HOH898 3.3 45.6 1.0
OG A:SER26 3.3 20.6 0.3
CB A:SER26 3.4 20.6 0.5
CB A:SER26 3.4 21.6 0.2
CB A:SER26 3.4 22.6 0.3
CB A:THR24 3.6 23.8 1.0
O A:HOH610 3.6 41.3 1.0
OG1 A:THR24 3.6 27.1 1.0
N A:ASP25 3.6 22.3 1.0
CA A:SER26 3.8 22.0 0.5
CA A:SER26 3.8 21.3 0.2
O A:HOH665 3.8 33.2 1.0
CA A:SER26 3.8 20.9 0.3
C A:ASP25 3.9 19.3 1.0
CB A:ASP25 4.0 25.3 1.0
CA A:ASP25 4.0 22.1 1.0
C A:THR24 4.2 21.2 1.0
NH2 A:ARG29 4.5 26.9 1.0
CA A:THR24 4.5 20.5 1.0
CG2 A:THR24 4.6 21.8 1.0
OG A:SER26 4.6 24.0 0.2
O A:HOH762 4.7 47.9 1.0
NH1 A:ARG29 4.9 27.8 1.0

Bromine binding site 5 out of 12 in 7pd1

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Bromine binding site 5 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br413

b:43.6
occ:0.30
 O1 A:SO4406 1.1 27.9 0.7
S A:SO4406 1.2 28.4 0.7
O3 A:SO4406 1.8 28.8 0.7
O4 A:SO4406 1.8 27.0 0.7
O2 A:SO4406 2.6 29.3 0.7
NH1 A:ARG311 2.6 19.4 0.4
NH1 A:ARG311 2.9 15.1 0.2
O A:HOH570 3.0 23.9 1.0
NH2 A:ARG311 3.3 25.7 0.2
NE2 A:HIS62 3.5 17.5 1.0
O A:HOH837 3.6 23.0 0.8
CZ A:ARG311 3.6 21.0 0.2
CZ A:ARG311 3.8 20.3 0.4
NH2 A:ARG311 4.0 31.4 0.4
NE A:ARG311 4.1 27.7 0.4
NE A:ARG71 4.1 31.6 1.0
NH2 A:ARG311 4.2 16.2 0.4
NH2 A:ARG71 4.3 41.5 1.0
CE1 A:HIS62 4.3 17.6 1.0
CD2 A:HIS62 4.4 16.2 1.0
CZ A:ARG311 4.5 20.7 0.4
CZ A:ARG71 4.7 28.1 1.0
O A:HOH579 4.8 30.6 1.0
NE A:ARG311 4.8 23.9 0.4
NE A:ARG311 4.9 31.6 0.2

Bromine binding site 6 out of 12 in 7pd1

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Bromine binding site 6 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br414

b:47.7
occ:0.41
 O A:HOH880 2.5 40.7 1.0
O A:HOH890 3.3 39.1 1.0
N A:GLY335 3.4 17.4 1.0
O A:HOH781 3.7 23.4 1.0
CA A:GLY335 3.9 16.9 1.0
O A:PHE337 4.3 15.7 1.0
O A:HOH575 4.3 19.6 1.0
C A:VAL334 4.4 18.3 1.0
CA A:GLN338 4.6 16.7 1.0
C A:GLY335 4.6 16.6 1.0
CA A:VAL334 4.6 21.5 1.0
O A:GLY335 4.6 17.6 1.0
C A:PHE337 4.6 15.9 1.0
O A:ALA333 4.7 23.7 1.0
N A:GLN338 4.8 15.1 1.0
CG1 A:VAL334 4.9 24.4 1.0
OG1 A:THR323 4.9 16.2 1.0
CB A:GLN338 5.0 17.4 1.0

Bromine binding site 7 out of 12 in 7pd1

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Bromine binding site 7 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br408

b:64.3
occ:0.52
 O B:HOH762 2.8 41.3 1.0
NH2 B:ARG33 3.7 50.2 1.0
NH2 B:ARG29 3.9 46.2 1.0
NE B:ARG29 4.0 46.6 1.0
NH1 B:ARG33 4.1 49.5 1.0
CZ B:ARG33 4.3 47.9 1.0
CZ B:ARG29 4.5 45.3 1.0
OG B:SER26 4.9 47.0 1.0

Bromine binding site 8 out of 12 in 7pd1

Go back to Bromine Binding Sites List in 7pd1
Bromine binding site 8 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br409

b:68.1
occ:0.59
 O B:LEU54 4.2 18.2 1.0
CB B:LEU54 4.2 18.2 1.0
C B:LEU54 4.4 18.0 1.0
OE2 B:GLU55 4.4 30.8 1.0
CD B:GLU55 4.4 35.9 1.0
CB B:ALA58 4.5 15.6 1.0
OE1 B:GLU55 4.5 51.0 1.0
O B:HOH923 4.5 33.4 1.0
CG1 B:VAL280 4.6 19.9 1.0
N B:GLU55 4.7 18.7 1.0
CA B:GLU55 4.8 20.0 1.0
O B:HOH931 4.9 48.2 1.0
CD1 B:LEU284 4.9 15.1 1.0
CA B:LEU54 5.0 16.5 1.0

Bromine binding site 9 out of 12 in 7pd1

Go back to Bromine Binding Sites List in 7pd1
Bromine binding site 9 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br410

b:25.4
occ:0.42
 O B:HOH541 3.8 26.8 1.0
O B:HOH923 4.2 33.4 1.0
O B:HOH899 4.3 26.8 1.0
OE2 B:GLU55 4.5 30.8 1.0

Bromine binding site 10 out of 12 in 7pd1

Go back to Bromine Binding Sites List in 7pd1
Bromine binding site 10 out of 12 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br411

b:62.4
occ:0.44
 O B:HOH838 2.9 58.8 1.0
NH2 B:ARG262 3.3 20.1 1.0
NH1 B:ARG262 3.6 23.9 1.0
CZ B:ARG262 3.8 20.5 1.0
OG B:SER340 3.9 23.4 1.0
O B:HOH621 4.4 43.8 1.0
NE2 B:GLN338 4.5 44.2 1.0
CB B:SER340 4.5 19.0 1.0
CA B:SER340 4.7 16.4 1.0

Reference:

P.Amara, C.Saragaglia, J.M.Mouesca, L.Martin, Y.Nicolet. L-Tyrosine-Bound Thih Structure Reveals C-C Bond Break Differences Within Radical Sam Aromatic Amino Acid Lyases. Nat Commun V. 13 2284 2022.
ISSN: ESSN 2041-1723
PubMed: 35477710
DOI: 10.1038/S41467-022-29980-4
Page generated: Tue Apr 4 17:34:27 2023

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