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Caesium in PDB 5tcg: Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form

Enzymatic activity of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form

All present enzymatic activity of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form, PDB code: 5tcg was solved by K.Michalska, N.Maltseva, R.Jedrzejczak, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.183, 159.433, 165.230, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.6

Caesium Binding Sites:

The binding sites of Caesium atom in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form (pdb code 5tcg). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 9 binding sites of Caesium where determined in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form, PDB code: 5tcg:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Caesium binding site 1 out of 9 in 5tcg

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Caesium binding site 1 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs502

b:54.5
occ:0.80
OG1 B:THR284 3.0 22.5 1.0
O B:HOH644 3.0 43.8 1.0
O B:TYR320 3.0 25.4 1.0
O B:GLY322 3.1 23.5 1.0
O B:HOH690 3.2 20.5 1.0
O B:GLY246 3.3 23.5 1.0
O B:ALA282 3.3 23.0 1.0
O B:VAL245 3.9 23.5 1.0
CB B:THR284 3.9 22.9 1.0
C B:GLY246 4.1 22.8 1.0
C B:TYR320 4.2 25.4 1.0
C B:GLY322 4.2 23.5 1.0
O B:LEU318 4.3 23.0 1.0
CA B:GLY246 4.4 22.6 1.0
C B:ALA282 4.5 23.9 1.0
N B:THR284 4.5 23.2 1.0
N B:GLY322 4.7 25.2 1.0
CB B:ALA282 4.7 24.0 1.0
CB B:TYR320 4.7 24.2 1.0
C B:VAL245 4.8 22.8 1.0
CB B:VAL323 4.8 22.2 1.0
C B:PRO321 4.8 26.2 1.0
CA B:THR284 4.9 23.5 1.0
CD2 B:TYR320 4.9 24.2 1.0
CA B:TYR320 4.9 24.9 1.0
N B:TYR320 4.9 24.7 1.0
CG2 B:THR284 4.9 23.4 1.0

Caesium binding site 2 out of 9 in 5tcg

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Caesium binding site 2 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs503

b:36.1
occ:0.50
O B:TRP403 3.1 27.6 1.0
O B:LYS402 3.4 30.3 1.0
C B:TRP403 3.8 27.3 1.0
CA B:TRP403 4.1 26.9 1.0
C B:LYS402 4.4 29.6 1.0
N B:GLY405 4.5 31.3 1.0
N B:TRP403 4.8 27.6 1.0
N B:PHE404 4.8 27.1 1.0

Caesium binding site 3 out of 9 in 5tcg

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Caesium binding site 3 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cs502

b:52.5
occ:0.80
OG1 H:THR284 2.9 21.6 1.0
O H:TYR320 3.0 24.3 1.0
O H:HOH621 3.1 32.0 1.0
O H:GLY322 3.1 21.5 1.0
O H:ALA282 3.2 22.6 1.0
O H:HOH730 3.2 14.7 1.0
O H:GLY246 3.4 22.0 1.0
CB H:THR284 3.9 21.9 1.0
O H:VAL245 4.1 22.6 1.0
C H:TYR320 4.1 24.1 1.0
C H:GLY246 4.2 21.8 1.0
C H:GLY322 4.3 22.0 1.0
C H:ALA282 4.3 23.1 1.0
O H:LEU318 4.3 22.5 1.0
CA H:GLY246 4.4 21.6 1.0
N H:THR284 4.5 22.2 1.0
CB H:ALA282 4.6 22.9 1.0
N H:GLY322 4.7 23.6 1.0
C H:PRO321 4.8 24.7 1.0
CB H:TYR320 4.8 22.5 1.0
CA H:THR284 4.8 22.5 1.0
CB H:VAL323 4.8 21.0 1.0
C H:VAL245 4.9 21.9 1.0
CG2 H:THR284 4.9 22.2 1.0
CA H:TYR320 4.9 23.5 1.0
CD2 H:TYR320 4.9 22.3 1.0
CA H:PRO321 5.0 25.2 1.0
CB H:GLU270 5.0 21.8 1.0

Caesium binding site 4 out of 9 in 5tcg

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Caesium binding site 4 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cs502

b:58.3
occ:0.80
O F:HOH627 2.9 41.2 1.0
OG1 F:THR284 3.0 24.7 1.0
O F:TYR320 3.0 26.9 1.0
O F:GLY322 3.0 23.8 1.0
O F:ALA282 3.2 25.7 1.0
O F:HOH676 3.2 27.8 1.0
O F:GLY246 3.3 23.8 1.0
CB F:THR284 3.9 25.1 1.0
O F:VAL245 4.0 23.0 1.0
C F:GLY246 4.1 22.7 1.0
C F:TYR320 4.1 26.9 1.0
C F:GLY322 4.2 24.0 1.0
C F:ALA282 4.3 26.4 1.0
O F:LEU318 4.4 25.9 1.0
N F:THR284 4.4 25.8 1.0
CA F:GLY246 4.5 22.4 1.0
N F:GLY322 4.7 25.6 1.0
CB F:ALA282 4.8 26.3 1.0
CB F:VAL323 4.8 23.1 1.0
C F:PRO321 4.8 26.8 1.0
CA F:THR284 4.8 26.1 1.0
CB F:TYR320 4.9 26.2 1.0
C F:VAL245 4.9 22.0 1.0
CD2 F:TYR320 4.9 26.5 1.0
CA F:TYR320 4.9 26.8 1.0
CG2 F:THR284 5.0 25.7 1.0

Caesium binding site 5 out of 9 in 5tcg

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Caesium binding site 5 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cs503

b:45.7
occ:0.80
O F:LEU142 3.0 25.3 1.0
O F:HOH658 3.2 28.6 1.0
O H:HOH639 3.3 20.2 1.0
O F:HOH662 3.3 15.1 1.0
O F:HOH614 3.6 28.1 1.0
O F:CYS137 3.8 22.5 1.0
O F:GLY167 3.9 25.1 1.0
O1 F:FMT505 3.9 48.2 1.0
C F:LEU142 4.0 25.5 1.0
C F:CYS137 4.2 21.7 1.0
N F:ALA138 4.3 21.8 1.0
CA F:ALA138 4.3 22.7 1.0
C F:GLY167 4.5 24.5 1.0
CA F:ASP143 4.6 26.2 1.0
O F:LEU166 4.6 23.2 1.0
N F:ASP143 4.6 26.1 1.0
N F:LEU142 4.7 25.1 1.0
CB F:CYS137 4.7 21.0 1.0
N F:CYS144 4.8 24.7 1.0
CB F:CYS144 4.9 23.6 1.0
CA F:GLY167 4.9 24.6 1.0
C F:ASP143 4.9 25.2 1.0
CA F:LEU142 5.0 25.5 1.0
C F:FMT505 5.0 49.1 1.0

Caesium binding site 6 out of 9 in 5tcg

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Caesium binding site 6 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cs504

b:61.3
occ:0.50
O H:GLY67 2.9 22.7 1.0
O F:GLY67 3.0 23.3 1.0
O H:HOH780 3.0 27.3 1.0
O F:HOH735 3.0 31.1 1.0
O F:PRO69 3.4 20.4 1.0
O H:PRO69 3.6 19.2 1.0
C F:GLY67 3.9 22.7 1.0
O F:HOH615 4.0 27.9 1.0
C H:GLY67 4.0 22.0 1.0
O F:HOH698 4.1 9.1 0.5
O H:HOH652 4.2 27.5 1.0
O H:HOH691 4.3 31.6 1.0
O F:HOH657 4.4 7.2 0.5
CA F:GLY67 4.5 22.6 1.0
C F:PRO69 4.5 19.7 1.0
CA H:GLY67 4.6 22.4 1.0
O H:HOH753 4.6 24.4 1.0
C H:PRO69 4.7 18.8 1.0
O H:HOH742 4.7 37.1 1.0
C F:ARG68 4.7 22.2 1.0
N F:ARG68 4.8 22.7 1.0
OE1 B:GLN52 4.9 34.1 1.0
O F:ARG68 4.9 23.3 1.0
N F:PRO69 5.0 21.5 1.0
C H:ARG68 5.0 20.7 1.0

Caesium binding site 7 out of 9 in 5tcg

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Caesium binding site 7 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs502

b:55.8
occ:0.80
OG1 D:THR284 3.0 21.5 1.0
O D:TYR320 3.0 23.6 1.0
O D:HOH692 3.0 33.9 1.0
O D:GLY322 3.1 21.1 1.0
O D:GLY246 3.1 22.3 1.0
O D:HOH712 3.1 26.1 1.0
O D:ALA282 3.2 21.5 1.0
CB D:THR284 3.9 21.8 1.0
O D:VAL245 3.9 21.8 1.0
C D:GLY246 4.0 21.4 1.0
C D:TYR320 4.2 23.6 1.0
C D:GLY322 4.2 21.7 1.0
O D:LEU318 4.3 23.5 1.0
CA D:GLY246 4.3 21.1 1.0
C D:ALA282 4.4 22.4 1.0
N D:THR284 4.5 22.0 1.0
CB D:ALA282 4.7 22.1 1.0
N D:GLY322 4.7 22.8 1.0
CB D:VAL323 4.8 21.5 1.0
C D:VAL245 4.8 20.9 1.0
C D:PRO321 4.8 23.7 1.0
CB D:TYR320 4.8 22.7 1.0
CA D:THR284 4.8 22.4 1.0
CG2 D:THR284 4.9 22.3 1.0
CA D:TYR320 4.9 23.4 1.0
OE1 D:GLU270 5.0 24.3 1.0

Caesium binding site 8 out of 9 in 5tcg

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Caesium binding site 8 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs503

b:47.2
occ:0.80
O D:LEU142 3.0 23.1 1.0
O D:HOH659 3.3 24.0 1.0
O B:HOH662 3.3 16.6 1.0
O D:HOH703 3.4 16.2 1.0
O D:CYS137 3.8 23.2 1.0
C D:LEU142 4.0 23.7 1.0
O D:GLY167 4.1 24.5 1.0
C D:CYS137 4.2 22.4 1.0
CA D:ALA138 4.4 22.9 1.0
N D:ALA138 4.4 22.2 1.0
N D:LEU142 4.6 24.2 1.0
CB D:CYS137 4.6 21.8 1.0
C D:GLY167 4.6 24.0 1.0
CA D:ASP143 4.6 24.0 1.0
N D:ASP143 4.6 24.2 1.0
O D:LEU166 4.7 22.9 1.0
N D:CYS144 4.7 22.5 1.0
CA D:GLY167 4.9 24.3 1.0
CA D:LEU142 4.9 24.0 1.0
CB D:CYS144 5.0 21.2 1.0
C D:ASP143 5.0 23.0 1.0

Caesium binding site 9 out of 9 in 5tcg

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Caesium binding site 9 out of 9 in the Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Crystal Structure of Tryptophan Synthase From M. Tuberculosis - Aminoacrylate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs504

b:65.8
occ:0.50
O B:GLY67 2.9 23.5 1.0
O D:GLY67 2.9 22.8 1.0
O B:HOH756 3.0 30.2 1.0
O B:HOH758 3.1 32.7 1.0
O D:PRO69 3.3 20.8 1.0
O B:PRO69 3.6 22.1 1.0
C B:GLY67 4.0 23.1 1.0
C D:GLY67 4.0 22.7 1.0
O D:HOH636 4.1 34.9 1.0
O D:HOH667 4.3 34.1 1.0
C D:PRO69 4.4 20.0 1.0
O D:HOH713 4.4 23.8 1.0
O B:HOH663 4.4 32.4 1.0
NE2 H:GLN52 4.4 28.1 0.5
O B:HOH712 4.5 21.9 1.0
CA B:GLY67 4.5 23.4 1.0
CA D:GLY67 4.7 22.7 1.0
C B:PRO69 4.7 21.1 1.0
C D:ARG68 4.7 22.3 1.0
N D:PRO69 4.8 21.5 1.0
O D:ARG68 4.8 23.5 1.0
C B:ARG68 4.9 22.5 1.0
N D:ARG68 4.9 22.7 1.0
N B:ARG68 5.0 22.8 1.0
O B:ARG68 5.0 22.8 1.0
OE1 H:GLN52 5.0 27.5 0.5

Reference:

S.Wellington, P.P.Nag, K.Michalska, S.E.Johnston, R.P.Jedrzejczak, V.K.Kaushik, A.E.Clatworthy, N.Siddiqi, P.Mccarren, B.Bajrami, N.I.Maltseva, S.Combs, S.L.Fisher, A.Joachimiak, S.L.Schreiber, D.T.Hung. A Small-Molecule Allosteric Inhibitor of Mycobacterium Tuberculosis Tryptophan Synthase. Nat. Chem. Biol. V. 13 943 2017.
ISSN: ESSN 1552-4469
PubMed: 28671682
DOI: 10.1038/NCHEMBIO.2420
Page generated: Sun Dec 13 10:56:50 2020

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