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Chlorine in PDB 6dz4: Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.

Enzymatic activity of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.

All present enzymatic activity of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.:
4.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site., PDB code: 6dz4 was solved by E.Hilario, M.F.Dunn, L.J.Mueller, L.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.94 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.509, 59.300, 67.325, 90.00, 94.69, 90.00
R / Rfree (%) 14.7 / 18.6

Other elements in 6dz4:

The structure of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. (pdb code 6dz4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site., PDB code: 6dz4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6dz4

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Chlorine binding site 1 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:41.9
occ:1.00
 O A:HOH592 2.3 44.6 1.0
N A:ILE95 3.1 19.1 1.0
OG1 A:THR94 3.2 27.5 1.0
N A:THR94 3.2 20.7 1.0
C A:HIS92 3.6 19.6 1.0
CB A:HIS92 3.6 19.5 1.0
CB A:ILE95 3.7 19.7 1.0
N A:PRO93 3.7 20.6 1.0
CA A:HIS92 3.7 19.4 1.0
CG2 A:ILE95 3.8 18.9 1.0
O A:HOH467 3.8 42.3 1.0
CA A:THR94 3.8 21.4 1.0
C A:THR94 3.9 19.5 1.0
CD A:PRO93 3.9 21.8 1.0
CA A:ILE95 3.9 19.5 1.0
O A:HIS92 4.0 20.4 1.0
CB A:THR94 4.1 22.9 1.0
O A:HOH583 4.2 42.5 1.0
C A:PRO93 4.3 21.3 1.0
O A:HOH437 4.5 43.6 1.0
CA A:PRO93 4.5 21.4 1.0
CG A:PRO93 4.6 22.8 1.0
CG A:HIS92 4.6 20.2 1.0
ND1 A:HIS92 4.6 21.6 1.0
CG2 A:THR94 4.9 24.7 1.0
O A:THR94 5.0 21.6 1.0

Chlorine binding site 2 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 2 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:56.2
occ:1.00
 NH1 A:ARG225 3.4 38.1 1.0
CD A:ARG225 4.1 40.8 1.0
O A:SER221 4.5 26.5 0.5
CZ A:ARG225 4.5 40.7 1.0
O A:SER221 4.5 27.2 0.6
CB A:ARG225 4.6 33.0 1.0
CG A:ARG225 4.6 36.7 1.0
NE A:ARG225 4.7 42.9 1.0
CB A:SER221 4.7 24.5 0.6
CB A:SER221 4.8 24.1 0.5

Chlorine binding site 3 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 3 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:61.9
occ:1.00
 O B:ARG150 3.9 22.7 1.0
C B:ARG150 4.1 21.8 1.0
CA B:LEU151 4.2 20.0 1.0
N B:LEU151 4.2 19.9 1.0
CD2 B:LEU151 4.4 20.6 1.0
CE1 B:PHE147 4.5 29.2 1.0
CB B:ARG150 4.5 25.0 1.0
CG B:LEU151 4.8 21.0 1.0
CA B:ARG150 4.9 21.6 1.0

Chlorine binding site 4 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 4 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:62.7
occ:1.00
 C B:GLU220 3.6 15.8 1.0
O B:LYS219 3.7 18.9 1.0
N B:GLY221 3.7 16.1 1.0
O B:HOH814 3.7 58.2 1.0
O B:GLU220 3.9 18.5 1.0
C B:LYS219 4.0 16.1 1.0
CA B:GLU220 4.0 15.2 1.0
CA B:GLY221 4.1 17.7 1.0
O B:HOH934 4.1 49.0 1.0
N B:GLU220 4.1 15.2 1.0
O B:ASP218 4.2 18.2 1.0
O B:HOH744 4.7 49.1 1.0
O B:LEU217 4.9 18.0 1.0

Chlorine binding site 5 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 5 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:57.0
occ:1.00
 O B:HOH671 3.3 31.9 1.0
O B:GLY274 3.5 20.3 1.0
O B:HOH762 3.7 18.5 0.5
O B:HOH762 4.0 15.6 0.5
O B:LEU271 4.1 15.2 1.0
C B:GLY274 4.1 18.8 1.0
CA B:ARG275 4.1 17.4 0.7
CA B:ARG275 4.1 17.6 0.3
N B:VAL276 4.2 15.7 1.0
CG2 B:VAL276 4.4 19.8 1.0
N B:ARG275 4.4 18.4 0.3
N B:ARG275 4.4 18.3 0.7
C B:ARG275 4.5 15.8 0.7
O B:PRO270 4.5 13.1 1.0
C B:ARG275 4.5 16.2 0.3
CB B:PRO285 4.7 13.5 1.0
O B:HOH951 4.7 31.1 1.0
CG B:PRO285 4.8 13.1 1.0

Chlorine binding site 6 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 6 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:0.8
occ:1.00
 O B:HOH756 2.9 41.9 1.0
O B:HOH691 5.0 48.9 1.0

Chlorine binding site 7 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 7 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:66.1
occ:1.00
 O B:HOH888 4.1 39.4 1.0
O B:HOH972 4.7 34.8 1.0
O B:HOH909 4.7 47.4 1.0
O B:HOH861 4.8 19.2 1.0
O B:HOH900 4.8 25.3 1.0
O B:HOH531 4.8 22.3 1.0
O B:HOH966 4.8 27.4 1.0
O B:HOH920 4.9 56.4 1.0
O B:HOH941 5.0 23.2 1.0

Chlorine binding site 8 out of 8 in 6dz4

Go back to Chlorine Binding Sites List in 6dz4
Chlorine binding site 8 out of 8 in the Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5- Phosphonooxymethyl-Pyridin-4-Ylmethyl]-Serine (Pls) at the Beta-Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:50.9
occ:1.00
 NZ B:LYS283 2.7 24.4 1.0
O A:HOH442 3.5 25.5 1.0
CG A:PRO138 3.5 17.2 1.0
CD1 A:ILE111 3.7 16.7 1.0
CE B:LYS283 3.7 19.0 1.0
O B:HOH899 3.8 41.3 1.0
OH B:TYR16 4.0 17.9 1.0
O B:HOH957 4.0 34.4 1.0
CB A:PRO138 4.2 16.0 1.0
CE1 A:PHE139 4.4 14.4 1.0
O B:HOH594 4.5 43.9 1.0
CE1 A:PHE107 4.5 19.1 1.0
CD1 A:PHE107 4.5 16.7 1.0
CZ A:PHE139 4.7 13.8 1.0
CD A:PRO138 4.8 15.1 1.0
CD1 B:ILE278 4.8 14.9 1.0

Reference:

E.Hilario, M.F.Dunn, L.J.Mueller, L.Fan. Crystal Structure of Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site and [3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl] -Serine (Pls) at the Beta-Site. To Be Published.
Page generated: Sat Jul 27 21:59:37 2024

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