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Chlorine in PDB 3obk: Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen

Enzymatic activity of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen

All present enzymatic activity of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen:
4.2.1.24;

Protein crystallography data

The structure of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen, PDB code: 3obk was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.93 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 177.110, 187.170, 95.860, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.2

Other elements in 3obk:

The structure of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen (pdb code 3obk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen, PDB code: 3obk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in 3obk

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Chlorine binding site 1 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl400

b:49.9
occ:1.00
 O A:HOH401 3.6 6.1 1.0
O A:HOH438 4.0 2.0 1.0
CD1 C:TYR356 4.2 14.3 1.0
CB A:PHE351 4.5 16.4 1.0
CE1 C:TYR356 4.6 14.7 1.0
CD1 A:PHE351 4.6 14.8 1.0
CG A:PHE351 4.8 16.1 1.0
CB A:LEU315 4.9 11.2 1.0
CD1 A:LEU315 4.9 11.4 1.0

Chlorine binding site 2 out of 16 in 3obk

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Chlorine binding site 2 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:47.1
occ:1.00
 OD1 A:ASP204 3.5 34.5 1.0
CB C:ARG24 4.0 16.6 1.0
CG C:ARG25 4.2 16.8 1.0
N C:ARG25 4.3 15.4 1.0
C C:ARG24 4.4 15.5 1.0
CD C:ARG22 4.6 21.8 1.0
CA A:ASP204 4.6 20.9 1.0
CA C:ARG25 4.6 15.7 1.0
O A:THR203 4.6 20.9 1.0
CG A:ASP204 4.6 26.9 1.0
OD2 D:ASP187 4.8 23.7 1.0
O C:ARG24 4.8 14.4 1.0
CA C:ARG24 4.8 15.8 1.0
CB C:ARG22 4.9 19.8 1.0
NE C:ARG24 5.0 19.2 1.0
CZ C:ARG24 5.0 18.1 1.0

Chlorine binding site 3 out of 16 in 3obk

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Chlorine binding site 3 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:39.6
occ:1.00
 O A:HOH364 3.4 6.5 1.0
CB B:ARG24 3.8 12.1 1.0
CG B:ARG25 4.1 11.7 1.0
OD1 E:ASP204 4.1 34.9 1.0
N B:ARG25 4.2 11.2 1.0
C B:ARG24 4.3 11.3 1.0
O A:HOH398 4.4 2.9 1.0
O A:HOH431 4.4 2.2 1.0
CA B:ARG25 4.5 11.8 1.0
O E:THR203 4.5 22.2 1.0
CA E:ASP204 4.6 22.9 1.0
O B:ARG24 4.6 11.0 1.0
CD B:ARG22 4.6 14.8 1.0
CA B:ARG24 4.7 11.8 1.0
OD2 A:ASP187 4.8 18.0 1.0
NE B:ARG24 4.9 12.9 1.0
CB B:ARG25 4.9 11.9 1.0
CB B:ARG22 5.0 14.3 1.0
CZ B:ARG24 5.0 13.2 1.0

Chlorine binding site 4 out of 16 in 3obk

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Chlorine binding site 4 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl400

b:50.5
occ:1.00
 O B:HOH374 3.6 2.0 1.0
O B:HOH398 3.9 8.5 1.0
CD1 E:TYR356 4.3 13.2 1.0
CD1 B:PHE351 4.3 15.6 1.0
CB B:PHE351 4.5 17.6 1.0
O A:HOH528 4.5 6.4 1.0
CE1 E:TYR356 4.6 13.3 1.0
CG B:PHE351 4.6 16.8 1.0
CD1 B:LEU315 4.7 11.8 1.0
CB B:LEU315 4.8 11.2 1.0

Chlorine binding site 5 out of 16 in 3obk

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Chlorine binding site 5 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl395

b:62.2
occ:1.00
 OE1 A:GLN349 4.1 32.4 1.0
O C:SER84 4.1 18.4 1.0
O C:ARG83 4.1 18.3 1.0
O A:HOH413 4.2 10.8 1.0
CA C:GLY86 4.3 13.5 1.0
N C:GLY86 4.3 14.4 1.0
C C:SER84 4.6 17.7 1.0
CD A:GLN349 4.7 31.3 1.0
NE2 A:GLN349 4.8 31.8 1.0
C C:TYR85 4.9 15.3 1.0
O C:HOH363 5.0 5.0 1.0

Chlorine binding site 6 out of 16 in 3obk

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Chlorine binding site 6 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl400

b:59.1
occ:1.00
 O C:HOH420 3.3 2.0 1.0
CD1 C:LEU315 4.1 13.4 1.0
CB C:LEU315 4.2 12.3 1.0
CD1 C:PHE351 4.4 15.2 1.0
O C:HOH403 4.5 8.9 1.0
CD1 A:TYR356 4.6 11.5 1.0
CG C:PHE351 4.6 16.7 1.0
CB C:PHE351 4.7 18.4 1.0
CE1 A:TYR356 4.8 13.0 1.0
CG C:LEU315 4.8 14.0 1.0

Chlorine binding site 7 out of 16 in 3obk

Go back to Chlorine Binding Sites List in 3obk
Chlorine binding site 7 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:40.6
occ:1.00
 O C:HOH369 3.4 2.0 1.0
CB D:ARG24 3.9 14.8 1.0
CG D:ARG25 4.1 13.9 1.0
N D:ARG25 4.2 14.3 1.0
C D:ARG24 4.3 14.5 1.0
O C:HOH422 4.4 11.1 1.0
O H:THR203 4.5 24.6 1.0
CD D:ARG22 4.5 18.0 1.0
CA D:ARG25 4.5 15.0 1.0
CA H:ASP204 4.6 25.6 1.0
O D:ARG24 4.7 14.3 1.0
O C:HOH376 4.7 2.0 1.0
CA D:ARG24 4.7 14.5 1.0
OD2 C:ASP187 4.7 18.5 1.0
CB D:ARG22 4.8 16.7 1.0
OD1 H:ASP204 4.9 36.5 1.0
CB D:ARG25 4.9 14.8 1.0
N H:ASP204 4.9 25.7 1.0
C H:THR203 4.9 25.0 1.0
NE D:ARG24 4.9 15.0 1.0
CG H:ASP204 5.0 31.1 1.0
CD D:ARG24 5.0 14.4 1.0

Chlorine binding site 8 out of 16 in 3obk

Go back to Chlorine Binding Sites List in 3obk
Chlorine binding site 8 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


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 Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl400

b:50.9
occ:1.00
 O D:HOH505 3.3 4.8 1.0
O D:HOH377 3.5 2.0 1.0
CD1 H:TYR356 4.0 14.7 1.0
O H:HOH540 4.3 16.7 1.0
O C:HOH378 4.3 6.8 1.0
CE1 H:TYR356 4.3 14.1 1.0
CB D:LEU315 4.6 13.4 1.0
CD1 D:PHE351 4.7 15.7 1.0
CD1 D:LEU315 4.7 14.4 1.0
CB D:PHE351 4.8 16.0 1.0
CG D:PHE351 4.9 15.6 1.0
CG H:TYR356 5.0 14.3 1.0

Chlorine binding site 9 out of 16 in 3obk

Go back to Chlorine Binding Sites List in 3obk
Chlorine binding site 9 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl395

b:52.2
occ:1.00
 O E:HOH380 3.5 2.0 1.0
O E:ARG83 4.2 21.6 1.0
O E:SER84 4.3 21.1 1.0
CA E:GLY86 4.3 16.0 1.0
N E:GLY86 4.4 16.6 1.0
CD B:GLN349 4.5 34.7 1.0
NE2 B:GLN349 4.5 37.1 1.0
CG B:GLN349 4.7 32.0 1.0
C E:SER84 4.8 20.9 1.0
OE1 B:GLN349 4.9 36.2 1.0
C E:TYR85 4.9 17.8 1.0
O E:HOH358 4.9 2.0 1.0

Chlorine binding site 10 out of 16 in 3obk

Go back to Chlorine Binding Sites List in 3obk
Chlorine binding site 10 out of 16 in the Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Delta-Aminolevulinic Acid Dehydratase (Porphobilinogen Synthase) From Toxoplasma Gondii ME49 in Complex with the Reaction Product Porphobilinogen within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl400

b:57.5
occ:1.00
 O E:HOH520 3.6 2.0 1.0
O E:HOH385 4.1 2.0 1.0
CD1 B:TYR356 4.2 15.2 1.0
CD1 E:PHE351 4.3 15.6 1.0
CB E:PHE351 4.3 19.1 1.0
CG E:PHE351 4.5 17.8 1.0
CE1 B:TYR356 4.5 15.5 1.0
CB E:LEU315 4.5 14.1 1.0
CD2 E:LEU315 4.7 14.3 1.0
CG E:LEU315 4.9 14.3 1.0

Reference:

E.K.Jaffe, D.Shanmugam, A.Gardberg, S.Dieterich, B.Sankaran, L.J.Stewart, P.J.Myler, D.S.Roos. Crystal Structure of Toxoplasma Gondii Porphobilinogen Synthase: Insights on Octameric Structure and Porphobilinogen Formation. J.Biol.Chem. V. 286 15298 2011.
ISSN: ISSN 0021-9258
PubMed: 21383008
DOI: 10.1074/JBC.M111.226225
Page generated: Fri Jul 11 08:38:10 2025

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