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Magnesium 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:

Chlorine (Cl) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3obk

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Magnesium binding site 1 out of 8 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 Magnesium with other atoms in the Mg 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:Mg365

b:16.3
occ:1.00
 OE1 A:GLU252 1.9 18.7 1.0
O A:HOH466 2.0 11.1 1.0
O A:HOH423 2.1 5.5 1.0
O A:HOH416 2.2 4.0 1.0
O A:HOH422 2.2 8.8 1.0
O A:HOH403 2.4 8.7 1.0
CD A:GLU252 3.0 18.8 1.0
OE2 A:GLU252 3.4 21.0 1.0
O A:HOH598 3.6 21.6 1.0
NH1 A:ARG189 3.8 19.2 1.0
OD1 A:ASP256 3.8 14.7 1.0
O A:HOH359 3.9 5.7 1.0
O A:HOH479 4.0 8.5 1.0
CG A:GLU252 4.3 17.1 1.0
O A:MET186 4.3 15.1 1.0
OD2 A:ASP256 4.4 13.7 1.0
CB A:GLU252 4.5 16.6 1.0
OD1 A:ASP187 4.5 16.8 1.0
CG A:ASP256 4.5 14.7 1.0
CA A:GLU252 4.8 16.8 1.0
O A:GLU252 4.9 17.2 1.0
O A:SER211 4.9 16.7 1.0
CA A:ASP187 4.9 15.3 1.0
CZ A:ARG189 5.0 18.6 1.0
N A:GLY188 5.0 15.8 1.0

Magnesium binding site 2 out of 8 in 3obk

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Magnesium binding site 2 out of 8 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 Magnesium with other atoms in the Mg 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
B:Mg365

b:20.1
occ:1.00
 OE1 B:GLU252 1.9 22.7 1.0
O B:HOH469 2.1 8.2 1.0
O B:HOH467 2.1 14.5 1.0
O B:HOH397 2.2 11.5 1.0
O B:HOH521 2.2 13.4 1.0
O B:HOH468 2.4 25.7 1.0
CD B:GLU252 2.8 22.6 1.0
OE2 B:GLU252 3.2 24.6 1.0
NH2 B:ARG189 3.8 25.8 1.0
O B:MET186 4.0 24.3 1.0
CG B:GLU252 4.2 19.8 1.0
OD1 B:ASP256 4.2 20.4 1.0
OD1 B:ASP187 4.4 24.8 1.0
O B:HOH363 4.4 2.0 1.0
OD2 B:ASP256 4.5 20.6 1.0
CB B:GLU252 4.5 19.4 1.0
O B:SER211 4.6 21.6 1.0
CG B:ASP256 4.8 18.7 1.0
SD B:MET185 4.8 23.5 1.0
CA B:ASP187 4.8 24.0 1.0
CA B:GLU252 4.8 19.5 1.0
C B:MET186 4.9 24.0 1.0
CZ B:ARG189 4.9 24.8 1.0

Magnesium binding site 3 out of 8 in 3obk

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Magnesium binding site 3 out of 8 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 Magnesium with other atoms in the Mg 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
C:Mg365

b:17.9
occ:1.00
 O C:HOH417 1.9 4.6 1.0
O C:HOH387 2.1 2.0 1.0
OE1 C:GLU252 2.1 19.9 1.0
O C:HOH415 2.2 28.1 1.0
O C:HOH388 2.2 2.0 1.0
O C:HOH416 2.3 10.3 1.0
CD C:GLU252 3.2 19.3 1.0
OE2 C:GLU252 3.6 20.9 1.0
NH1 C:ARG189 3.6 21.1 1.0
OD1 C:ASP256 3.9 16.9 1.0
O C:HOH412 4.0 5.0 1.0
O C:HOH391 4.0 2.0 1.0
O C:MET186 4.0 18.6 1.0
OD2 C:ASP256 4.3 14.5 1.0
OD1 C:ASP187 4.5 19.4 1.0
CG C:ASP256 4.5 15.4 1.0
CG C:GLU252 4.5 18.0 1.0
CA C:ASP187 4.8 18.6 1.0
CB C:GLU252 4.8 17.2 1.0
CZ C:ARG189 4.8 21.9 1.0
O C:SER211 4.9 17.1 1.0
O C:GLU252 4.9 17.3 1.0
SD C:MET185 4.9 16.7 1.0
C C:MET186 4.9 18.2 1.0
CA C:GLU252 5.0 17.5 1.0
CE C:MET185 5.0 16.2 1.0

Magnesium binding site 4 out of 8 in 3obk

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Magnesium binding site 4 out of 8 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 Magnesium with other atoms in the Mg 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
D:Mg365

b:32.8
occ:1.00
 O D:HOH530 1.9 5.1 1.0
OE1 D:GLU252 1.9 24.1 1.0
O D:HOH402 1.9 13.5 1.0
O D:HOH593 2.1 11.2 0.5
O D:HOH403 2.2 4.0 1.0
O D:HOH592 2.3 2.0 0.5
CD D:GLU252 3.0 22.4 1.0
OE2 D:GLU252 3.5 23.9 1.0
NH1 D:ARG189 3.5 24.8 1.0
O D:HOH410 3.9 14.5 1.0
O D:MET186 4.0 21.2 1.0
OD1 D:ASP256 4.1 19.8 1.0
O D:HOH409 4.2 8.8 1.0
OD2 D:ASP256 4.3 18.2 1.0
CG D:GLU252 4.3 20.4 1.0
CB D:GLU252 4.5 19.8 1.0
OD1 D:ASP187 4.6 22.4 1.0
CG D:ASP256 4.6 17.6 1.0
O D:SER211 4.7 20.3 1.0
CA D:ASP187 4.8 21.7 1.0
CZ D:ARG189 4.8 24.6 1.0
CA D:GLU252 4.9 19.7 1.0
SD D:MET185 4.9 20.3 1.0
C D:MET186 4.9 21.6 1.0

Magnesium binding site 5 out of 8 in 3obk

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Magnesium binding site 5 out of 8 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 Magnesium with other atoms in the Mg 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
E:Mg365

b:31.4
occ:1.00
 O E:HOH406 1.8 21.9 1.0
OE1 E:GLU252 1.9 24.1 1.0
O E:HOH460 1.9 14.3 1.0
O E:HOH459 2.0 17.5 1.0
O E:HOH407 2.1 5.9 1.0
O E:HOH458 2.4 3.2 1.0
CD E:GLU252 3.0 21.6 1.0
OE2 E:GLU252 3.5 22.9 1.0
NH1 E:ARG189 3.5 24.7 1.0
OD1 E:ASP256 3.9 18.2 1.0
O E:MET186 4.1 21.4 1.0
O E:HOH373 4.2 2.0 1.0
OD2 E:ASP256 4.3 17.4 1.0
CG E:GLU252 4.3 19.9 1.0
CB E:GLU252 4.4 19.4 1.0
CG E:ASP256 4.5 17.1 1.0
CE E:MET185 4.6 22.5 1.0
O E:SER211 4.7 20.8 1.0
OD1 E:ASP187 4.7 23.1 1.0
CZ E:ARG189 4.8 24.6 1.0
SD E:MET185 4.8 22.1 1.0
CA E:GLU252 4.8 19.3 1.0
O E:GLU252 5.0 18.8 1.0

Magnesium binding site 6 out of 8 in 3obk

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Magnesium binding site 6 out of 8 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 Magnesium with other atoms in the Mg 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
F:Mg365

b:35.5
occ:1.00
 O F:HOH451 2.1 12.6 1.0
O F:HOH594 2.1 9.6 0.5
O F:HOH386 2.2 2.0 1.0
O F:HOH405 2.3 16.0 1.0
OE1 F:GLU252 2.3 22.1 1.0
O F:HOH378 2.7 13.9 1.0
CD F:GLU252 3.3 21.2 1.0
NH1 F:ARG189 3.4 23.1 1.0
O F:HOH379 3.4 9.7 1.0
OE2 F:GLU252 3.5 23.8 1.0
O F:MET186 3.8 20.9 1.0
OD1 F:ASP256 4.2 20.2 1.0
OD2 F:ASP256 4.4 19.6 1.0
OD1 F:ASP187 4.4 19.7 1.0
CA F:ASP187 4.6 20.8 1.0
C F:MET186 4.6 20.9 1.0
CZ F:ARG189 4.6 24.3 1.0
CG F:GLU252 4.7 19.9 1.0
CG F:ASP256 4.7 18.1 1.0
N F:GLY188 4.9 20.0 1.0
N F:ASP187 5.0 20.7 1.0
O F:MET185 5.0 21.5 1.0

Magnesium binding site 7 out of 8 in 3obk

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Magnesium binding site 7 out of 8 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 Magnesium with other atoms in the Mg 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
G:Mg365

b:34.4
occ:1.00
 OE1 G:GLU252 1.8 26.3 1.0
O G:HOH461 2.0 13.5 1.0
O G:HOH463 2.1 10.3 1.0
O G:HOH595 2.1 2.0 0.5
O G:HOH532 2.2 9.5 1.0
O G:HOH405 2.5 20.6 1.0
CD G:GLU252 3.0 23.8 1.0
OE2 G:GLU252 3.5 26.0 1.0
O G:HOH366 3.6 4.2 1.0
NH1 G:ARG189 4.0 27.1 1.0
OD1 G:ASP256 4.1 22.4 1.0
CG G:GLU252 4.2 22.8 1.0
O G:MET186 4.2 24.3 1.0
O G:HOH377 4.3 8.2 1.0
CB G:GLU252 4.3 21.8 1.0
OD1 G:ASP187 4.4 25.7 1.0
OD2 G:ASP256 4.4 21.9 1.0
CG G:ASP256 4.7 19.8 1.0
CA G:GLU252 4.7 21.4 1.0
O G:SER211 4.7 22.0 1.0
CA G:ASP187 4.9 26.0 1.0
SD G:MET185 4.9 22.9 1.0
O G:GLU252 4.9 21.4 1.0

Magnesium binding site 8 out of 8 in 3obk

Go back to Magnesium Binding Sites List in 3obk
Magnesium binding site 8 out of 8 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 Magnesium with other atoms in the Mg 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
H:Mg365

b:21.7
occ:1.00
 O H:HOH526 1.8 17.4 1.0
OE1 H:GLU252 1.9 24.9 1.0
O H:HOH465 1.9 16.9 1.0
O H:HOH452 2.1 4.5 1.0
O H:HOH597 2.2 2.0 0.5
O H:HOH393 2.4 27.0 1.0
CD H:GLU252 2.9 24.4 1.0
OE2 H:GLU252 3.2 27.3 1.0
O H:HOH522 3.7 17.9 1.0
NH1 H:ARG189 3.7 25.6 1.0
O H:HOH533 3.9 13.9 1.0
OD1 H:ASP256 3.9 19.9 1.0
O H:MET186 4.0 23.1 1.0
CG H:GLU252 4.3 21.6 1.0
OD1 H:ASP187 4.4 23.1 1.0
CB H:GLU252 4.6 20.6 1.0
CG H:ASP256 4.7 19.5 1.0
OD2 H:ASP256 4.7 20.8 1.0
C H:MET186 4.8 22.9 1.0
CA H:GLU252 4.8 20.9 1.0
CA H:ASP187 4.8 23.6 1.0
CZ H:ARG189 4.9 24.6 1.0
O H:GLU252 4.9 21.6 1.0
CE H:MET185 4.9 21.4 1.0
O H:SER211 5.0 21.2 1.0
SD H:MET185 5.0 24.0 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: Mon Dec 14 08:31:37 2020

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