Atomistry » Magnesium » PDB 3o1n-3oha » 3obk
Atomistry »
  Magnesium »
    PDB 3o1n-3oha »
      3obk »

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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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

Go back to Magnesium Binding Sites List in 3obk
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: Thu Aug 15 08:14:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy