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Zinc in PDB 1w54: Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C)

Enzymatic activity of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C)

All present enzymatic activity of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C):
4.2.1.24;

Protein crystallography data

The structure of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C), PDB code: 1w54 was solved by F.Frere, H.Reents, W.-D.Schubert, D.W.Heinz, D.Jahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.71 / 2.20
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.231, 125.232, 86.030, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 21.7

Other elements in 1w54:

The structure of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C) (pdb code 1w54). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C), PDB code: 1w54:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1w54

Go back to Zinc Binding Sites List in 1w54
Zinc binding site 1 out of 2 in the Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1340

b:38.2
occ:0.50
 OD2 A:ASP131 1.8 49.5 1.0
O A:HOH2177 2.1 28.3 1.0
SG A:CYS139 2.4 59.7 1.0
O A:HOH2178 2.7 36.2 1.0
CG A:ASP131 2.9 43.4 1.0
CB A:CYS139 3.3 50.9 1.0
CB A:ALA129 3.5 22.9 1.0
CB A:ASP131 3.7 35.9 1.0
OD1 A:ASP131 3.9 53.6 1.0
CA A:CYS139 3.9 46.7 1.0
O A:HOH2106 4.1 45.6 1.0
CA A:ASP176 4.1 35.5 1.0
N A:ASP131 4.2 27.6 1.0
OG A:SER175 4.2 18.1 1.0
O A:SER175 4.3 32.2 1.0
N A:ASP176 4.4 24.5 1.0
CA A:ALA129 4.5 21.8 1.0
C A:SER175 4.5 22.5 1.0
CA A:ASP131 4.5 31.4 1.0
O A:HOH2083 4.6 41.1 1.0
N A:LEU130 4.6 25.4 1.0
NZ A:LYS205 4.7 43.9 1.0
CB A:ASP176 4.8 33.7 1.0
N A:CYS139 4.8 37.5 1.0
C A:ALA129 5.0 21.1 1.0
C A:CYS139 5.0 39.9 1.0

Zinc binding site 2 out of 2 in 1w54

Go back to Zinc Binding Sites List in 1w54
Zinc binding site 2 out of 2 in the Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Stepwise Introduction of A Zinc Binding Site Into Porphobilinogen Synthase From Pseudomonas Aeruginosa (Mutation D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1340

b:74.0
occ:0.50
 OD2 B:ASP131 2.1 78.1 1.0
CG B:ASP131 3.3 74.0 1.0
SG B:CYS139 3.3 0.5 1.0
CB B:ALA129 3.6 54.7 1.0
OG B:SER175 3.7 46.0 1.0
O B:HOH2080 4.0 50.9 1.0
O B:SER175 4.0 50.6 1.0
OD1 B:ASP131 4.0 77.0 1.0
NZ B:LYS205 4.0 49.5 1.0
CB B:CYS139 4.1 1.0 1.0
CA B:ASP176 4.1 64.8 1.0
C B:SER175 4.3 49.4 1.0
N B:ASP176 4.3 55.8 1.0
CB B:ASP131 4.3 69.7 1.0
CB B:SER175 4.7 49.2 1.0
CA B:ALA129 4.8 52.4 1.0
CA B:CYS139 4.9 99.7 1.0
N B:ASP131 4.9 62.9 1.0
CB B:ASP176 5.0 69.7 1.0

Reference:

F.Frere, H.Reents, W.-D.Schubert, D.W.Heinz, D.Jahn. Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro J.Mol.Biol. V. 345 1059 2005.
ISSN: ISSN 0022-2836
PubMed: 15644204
DOI: 10.1016/J.JMB.2004.10.053
Page generated: Tue Aug 19 23:54:19 2025

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