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Sodium in PDB 2c19: 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

Enzymatic activity of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa:
4.2.1.24;

Protein crystallography data

The structure of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c19 was solved by F.Frere, M.Nentwich, S.Gacond, D.W.Heinz, R.Neier, N.Frankenberg-Dinkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.80 / 2.05
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.203, 127.203, 85.848, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 20.1

Other elements in 2c19:

The structure of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa (pdb code 2c19). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c19:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2c19

Go back to Sodium Binding Sites List in 2c19
Sodium binding site 1 out of 2 in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1337

b:19.7
occ:1.00
 O A:HOH2056 2.4 14.7 1.0
O A:LEU27 2.7 17.1 1.0
C A:LEU27 3.7 16.4 1.0
O A:ARG29 4.1 14.3 1.0
O A:ARG26 4.1 14.5 1.0
CA A:LEU27 4.3 15.7 1.0
N A:VAL28 4.7 14.6 1.0
C A:VAL28 4.9 15.4 1.0
N A:ARG29 5.0 14.9 1.0
CA A:VAL28 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 2c19

Go back to Sodium Binding Sites List in 2c19
Sodium binding site 2 out of 2 in the 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1338

b:18.6
occ:1.00
 O A:ASP319 2.3 13.5 1.0
OD1 A:ASP37 2.4 13.0 1.0
O A:HOH2322 2.7 2.0 0.5
C A:ASP319 3.3 14.0 1.0
CG A:ASP37 3.5 15.6 1.0
CA A:ASP37 3.8 15.7 1.0
CA A:ASP319 3.9 13.8 1.0
O A:ASP36 4.0 16.7 1.0
O A:HOH2318 4.0 19.7 1.0
CB A:ASP37 4.1 15.4 1.0
CB A:ASP319 4.1 13.6 1.0
O A:HOH2075 4.2 13.7 1.0
N A:ASP37 4.2 15.6 1.0
C A:ASP36 4.2 16.3 1.0
N A:GLY320 4.4 13.6 1.0
OD2 A:ASP37 4.5 15.3 1.0
O A:HOH2079 4.6 20.1 1.0
CE A:LYS314 4.7 15.0 1.0
CA A:GLY320 4.8 13.6 1.0
CB A:ASP36 4.8 16.6 1.0
NZ A:LYS314 4.8 14.4 1.0
OD1 A:ASP319 4.9 16.8 1.0

Reference:

F.Frere, M.Nentwich, S.Gacond, D.W.Heinz, R.Neier, N.Frankenberg-Dinkel. Probing the Active Site of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors. Biochemistry V. 45 8243 2006.
ISSN: ISSN 0006-2960
PubMed: 16819823
DOI: 10.1021/BI052611F
Page generated: Tue Dec 15 05:46:26 2020

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