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Sodium in PDB 2c18: 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

Enzymatic activity of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa:
4.2.1.24;

Protein crystallography data

The structure of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c18 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 / 1.93
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.596, 125.596, 86.573, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.6

Other elements in 2c18:

The structure of 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa (pdb code 2c18). 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-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa, PDB code: 2c18:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2c18

Go back to Sodium Binding Sites List in 2c18
Sodium binding site 1 out of 2 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1339

b:20.7
occ:1.00
OD1 A:ASP37 2.2 16.5 1.0
O A:ASP319 2.2 14.7 1.0
C A:ASP319 3.3 15.1 1.0
CG A:ASP37 3.4 16.6 1.0
CA A:ASP319 3.9 15.0 1.0
CA A:ASP37 3.9 17.0 1.0
O A:ASP36 4.0 17.9 1.0
CB A:ASP37 4.1 16.6 1.0
O A:HOH2073 4.1 25.2 1.0
N A:ASP37 4.3 17.1 1.0
CB A:ASP319 4.3 14.7 1.0
C A:ASP36 4.4 17.4 1.0
O A:HOH2076 4.4 39.1 1.0
O A:HOH2306 4.4 36.7 1.0
OD2 A:ASP37 4.4 14.9 1.0
N A:GLY320 4.4 14.6 1.0
CE A:LYS314 4.5 17.2 1.0
CA A:GLY320 4.8 14.3 1.0
CB A:ASP36 4.8 18.3 1.0
NZ A:LYS314 4.9 17.2 1.0

Sodium binding site 2 out of 2 in 2c18

Go back to Sodium Binding Sites List in 2c18
Sodium binding site 2 out of 2 in the 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic 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-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid Bound to Porphobilinogen Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1339

b:22.1
occ:1.00
O B:HOH2085 2.2 50.6 1.0
O B:ASP319 2.2 15.1 1.0
OD1 B:ASP37 2.3 16.5 1.0
C B:ASP319 3.3 14.5 1.0
CG B:ASP37 3.5 15.8 1.0
CA B:ASP319 3.8 14.1 1.0
CA B:ASP37 4.0 16.3 1.0
O B:ASP36 4.1 16.2 1.0
CB B:ASP37 4.1 16.1 1.0
O B:HOH2076 4.3 24.8 1.0
CB B:ASP319 4.3 13.7 1.0
N B:ASP37 4.4 15.1 1.0
O B:HOH2082 4.4 35.4 1.0
N B:GLY320 4.4 13.7 1.0
C B:ASP36 4.4 15.3 1.0
OD2 B:ASP37 4.4 17.7 1.0
CE B:LYS314 4.5 18.4 1.0
NZ B:LYS314 4.6 15.3 1.0
CA B:GLY320 4.7 13.8 1.0
CB B:ASP36 4.9 16.4 1.0
OD1 B:ASP319 5.0 17.0 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 05:46:25 2020

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