Atomistry » Sodium » PDB 2bii-2c8x » 2c19
Atomistry »
  Sodium »
    PDB 2bii-2c8x »
      2c19 »

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: Mon Oct 7 02:03:57 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