Sodium in PDB 6q9p: Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh:
3.5.3.1;

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh, PDB code: 6q9p was solved by Y.Grobben, J.C.M.Uitdehaag, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.99 / 1.66
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	89.980, 89.980, 69.131, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 17.8

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh (pdb code 6q9p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh, PDB code: 6q9p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.2 occ:1.00 OD2 A:ASP234 2.2 19.2 1.0 O3 A:ABH403 2.2 20.8 1.0 O A:HOH593 2.3 19.3 1.0 OD2 A:ASP232 2.5 18.2 1.0 OD1 A:ASP232 2.6 15.5 1.0 CG A:ASP232 2.9 16.4 1.0 CG A:ASP234 3.1 16.5 1.0 MN A:MN402 3.2 18.5 1.0 CG A:GLU277 3.3 17.2 1.0 B A:ABH403 3.3 23.1 1.0 CD A:GLU277 3.5 20.6 1.0 OG1 A:THR246 3.5 21.2 1.0 CB A:GLU277 3.5 17.0 1.0 O A:HOH639 3.5 27.0 1.0 O2 A:ABH403 3.6 26.8 1.0 O1 A:ABH403 3.7 21.2 1.0 OE1 A:GLU277 3.8 23.1 1.0 CB A:ASP234 3.8 16.2 1.0 OE2 A:GLU277 3.9 18.4 1.0 OD1 A:ASP234 4.0 13.7 1.0 MN A:MN401 4.2 17.2 1.0 OG1 A:THR244 4.3 16.5 1.0 CB A:ASP232 4.4 16.4 1.0 CE A:ABH403 4.7 21.4 1.0 ND1 A:HIS126 4.7 16.4 1.0 N A:ASP234 4.7 15.5 1.0 CB A:THR246 4.8 18.3 1.0 N A:THR246 4.9 17.8 1.0 OD1 A:ASP124 4.9 17.2 1.0 CA A:ASP234 4.9 15.8 1.0 ND1 A:HIS141 4.9 17.7 1.0 CE1 A:HIS126 4.9 14.9 1.0 O A:HOH511 5.0 18.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:38.4 occ:1.00 O3 B:ABH403 2.1 23.0 1.0 O B:HOH536 2.4 22.5 1.0 OD2 B:ASP234 2.4 20.9 1.0 OD2 B:ASP232 2.5 16.9 1.0 OD1 B:ASP232 2.7 16.9 1.0 CG B:ASP232 2.9 18.1 1.0 MN B:MN402 3.1 21.7 1.0 CG B:ASP234 3.1 17.7 1.0 B B:ABH403 3.3 20.6 1.0 OG1 B:THR246 3.3 21.8 1.0 CG B:GLU277 3.4 21.9 1.0 CD B:GLU277 3.5 22.1 1.0 O B:HOH598 3.5 29.5 1.0 O2 B:ABH403 3.6 23.4 1.0 CB B:GLU277 3.6 20.9 1.0 OE1 B:GLU277 3.8 25.6 1.0 O1 B:ABH403 3.8 18.0 1.0 OD1 B:ASP234 3.8 16.4 1.0 CB B:ASP234 3.8 16.0 1.0 OE2 B:GLU277 4.0 24.1 1.0 MN B:MN401 4.2 20.3 1.0 OG1 B:THR244 4.3 21.0 1.0 CB B:ASP232 4.4 17.0 1.0 CE B:ABH403 4.6 20.8 1.0 CB B:THR246 4.7 18.7 1.0 ND1 B:HIS126 4.8 17.5 1.0 OD1 B:ASP124 4.8 18.5 1.0 N B:ASP234 4.8 15.2 1.0 ND1 B:HIS141 4.9 18.5 1.0 CA B:ASP234 4.9 15.9 1.0 O B:HOH575 5.0 20.7 1.0 CE1 B:HIS126 5.0 16.5 1.0 N B:THR246 5.0 18.6 1.0

Y.Grobben, J.C.M.Uitdehaag, G.J.R.Zaman. Structural Insights Into Human Arginase-1 pH Dependence and Its Inhibition By the Small Molecule Inhibitor Cb-1158 J.Struct.Biol. 2019.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.YJSBX.2019.100014