Sodium in PDB 6q92: Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh:
3.5.3.1;

The structure of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh, PDB code: 6q92 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)	39.14 / 1.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.380, 90.380, 69.254, 90.00, 90.00, 120.00
R / Rfree (%)	13.5 / 14.7

The structure of Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh (pdb code 6q92). 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 7.0 in Complex with Abh, PDB code: 6q92:
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 7.0 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 7.0 in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:12.2 occ:1.00 O A:HOH600 2.1 12.7 1.0 OD2 A:ASP234 2.3 8.7 1.0 O3 A:ABH403 2.3 9.4 1.0 OD2 A:ASP232 2.5 7.2 1.0 OD1 A:ASP232 2.5 7.4 1.0 CG A:ASP232 2.8 7.3 1.0 CG A:ASP234 3.1 7.7 1.0 OG1 A:THR246 3.3 11.5 1.0 CG A:GLU277 3.4 9.9 1.0 B A:ABH403 3.4 9.9 1.0 MN A:MN402 3.4 6.2 1.0 CB A:GLU277 3.5 9.4 1.0 CD A:GLU277 3.6 11.0 1.0 CB A:ASP234 3.7 7.6 1.0 O1 A:ABH403 3.7 9.7 1.0 O2 A:ABH403 3.8 11.0 1.0 O A:HOH615 3.9 19.2 1.0 OE1 A:GLU277 4.0 13.2 1.0 OD1 A:ASP234 4.0 7.4 1.0 OE2 A:GLU277 4.1 11.0 1.0 MN A:MN401 4.2 7.8 1.0 OG1 A:THR244 4.2 9.7 1.0 CB A:ASP232 4.3 7.3 1.0 N A:ASP234 4.6 7.4 1.0 CB A:THR246 4.7 10.9 1.0 CA A:ASP234 4.7 7.3 1.0 CE A:ABH403 4.8 10.2 1.0 N A:THR246 4.8 11.1 1.0 ND1 A:HIS126 4.9 8.2 1.0 OD1 A:ASP124 4.9 6.7 1.0 O A:THR246 5.0 10.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Arginase-1 at pH 7.0 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 7.0 in Complex with Abh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:14.1 occ:1.00 O3 B:ABH403 2.2 11.8 1.0 O B:HOH569 2.3 13.5 1.0 OD2 B:ASP234 2.3 10.4 1.0 OD2 B:ASP232 2.5 8.7 1.0 OD1 B:ASP232 2.6 8.8 1.0 CG B:ASP232 2.9 9.0 1.0 CG B:ASP234 3.2 9.2 1.0 OG1 B:THR246 3.3 13.3 1.0 B B:ABH403 3.3 12.3 1.0 MN B:MN402 3.3 7.8 1.0 CG B:GLU277 3.4 13.0 1.0 CB B:GLU277 3.6 12.6 1.0 O1 B:ABH403 3.6 13.3 1.0 O2 B:ABH403 3.6 13.4 1.0 CD B:GLU277 3.7 13.7 1.0 CB B:ASP234 3.7 9.2 1.0 O B:HOH644 3.8 24.1 1.0 OD1 B:ASP234 4.1 10.1 1.0 OE2 B:GLU277 4.1 14.1 1.0 MN B:MN401 4.1 9.6 1.0 OE1 B:GLU277 4.1 15.8 1.0 OG1 B:THR244 4.3 11.5 1.0 CB B:ASP232 4.4 9.2 1.0 CE B:ABH403 4.7 12.9 1.0 N B:ASP234 4.7 9.2 1.0 CB B:THR246 4.7 12.3 1.0 ND1 B:HIS126 4.8 9.2 1.0 OD1 B:ASP124 4.8 7.7 1.0 CA B:ASP234 4.8 9.2 1.0 N B:THR246 4.8 11.6 1.0 O B:THR246 4.9 12.8 1.0 CE1 B:HIS126 5.0 9.0 1.0 O B:HOH510 5.0 13.4 1.0 ND1 B:HIS141 5.0 10.9 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