Sodium in PDB 6qaf: Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158:
3.5.3.1;

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158, PDB code: 6qaf was solved by Y.Grobben, J.C.M.Uitdehaag, W.W.A.Tabak, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.74 / 1.61
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	90.130, 90.130, 69.111, 90.00, 90.00, 120.00
R / Rfree (%)	14.7 / 17.7

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 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 Cb- 1158/INCB001158 (pdb code 6qaf). 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 Cb- 1158/INCB001158, PDB code: 6qaf:
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 Cb- 1158/INCB001158


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 Cb- 1158/INCB001158 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:HOH586 2.2 19.6 1.0 OD2 A:ASP234 2.4 15.2 1.0 O11 A:XC3403 2.5 18.0 1.0 OD1 A:ASP232 2.5 15.9 1.0 OD2 A:ASP232 2.7 16.8 1.0 CG A:GLU277 3.0 17.0 1.0 CG A:ASP232 3.0 14.9 1.0 CB A:GLU277 3.2 16.5 1.0 CG A:ASP234 3.3 15.0 1.0 CD A:GLU277 3.3 18.4 1.0 MN A:MN402 3.3 18.1 1.0 OG1 A:THR246 3.5 18.0 1.0 O A:HOH639 3.5 27.7 1.0 B9 A:XC3403 3.6 18.8 1.0 O10 A:XC3403 3.6 18.7 1.0 OE1 A:GLU277 3.6 20.4 1.0 OE2 A:GLU277 3.8 17.3 1.0 CB A:ASP234 3.9 15.0 1.0 OD1 A:ASP234 4.0 15.7 1.0 OG1 A:THR244 4.1 16.6 1.0 O12 A:XC3403 4.1 18.5 1.0 MN A:MN401 4.4 17.1 1.0 CB A:ASP232 4.5 15.0 1.0 N A:ASP234 4.7 14.4 1.0 CA A:GLU277 4.7 16.5 1.0 O A:HOH531 4.7 17.7 1.0 CB A:THR246 4.8 16.4 1.0 N A:THR246 4.9 15.5 1.0 C8 A:XC3403 4.9 18.7 1.0 CA A:ASP234 4.9 14.7 1.0 ND1 A:HIS126 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158


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 Cb- 1158/INCB001158 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:30.0 occ:1.00 O11 B:XC3403 2.2 19.2 1.0 O B:HOH531 2.2 19.7 1.0 OD2 B:ASP234 2.4 14.9 1.0 OD2 B:ASP232 2.7 16.6 1.0 OD1 B:ASP232 2.7 15.3 1.0 CG B:GLU277 3.0 20.3 1.0 CG B:ASP232 3.1 16.3 1.0 O B:HOH584 3.2 24.9 1.0 MN B:MN402 3.2 18.9 1.0 CB B:GLU277 3.3 19.4 1.0 CG B:ASP234 3.3 14.7 1.0 CD B:GLU277 3.3 21.5 1.0 OG1 B:THR246 3.3 20.7 1.0 B9 B:XC3403 3.4 18.2 1.0 OE1 B:GLU277 3.5 24.6 1.0 O10 B:XC3403 3.6 19.3 1.0 OE2 B:GLU277 3.9 21.6 1.0 OD1 B:ASP234 3.9 13.8 1.0 CB B:ASP234 4.0 14.0 1.0 O12 B:XC3403 4.0 17.8 1.0 OG1 B:THR244 4.1 17.8 1.0 MN B:MN401 4.4 18.0 1.0 O B:HOH502 4.6 22.1 1.0 CB B:ASP232 4.6 16.2 1.0 C8 B:XC3403 4.7 19.1 1.0 CB B:THR246 4.7 18.6 1.0 CA B:GLU277 4.7 18.2 1.0 N B:ASP234 4.8 14.5 1.0 N B:THR246 4.8 18.3 1.0 ND1 B:HIS126 4.9 16.4 1.0 ND1 B:HIS141 5.0 17.8 1.0

Y.Grobben, J.C.M.Uitdehaag, W.W.A.Tabak, G.J.R.Zaman. Structural Insights Into Human Arginase-1 pH Dependence and Its Inhibition By the Small Molecule Inhibitor Cb-1158 Journal of Structural 2019BIOLOGY: X.
ISSN: ESSN 2590-1524
DOI: 10.1016/J.YJSBX.2019.100014