Sodium in PDB 6xro: Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2

All present enzymatic activity of Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2:
3.4.21.105;

The structure of Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2, PDB code: 6xro was solved by S.Urban, S.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.08 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	111.710, 111.710, 124.380, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 24.7

The structure of Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2 (pdb code 6xro). 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 Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2, PDB code: 6xro:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2


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 Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:16.9 occ:1.00 O A:HOH622 2.4 37.1 1.0 CE A:MET249 3.0 43.2 1.0 O A:HOH630 3.0 37.4 1.0 NE2 A:HIS254 3.1 27.9 1.0 O A:HOH607 3.1 29.5 1.0 CE1 A:HIS254 3.3 22.7 1.0 O2 A:B2A501 3.3 50.7 1.0 O A:HOH621 3.3 31.9 1.0 CB A:SER201 3.6 13.3 1.0 OG A:SER201 3.9 17.6 1.0 NE1 A:TRP236 4.1 31.6 1.0 CD2 A:HIS254 4.2 25.6 1.0 B A:B2A501 4.3 21.7 1.0 ND1 A:HIS254 4.4 25.9 1.0 CE2 A:TYR205 4.4 26.8 1.0 OH A:TYR205 4.6 28.8 1.0 SD A:MET249 4.6 41.7 1.0 ND2 A:ASN154 4.7 18.3 1.0 CE2 A:PHE245 4.7 45.2 1.0 CD1 A:TRP236 4.7 34.9 1.0 NA A:NA505 4.8 24.1 1.0 O B:SER500 4.8 22.9 1.0 O1 A:B2A501 4.9 16.0 1.0 CE2 A:TRP236 4.9 41.4 1.0 CG A:HIS254 4.9 23.2 1.0 CZ A:TYR205 5.0 31.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2


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 Glpg in Complex with Peptide Boronate Inhibitor, Ac-Krfrsmqysa-B(Oh)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:24.1 occ:1.00 O A:HOH636 2.9 19.4 1.0 O1 A:B2A501 3.1 16.0 1.0 OD1 A:ASN154 3.1 23.2 1.0 O A:HOH622 3.3 37.1 1.0 CB A:HIS150 3.5 31.0 1.0 O2 A:B2A501 3.5 50.7 1.0 ND1 A:HIS150 3.6 51.0 1.0 CG A:HIS150 3.9 45.4 1.0 CD2 A:HIS145 3.9 15.5 1.0 CB B:SER500 3.9 24.5 1.0 B A:B2A501 4.0 21.7 1.0 CA A:GLY199 4.1 13.2 1.0 CG A:ASN154 4.2 20.1 1.0 O A:HOH630 4.4 37.4 1.0 OG B:SER500 4.4 39.5 1.0 C B:SER500 4.4 26.5 1.0 O A:GLY198 4.5 16.8 1.0 N A:B2A501 4.5 27.6 1.0 ND2 A:ASN154 4.6 18.3 1.0 CA B:SER500 4.6 26.6 1.0 CA A:HIS150 4.6 25.4 1.0 NE2 A:HIS145 4.7 18.8 1.0 CE1 A:HIS150 4.7 61.0 1.0 C A:GLY199 4.7 17.6 1.0 N A:LEU200 4.7 17.1 1.0 O A:HIS150 4.8 20.6 1.0 C A:HIS150 4.8 19.0 1.0 NA A:NA504 4.8 16.9 1.0 OG A:SER201 4.8 17.6 1.0 CB A:SER201 4.9 13.3 1.0 CG A:HIS145 4.9 16.2 1.0 O B:SER500 5.0 22.9 1.0 CA A:B2A501 5.0 19.9 1.0

S.Gandhi, R.P.Baker, S.Cho, S.Stanchev, K.Strisovsky, S.Urban. Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria. Cell Chem Biol V. 27 1410 2020.
ISSN: ESSN 2451-9456
PubMed: 32888502
DOI: 10.1016/J.CHEMBIOL.2020.08.011