Sodium in PDB 6q4r: High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor

The structure of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor, PDB code: 6q4r was solved by P.Giastas, M.Neu, P.Rowland, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.45 / 1.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.683, 116.669, 147.267, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

The structure of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor (pdb code 6q4r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor, PDB code: 6q4r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1044 b:35.0 occ:1.00 H30 A:HJ51009 2.7 24.2 1.0 OG A:SER870 3.0 19.3 1.0 O A:HOH1489 3.0 28.8 0.7 NE2 A:GLN315 3.2 19.1 1.0 N A:SER870 3.2 17.3 1.0 OG A:SER868 3.5 18.9 0.1 N A:SER869 3.5 17.4 1.0 H7 A:HJ51009 3.6 33.6 1.0 C30 A:HJ51009 3.6 20.2 1.0 CG A:GLN315 3.7 17.4 1.0 CB A:SER870 3.8 18.4 1.0 CB A:SER869 3.8 23.5 1.0 H6 A:HJ51009 3.8 33.2 1.0 H29 A:HJ51009 3.8 25.7 1.0 CB A:SER868 3.9 17.0 0.1 CD A:GLN315 3.9 20.9 1.0 CB A:SER868 3.9 16.4 0.9 CA A:SER869 4.0 19.3 1.0 C A:SER869 4.0 18.6 1.0 CA A:SER870 4.0 13.3 1.0 C7 A:HJ51009 4.1 28.0 1.0 C29 A:HJ51009 4.2 21.4 1.0 C6 A:HJ51009 4.2 27.7 1.0 C A:SER868 4.3 17.3 1.0 O A:HOH1523 4.3 26.6 0.8 CA A:SER868 4.5 15.4 0.9 CA A:SER868 4.5 16.7 0.1 OG A:SER868 4.5 15.8 0.9 OG A:SER869 4.6 26.3 1.0 O A:HOH1493 4.7 26.1 0.9 C31 A:HJ51009 4.7 21.3 1.0 H31 A:HJ51009 4.8 25.6 1.0 O A:GLN315 4.9 17.1 1.0 CB A:GLN315 4.9 12.2 1.0 O A:HOH1274 4.9 25.5 1.0

Sodium binding site 2 out of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1045 b:35.0 occ:1.00 O A:HOH1401 2.9 16.5 1.0 OG A:SER316 2.9 13.7 0.6 N A:SER316 3.0 12.8 1.0 H5 A:HJ51009 3.2 29.4 1.0 CE2 A:PHE314 3.4 17.7 1.0 N A:GLN315 3.4 13.9 1.0 H6 A:HJ51009 3.5 33.2 1.0 CB A:GLN315 3.5 12.2 1.0 CB A:SER316 3.6 15.7 0.6 CD2 A:PHE314 3.7 14.6 1.0 CZ A:PHE314 3.7 15.0 1.0 CB A:SER316 3.7 15.9 0.4 CG A:GLN181 3.7 18.7 1.0 CA A:GLN315 3.8 16.1 1.0 CD A:GLN181 3.8 19.1 1.0 C A:GLN315 3.8 18.9 1.0 OE1 A:GLN181 3.8 16.8 1.0 CA A:SER316 3.9 14.6 0.6 CA A:SER316 3.9 14.7 0.4 C5 A:HJ51009 4.0 24.5 1.0 C6 A:HJ51009 4.1 27.7 1.0 CE1 A:PHE314 4.2 16.9 1.0 CG A:PHE314 4.2 14.1 1.0 O A:HOH1663 4.5 51.0 1.0 CD1 A:PHE314 4.5 14.1 1.0 NE2 A:GLN181 4.5 19.0 1.0 C A:PHE314 4.5 13.0 1.0 CB A:GLN181 4.5 16.9 1.0 O A:PHE159 4.6 15.9 1.0 C A:SER316 4.6 15.4 1.0 CG A:GLN315 4.6 17.4 1.0 O A:SER316 4.7 15.7 1.0 CA A:PHE314 5.0 13.8 1.0

Sodium binding site 3 out of 3 in the High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Crystal Structure of ERAP1 with Bound Phosphinic Transition-State Analogue Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1046 b:35.0 occ:1.00 O A:HOH1853 2.7 27.1 1.0 OE2 A:GLU431 2.8 22.3 1.0 O A:HOH1600 2.9 21.6 1.0 N A:CYS907 3.1 17.0 1.0 SG A:CYS907 3.4 19.4 1.0 CB A:CYS907 3.5 20.1 1.0 CD A:GLU431 3.6 21.9 1.0 N A:ARG906 3.6 16.2 1.0 CG A:GLU431 3.6 15.9 1.0 CD2 A:LEU905 3.9 21.5 1.0 CA A:CYS907 3.9 16.6 1.0 CB A:LEU905 4.1 16.4 1.0 C A:ARG906 4.1 18.1 1.0 CA A:ARG906 4.1 17.4 1.0 C A:LEU905 4.2 16.3 1.0 CB A:ARG906 4.3 17.7 1.0 O A:HOH1641 4.3 31.4 1.0 CA A:GLY867 4.3 15.2 1.0 CB A:ALA872 4.4 15.5 1.0 CA A:LEU905 4.4 19.5 1.0 O A:HOH1400 4.4 30.3 1.0 CG A:LEU905 4.5 20.2 1.0 O A:GLY867 4.6 20.8 1.0 OE1 A:GLU431 4.7 23.0 1.0 CB A:GLU431 4.7 15.7 1.0 C A:GLY867 4.7 17.0 1.0 O A:HOH1406 4.8 17.2 0.8 CA A:ALA872 4.9 15.5 1.0 N A:GLY867 4.9 17.6 1.0

P.Giastas, M.Neu, P.Rowland, E.Stratikos. High-Resolution Crystal Structure of Endoplasmic Reticulum Aminopeptidase 1 with Bound Phosphinic Transition-State Analogue Inhibitor. Acs Med.Chem.Lett. V. 10 708 2019.
ISSN: ISSN 1948-5875
PubMed: 31097987
DOI: 10.1021/ACSMEDCHEMLETT.9B00002