Sodium in PDB 6rqx: High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide

The structure of High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide, PDB code: 6rqx was solved by P.Giastas, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.68 / 1.68
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.004, 116.439, 147.363, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.9

The structure of High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide (pdb code 6rqx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide, PDB code: 6rqx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide


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 in Complex with 10MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1045 b:38.6 occ:1.00 O B:HOH110 2.5 37.6 1.0 OG A:SER870 2.6 23.9 1.0 O A:GLN315 3.1 19.9 1.0 O A:HOH1750 3.4 47.1 1.0 NH2 A:ARG328 3.4 20.7 1.0 CB A:SER870 3.6 16.9 1.0 CG A:PRO833 3.8 18.6 1.0 CG A:GLN315 3.8 22.7 1.0 N A:SCN1013 3.9 38.5 1.0 C A:GLN315 4.0 20.9 1.0 C A:SCN1013 4.1 36.1 1.0 CA A:SER870 4.2 18.4 1.0 CE1 A:PHE864 4.3 19.0 1.0 CE1 B:HIS4 4.3 44.9 1.0 NE2 B:HIS4 4.3 44.0 1.0 CA A:GLN315 4.4 17.4 1.0 O A:HOH1193 4.4 50.0 1.0 CB A:PRO833 4.5 22.3 1.0 CD1 A:PHE864 4.5 21.7 1.0 CD A:PRO833 4.6 17.8 1.0 O A:GLN830 4.6 18.6 1.0 CZ A:ARG328 4.7 19.0 1.0 CB A:GLN315 4.7 16.9 1.0 NE2 A:GLN315 4.8 20.5 1.0 S A:SCN1013 4.8 33.1 1.0 N A:SER870 4.8 16.6 1.0 CD A:GLN315 4.9 27.2 1.0

Sodium binding site 2 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide


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 in Complex with 10MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1046 b:39.0 occ:1.00 O A:HOH1348 2.4 34.7 1.0 OH A:TYR608 2.7 18.2 1.0 OG1 A:THR568 2.7 21.7 1.0 OD1 A:ASN601 3.3 21.0 1.0 O A:PRO566 3.4 23.6 1.0 CZ A:TYR608 3.5 20.6 1.0 CE2 A:TYR608 3.5 19.2 1.0 N A:THR568 3.6 17.4 1.0 N A:GLY606 3.7 25.1 1.0 CG2 A:THR568 3.7 24.0 1.0 CB A:THR568 3.7 19.4 1.0 CA A:GLY606 3.8 18.8 1.0 CA A:ASN601 3.9 17.4 1.0 CG A:ASN601 4.0 18.5 1.0 C A:LEU567 4.1 20.3 1.0 CA A:THR568 4.2 16.9 1.0 C A:ASN605 4.4 23.9 1.0 CA A:LEU567 4.4 20.1 1.0 N A:VAL602 4.4 16.3 1.0 CB A:ASN601 4.5 17.2 1.0 C A:PRO566 4.5 26.5 1.0 C A:ASN601 4.5 16.9 1.0 N A:ASN601 4.7 17.1 1.0 O A:HOH1567 4.7 33.7 1.0 CE1 A:TYR608 4.8 16.8 1.0 CD2 A:TYR608 4.8 20.7 1.0 ND2 A:ASN601 4.8 19.2 1.0 CB A:ASN605 4.8 22.0 1.0 N A:ASN605 4.9 20.7 1.0 O A:THR568 4.9 15.7 1.0 CA A:ASN605 4.9 21.8 1.0 O A:LEU567 4.9 18.8 1.0 N A:LEU567 5.0 18.0 1.0

Sodium binding site 3 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide


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 in Complex with 10MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1047 b:49.8 occ:1.00 O A:HOH1685 2.6 45.6 1.0 O A:HOH1737 2.6 45.3 1.0 OD2 A:ASP635 3.1 32.5 1.0 OG A:SER632 3.2 22.8 1.0 N A:GLY603 3.6 21.1 1.0 CA A:GLY603 3.6 22.8 1.0 CB A:SER632 3.8 23.8 1.0 CG1 A:VAL602 3.8 20.5 1.0 O A:HOH1234 4.0 29.7 1.0 CG A:ASP635 4.1 36.2 1.0 C A:VAL602 4.4 22.4 1.0 OD1 A:ASP635 4.6 25.4 1.0 O A:HOH1631 4.7 46.8 1.0 O A:VAL602 4.9 21.2 1.0

Sodium binding site 4 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1048 b:50.7 occ:1.00 O B:HOH111 2.4 49.4 1.0 O A:HOH1481 2.5 28.7 1.0 OG A:SER869 2.9 26.1 0.4 CB A:SER869 3.2 25.4 0.6 CB A:SER869 3.2 25.2 0.4 O A:PHE433 3.2 21.7 1.0 CA A:SER869 3.6 20.2 0.6 CA A:SER869 3.6 20.4 0.4 CB A:ASP434 3.6 16.2 1.0 CE B:LYS2 3.7 44.5 1.0 CA A:ASP434 3.8 14.4 1.0 O A:HOH1671 3.8 51.9 1.0 OG A:SER869 3.9 26.8 0.6 O A:HOH1767 4.0 31.3 1.0 C A:PHE433 4.1 23.7 1.0 O A:HOH1459 4.2 27.4 1.0 N A:SER869 4.2 17.9 1.0 O A:HOH1535 4.3 31.0 1.0 CB A:ALA872 4.3 16.1 1.0 N A:ASP434 4.4 16.8 1.0 CD B:LYS2 4.5 43.7 1.0 O A:GLU431 4.7 18.2 1.0 O A:HOH1356 4.8 25.5 1.0 C A:SER869 4.8 18.3 1.0 NZ B:LYS2 4.9 45.3 1.0 C A:SER868 4.9 23.0 1.0 O A:SER868 5.0 20.7 1.0

P.Giastas, E.Stratikos. High-Resolution Crystal Structure of ERAP1 in Complex with 10MER Phosphinic Peptide To Be Published.