Sodium in PDB 6ryf: High-Resolution Crystal Structure of ERAP1 in Complex with 15MER Phosphinic Peptide

The structure of High-Resolution Crystal Structure of ERAP1 in Complex with 15MER Phosphinic Peptide, PDB code: 6ryf 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)	91.52 / 1.72
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.693, 117.157, 146.598, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.1

The structure of High-Resolution Crystal Structure of ERAP1 in Complex with 15MER 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 15MER Phosphinic Peptide (pdb code 6ryf). 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 15MER Phosphinic Peptide, PDB code: 6ryf:
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 15MER 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 15MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1024 b:42.6 occ:1.00 O A:MET189 2.7 33.1 1.0 O A:HIS99 3.0 44.6 1.0 O A:HOH1181 3.0 34.8 1.0 O A:HIS98 3.2 33.5 1.0 O A:HOH1218 3.3 40.5 1.0 CB A:HIS99 3.5 37.9 1.0 CD2 A:LEU100 3.6 31.6 1.0 C A:HIS99 3.6 40.9 1.0 O A:HOH1404 3.6 32.7 1.0 C A:MET189 3.6 35.6 1.0 CB A:MET189 3.8 38.7 1.0 CA A:MET189 3.8 36.5 1.0 CA A:HIS99 4.1 38.0 1.0 CG A:LEU100 4.2 33.2 1.0 CE A:MET189 4.3 36.0 1.0 C A:HIS98 4.3 37.3 1.0 O A:HOH1661 4.3 59.2 1.0 CG A:MET189 4.3 40.6 1.0 N A:LEU100 4.4 37.6 1.0 CZ A:PHE76 4.5 33.1 1.0 O A:ASN154 4.6 35.5 1.0 N A:HIS99 4.7 34.5 1.0 O A:HOH1640 4.7 50.9 1.0 CG A:HIS99 4.8 49.0 1.0 CA A:LEU100 4.8 34.0 1.0 N A:ALA190 4.9 37.4 1.0 CE1 A:PHE76 4.9 31.8 1.0

Sodium binding site 2 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 15MER 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 15MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1025 b:34.0 occ:1.00 O A:GLN527 2.7 24.8 1.0 O A:GLY529 2.8 22.7 1.0 NE1 A:TRP563 2.9 22.4 1.0 NZ A:LYS440 2.9 23.7 1.0 O A:THR523 3.5 25.2 1.0 O A:TRP524 3.6 25.2 1.0 O A:HOH1256 3.6 23.8 1.0 O A:LYS528 3.6 27.8 1.0 CE2 A:TRP563 3.7 23.4 1.0 C A:GLN527 3.7 28.4 1.0 C A:LYS528 3.8 26.4 1.0 CE A:LYS440 3.8 18.5 1.0 C A:GLY529 3.8 22.4 1.0 CA A:TRP524 3.9 21.2 1.0 CZ2 A:TRP563 3.9 25.4 1.0 C A:TRP524 3.9 22.1 1.0 CD1 A:TRP563 3.9 21.5 1.0 CG A:GLN527 4.0 41.4 1.0 CE3 A:TRP524 4.1 23.4 1.0 N A:GLY529 4.1 24.2 1.0 CA A:LYS528 4.4 24.7 1.0 C A:THR523 4.5 24.5 1.0 N A:LYS528 4.5 28.2 1.0 CA A:GLY529 4.6 21.7 1.0 CZ3 A:TRP524 4.7 22.5 1.0 N A:TRP524 4.7 24.2 1.0 CA A:GLN527 4.7 34.1 1.0 N A:PHE530 4.8 20.6 1.0 N A:GLN527 4.8 27.3 1.0 N A:THR525 4.9 21.3 1.0 CB A:GLN527 4.9 42.5 1.0 CB A:TRP524 4.9 23.8 1.0 CD2 A:TRP524 4.9 26.1 1.0 NA A:NA1026 4.9 34.5 1.0 NE2 A:GLN527 5.0 25.2 1.0 CD2 A:TRP563 5.0 26.8 1.0

Sodium binding site 3 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 15MER 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 15MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1026 b:34.5 occ:1.00 O A:HIS417 2.7 21.8 1.0 OD1 A:ASP411 2.7 23.2 1.0 NZ A:LYS440 2.8 23.7 1.0 O A:HOH1256 3.4 23.8 1.0 CA A:LYS528 3.5 24.7 1.0 CG A:ASP411 3.5 26.9 1.0 N A:GLY529 3.5 24.2 1.0 OD2 A:ASP411 3.5 23.6 1.0 CD A:LYS440 3.6 17.7 1.0 CE A:LYS440 3.7 18.5 1.0 C A:HIS417 3.7 25.6 1.0 CG1 A:VAL436 3.8 22.6 1.0 CA A:PRO418 3.8 24.5 1.0 OG A:SER416 3.9 23.4 1.0 C A:LYS528 3.9 26.4 1.0 N A:VAL419 4.0 23.7 1.0 CB A:LYS528 4.0 26.2 1.0 C A:PRO418 4.1 28.1 1.0 N A:PRO418 4.2 24.1 1.0 O A:GLN527 4.3 24.8 1.0 CG2 A:VAL419 4.4 23.2 1.0 CG2 A:VAL436 4.5 28.5 1.0 N A:LYS528 4.5 28.2 1.0 N A:HIS417 4.7 28.8 1.0 CA A:GLY529 4.7 21.7 1.0 C A:GLN527 4.8 28.4 1.0 CB A:VAL436 4.8 23.6 1.0 O A:GLY529 4.8 22.7 1.0 CA A:HIS417 4.8 30.1 1.0 CA A:VAL419 4.9 27.8 1.0 CB A:ASP411 4.9 27.4 1.0 NA A:NA1025 4.9 34.0 1.0 O A:PRO418 4.9 25.9 1.0

Sodium binding site 4 out of 4 in the High-Resolution Crystal Structure of ERAP1 in Complex with 15MER 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 15MER Phosphinic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1027 b:42.1 occ:1.00 O A:HOH1656 2.7 45.0 1.0 O A:HOH1438 2.7 38.5 1.0 OD1 A:ASN925 2.7 28.2 1.0 N A:ILE654 3.0 26.6 1.0 CG2 A:ILE654 3.6 32.5 1.0 CB A:ILE654 3.7 33.6 1.0 CA A:SER653 3.7 30.8 1.0 C A:SER653 3.8 28.5 1.0 CG A:ASN925 3.8 25.9 1.0 CG1 A:VAL647 3.9 25.1 1.0 CA A:ILE654 3.9 30.2 1.0 CE A:LYS924 4.0 41.7 1.0 CD A:LYS928 4.0 37.5 1.0 CE A:LYS928 4.3 49.0 1.0 O A:LEU652 4.3 33.0 1.0 ND2 A:ASN925 4.4 26.2 1.0 CB A:SER653 4.4 34.8 1.0 O A:HOH1630 4.4 49.1 1.0 NZ A:LYS924 4.5 46.6 1.0 CD A:LYS924 4.5 38.2 1.0 O A:HOH1271 4.5 36.6 1.0 O A:HOH1350 4.6 36.7 1.0 CG A:LYS924 4.7 39.4 1.0 OE1 A:GLU655 4.7 38.1 1.0 N A:SER653 4.8 28.4 1.0 O A:VAL647 5.0 30.3 1.0 C A:LEU652 5.0 31.8 1.0 O A:SER653 5.0 29.9 1.0

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