Sodium in PDB 5vcl: Structure of the Qdm Peptide Bound to Qa-1A

The structure of Structure of the Qdm Peptide Bound to Qa-1A, PDB code: 5vcl was solved by G.Ying, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.42 / 2.05
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.207, 75.876, 105.211, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.6

The binding sites of Sodium atom in the Structure of the Qdm Peptide Bound to Qa-1A (pdb code 5vcl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of the Qdm Peptide Bound to Qa-1A, PDB code: 5vcl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:41.3 occ:1.00 OD2 A:ASP29 2.6 28.2 1.0 O A:LEU179 2.6 29.6 1.0 OH A:TYR209 2.9 24.2 1.0 CB A:ASP29 3.4 23.9 1.0 CG A:ASP29 3.4 25.5 1.0 C A:LEU179 3.5 31.6 1.0 CE1 A:TYR209 3.5 25.4 1.0 CA A:LEU179 3.6 31.1 1.0 CZ A:TYR209 3.7 24.9 1.0 CB A:LEU179 3.7 32.0 1.0 CD2 A:LEU179 3.9 30.9 1.0 CG A:LEU179 4.4 31.2 1.0 O A:VAL28 4.6 25.6 1.0 ND1 A:HIS3 4.6 27.3 1.0 OD1 A:ASP29 4.6 27.8 1.0 O A:HOH437 4.7 34.2 1.0 OG1 A:THR31 4.7 25.5 1.0 N A:LYS180 4.7 31.4 1.0 CA A:ASP29 4.8 23.2 1.0 CD1 A:TYR209 4.8 25.0 1.0 CE1 A:HIS3 4.8 28.0 1.0 N A:ASP30 4.9 23.4 1.0

Sodium binding site 2 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:45.5 occ:1.00 O B:MET54 2.9 64.1 1.0 OG1 A:THR10 3.0 25.3 1.0 O A:PHE8 3.4 22.4 1.0 CB A:THR10 3.7 25.2 1.0 O A:ILE23 3.8 26.4 1.0 C A:PHE8 3.9 23.1 1.0 N A:THR10 4.0 23.2 1.0 CE2 B:PHE56 4.0 23.2 1.0 CD2 B:PHE56 4.0 24.1 1.0 C B:MET54 4.1 61.2 1.0 CG2 A:ILE23 4.1 32.8 1.0 C A:HIS9 4.2 23.7 1.0 CB A:PHE8 4.2 23.1 1.0 N A:HIS9 4.3 23.5 1.0 CB A:ILE23 4.3 32.2 1.0 CA B:SER55 4.3 44.1 1.0 C A:ILE23 4.3 27.7 1.0 CA A:HIS9 4.4 23.8 1.0 CG2 A:VAL25 4.4 28.9 1.0 CA A:THR10 4.5 24.6 1.0 N B:SER55 4.7 51.4 1.0 CA A:PHE8 4.7 22.4 1.0 N A:VAL25 4.7 23.7 1.0 O A:HIS9 4.7 22.5 1.0 N A:VAL24 4.9 25.8 1.0 C B:SER55 4.9 39.7 1.0 CG2 A:THR10 5.0 24.7 1.0 CE1 B:PHE62 5.0 25.6 1.0 CA A:VAL24 5.0 24.9 1.0 CG1 A:VAL25 5.0 26.2 1.0

Sodium binding site 3 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:44.1 occ:1.00 OE2 A:GLU116 2.8 41.6 1.0 OG1 P:THR6 2.8 37.5 1.0 OD1 A:ASN77 2.8 28.1 1.0 O P:LEU7 3.0 32.0 1.0 OE1 A:GLU116 3.4 40.0 1.0 CD A:GLU116 3.5 34.9 1.0 CG2 P:THR6 3.8 34.4 1.0 N P:LEU7 3.8 32.8 1.0 CB P:THR6 3.8 35.3 1.0 CE1 A:PHE74 3.9 25.9 1.0 C P:LEU7 3.9 32.2 1.0 CZ A:PHE74 4.0 26.3 1.0 CG A:ASN77 4.0 25.9 1.0 CA P:LEU7 4.2 32.7 1.0 CB P:LEU7 4.2 34.0 1.0 CD1 A:PHE74 4.3 25.9 1.0 CE2 A:PHE74 4.4 26.6 1.0 C P:THR6 4.5 32.3 1.0 CG P:LEU9 4.6 26.7 1.0 CD2 A:LEU95 4.6 26.1 1.0 CG A:PHE74 4.7 26.1 1.0 CA P:THR6 4.8 34.7 1.0 CD2 A:PHE74 4.8 25.9 1.0 CB A:ASN77 4.8 25.6 1.0 CD1 P:LEU9 4.8 25.9 1.0 CD2 P:LEU9 4.9 27.3 1.0 ND2 A:ASN77 4.9 23.7 1.0 CG A:GLU116 4.9 34.3 1.0

Sodium binding site 4 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:40.3 occ:1.00 OE1 A:GLN156 2.6 35.4 1.0 CD A:GLN156 3.6 35.0 1.0 CB A:TYR99 3.7 24.3 1.0 SG A:CYS114 3.7 28.3 1.0 CG A:TYR99 3.7 25.1 1.0 CB A:GLN156 3.9 33.6 1.0 CD2 A:TYR159 4.0 26.6 1.0 CD1 A:TYR99 4.0 25.1 1.0 CB A:CYS114 4.0 28.0 1.0 CZ2 A:TRP97 4.0 25.7 1.0 CD2 A:LEU160 4.1 31.1 1.0 CG A:GLN156 4.1 33.6 1.0 CG A:LEU160 4.1 30.6 1.0 CB P:ALA3 4.2 31.3 1.0 CD1 A:LEU160 4.3 30.2 1.0 CD2 A:TYR99 4.3 25.6 1.0 CE2 A:TYR159 4.3 26.4 1.0 CA A:GLN156 4.4 33.7 1.0 O A:GLN156 4.4 29.5 1.0 O A:TYR113 4.6 27.0 1.0 CE1 A:TYR99 4.7 26.1 1.0 CH2 A:TRP97 4.8 25.6 1.0 NE2 A:GLN156 4.8 33.2 1.0 C A:GLN156 4.8 32.2 1.0 CE2 A:TRP97 4.8 24.5 1.0 CG A:TYR159 4.9 27.5 1.0 CA A:CYS114 5.0 28.3 1.0 CE2 A:TYR99 5.0 25.7 1.0

Sodium binding site 5 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:58.7 occ:1.00 O A:SER2 3.7 32.9 1.0 OE1 A:GLU264 3.8 40.1 1.0 OD2 A:ASP29 4.3 28.2 1.0 ND1 A:HIS3 4.4 27.3 1.0 CG A:PRO210 4.4 27.9 1.0 CE1 A:HIS3 4.4 28.0 1.0 CG A:ASP29 4.5 25.5 1.0 CB A:PRO210 4.7 27.8 1.0 CD A:GLU264 4.8 38.6 1.0 O A:HOH471 4.8 43.4 1.0 C A:SER2 4.9 37.3 1.0 CB A:ASP29 4.9 23.9 1.0 OD1 A:ASP29 4.9 27.8 1.0 OE2 A:GLU264 4.9 38.2 1.0

Sodium binding site 6 out of 6 in the Structure of the Qdm Peptide Bound to Qa-1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Qdm Peptide Bound to Qa-1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:43.2 occ:1.00 OD1 A:ASP39 2.5 35.9 1.0 OG A:SER38 3.1 28.9 1.0 C A:SER38 3.6 30.6 1.0 N A:ASP39 3.6 31.3 1.0 O A:SER38 3.6 30.8 1.0 NH2 A:ARG14 3.6 66.8 1.0 CA A:ARG21 3.7 28.4 1.0 CG A:ASP39 3.8 36.0 1.0 NH1 A:ARG14 3.8 63.1 1.0 CB A:SER38 3.8 29.3 1.0 CA A:ASP39 3.9 34.2 1.0 CZ A:ARG14 4.0 64.3 1.0 CB A:ARG21 4.0 29.9 1.0 O A:PRO20 4.1 28.4 1.0 N A:ARG21 4.2 29.2 1.0 CG A:ARG21 4.3 32.1 1.0 CA A:SER38 4.3 28.8 1.0 O A:GLU19 4.4 35.6 1.0 C A:PRO20 4.4 31.4 1.0 CB A:ASP39 4.5 34.7 1.0 OD2 A:ASP39 4.7 36.0 1.0 NH2 A:ARG75 4.8 36.3 1.0 C A:ARG21 4.9 28.7 1.0 N A:PHE22 4.9 27.6 1.0 NE A:ARG14 5.0 60.0 1.0

G.Ying, J.Wang, V.Kumar, D.M.Zajonc. Crystal Structure of Qa-1A with Bound Qa-1 Determinant Modifier Peptide. Plos One V. 12 82296 2017.
ISSN: ESSN 1932-6203
PubMed: 28767728
DOI: 10.1371/JOURNAL.PONE.0182296