Sodium in PDB 8ral: CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor

The structure of CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor, PDB code: 8ral was solved by E.Erausquin, A.Urdiciain, P.Serra, P.Santamaria, J.Lopez-Sagaseta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.85 / 2.10
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.057, 76.032, 133.037, 90, 90, 90
R / Rfree (%)	21.6 / 24.8

The binding sites of Sodium atom in the CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor (pdb code 8ral). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor, PDB code: 8ral:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:44.3 occ:1.00 OG1 A:THR25 2.7 34.9 1.0 O A:ILE12 2.8 37.6 1.0 NE2 A:GLN23 3.1 35.5 1.0 N A:THR25 3.1 38.1 1.0 O A:GLN23 3.1 35.6 1.0 CG A:GLN23 3.4 38.7 1.0 C A:GLN23 3.4 39.2 1.0 CB A:THR25 3.5 39.9 1.0 C A:TYR24 3.5 39.8 1.0 CA A:TYR24 3.5 34.6 1.0 CG2 A:THR25 3.5 34.9 1.0 C A:ILE12 3.6 41.5 1.0 N A:TYR24 3.6 36.6 1.0 CB A:ILE12 3.7 41.9 1.0 CD A:GLN23 3.7 41.0 1.0 CA A:THR25 3.9 36.5 1.0 CG2 A:ILE12 3.9 40.1 1.0 CB A:GLN23 4.0 37.2 1.0 CG2 A:VAL14 4.2 37.9 1.0 CA A:ILE12 4.3 36.0 1.0 O A:HOH319 4.4 36.6 1.0 CA A:GLN23 4.4 40.6 1.0 O A:TYR24 4.5 36.6 1.0 N A:VAL14 4.5 39.8 1.0 N A:SER13 4.5 36.1 1.0 CB A:VAL14 4.7 39.8 1.0 O A:THR25 4.7 38.5 1.0 CA A:SER13 4.7 36.6 1.0 C A:THR25 4.8 37.4 1.0 CG1 A:ILE12 4.8 41.1 1.0 C A:SER13 4.9 39.4 1.0 O A:PHE139 5.0 42.8 1.0 OE1 A:GLN23 5.0 38.5 1.0 CB A:TYR24 5.0 31.1 1.0

Sodium binding site 2 out of 3 in the CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:60.6 occ:1.00 O A:HOH321 2.3 55.4 1.0 O A:HOH357 2.6 62.5 1.0 OE2 A:GLU42 2.8 56.0 1.0 O A:THR43 3.0 41.0 1.0 O A:HOH301 3.2 49.1 1.0 O A:HOH349 3.2 47.5 1.0 O A:HOH353 3.9 54.5 1.0 NE1 A:TRP45 3.9 41.2 1.0 CB A:THR43 4.0 39.2 1.0 C A:THR43 4.0 42.5 1.0 CD A:GLU42 4.1 57.1 1.0 O A:HOH316 4.1 51.7 1.0 CD1 A:TRP45 4.2 41.5 1.0 N A:THR43 4.3 39.6 1.0 CA A:THR43 4.3 39.7 1.0 CG2 A:THR43 4.8 35.8 1.0 CG A:GLU42 4.8 52.8 1.0 OE1 A:GLU42 4.9 52.9 1.0 OG1 A:THR43 4.9 43.4 1.0

Sodium binding site 3 out of 3 in the CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:49.4 occ:1.00 O A:GLN103 2.8 49.4 1.0 N A:LEU100 2.8 52.5 1.0 O A:HOH336 2.9 52.0 1.0 ND2 A:ASN105 3.1 44.2 1.0 O A:PRO98 3.2 43.6 1.0 O A:LEU100 3.2 52.3 1.0 CG A:PRO157 3.6 56.4 1.0 CA A:VAL99 3.6 47.4 1.0 C A:VAL99 3.7 49.8 1.0 CB A:ASN105 3.7 42.4 1.0 CB A:GLN103 3.7 57.6 1.0 CA A:LEU100 3.7 56.7 1.0 C A:GLN103 3.8 56.4 1.0 CG A:ASN105 3.9 46.4 1.0 C A:LEU100 3.9 58.7 1.0 CB A:LEU100 4.0 55.6 1.0 CG A:GLN103 4.1 66.4 1.0 C A:PRO98 4.1 49.3 1.0 O A:PRO104 4.2 52.4 1.0 CA A:GLN103 4.3 53.5 1.0 CD A:PRO157 4.3 57.1 1.0 N A:VAL99 4.3 40.1 1.0 C A:PRO104 4.5 47.6 1.0 CG A:LEU100 4.5 62.2 1.0 CD A:GLN103 4.6 67.9 1.0 CB A:VAL99 4.7 48.8 1.0 CB A:PRO157 4.7 60.8 1.0 N A:GLN103 4.7 58.6 1.0 CA A:ASN105 4.7 42.5 1.0 N A:ASN105 4.7 47.4 1.0 NE2 A:GLN103 4.8 68.2 1.0 CG1 A:VAL99 4.8 60.2 1.0 N A:PRO104 4.8 54.5 1.0 O A:VAL99 4.9 46.1 1.0

J.Lopez-Sagaseta, E.Erausquin, A.Urdiciain, P.Serra, P.Santamaria. CL3E Peptide Bound to the I-Ab Murine Mhc Class II Receptor To Be Published.