Sodium in PDB 9btx: Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde, PDB code: 9btx was solved by W.Awad, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.19 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	217.129, 70.405, 143.573, 90, 104.61, 90
R / Rfree (%)	18.5 / 21.8

The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde (pdb code 9btx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde, PDB code: 9btx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ F:Na102 b:56.3 occ:1.00 O F:LEU87 2.4 53.4 1.0 O F:HIS84 2.4 47.3 1.0 OD1 F:ASN83 2.5 54.3 1.0 O F:HOH234 2.5 56.9 1.0 O F:HOH230 2.6 51.5 1.0 O F:HOH235 2.7 55.7 1.0 C F:HIS84 3.3 47.8 1.0 CG F:ASN83 3.5 55.0 1.0 C F:LEU87 3.5 55.7 1.0 N F:HIS84 3.8 45.4 1.0 ND2 F:ASN83 4.0 53.7 1.0 N F:VAL85 4.0 47.6 1.0 CA F:VAL85 4.1 45.1 1.0 N F:LEU87 4.2 48.9 1.0 CA F:HIS84 4.2 46.1 1.0 CA F:LEU87 4.2 47.3 1.0 CB F:LEU87 4.3 50.6 1.0 C F:VAL85 4.4 46.8 1.0 O F:VAL85 4.5 50.2 1.0 O F:SER88 4.5 62.2 1.0 C F:SER88 4.5 60.5 1.0 N F:SER88 4.6 57.3 1.0 C F:ASN83 4.7 44.1 1.0 CB F:ASN83 4.8 47.8 1.0 CA F:SER88 4.8 57.7 1.0 O F:HOH240 4.9 55.5 1.0 N F:GLN89 4.9 57.6 1.0 CA F:ASN83 5.0 46.0 1.0

Sodium binding site 2 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:44.8 occ:1.00 O H:TYR64 2.3 45.9 1.0 O H:HOH476 2.4 45.6 1.0 O H:HOH499 2.5 45.2 1.0 O H:PRO61 2.5 44.8 1.0 OH H:TYR47 2.5 44.1 1.0 O H:HOH493 2.6 48.2 1.0 C H:PRO61 3.4 44.5 1.0 C H:TYR64 3.5 45.3 1.0 CZ H:TYR47 3.6 46.0 1.0 N H:TYR64 3.7 45.4 1.0 CE1 H:TYR47 3.7 45.0 1.0 CA H:ASN62 4.1 45.8 1.0 N H:GLY63 4.1 46.3 1.0 N H:ASN62 4.1 44.8 1.0 CB H:PRO61 4.2 44.0 1.0 CA H:TYR64 4.2 44.8 1.0 CA H:PRO61 4.3 43.5 1.0 C H:ASN62 4.4 45.6 1.0 ND2 H:ASN65 4.5 53.9 0.6 OD1 H:ASN65 4.5 55.1 0.6 O H:HOH561 4.5 49.9 1.0 CG H:ASN65 4.5 51.0 0.6 N H:ASN65 4.6 45.3 1.0 C H:GLY63 4.7 45.6 1.0 CE2 H:TYR47 4.8 37.4 1.0 CA H:ASN65 4.9 45.4 0.4 CB H:TYR64 4.9 43.5 1.0 OD1 H:ASN62 4.9 46.9 1.0 CA H:ASN65 4.9 45.5 0.6 CA H:GLY63 5.0 46.2 1.0

W.Awad, J.Rossjohn. Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3,4-Dihydroxybenzaldehyde J.Exp.Med. 2024.
ISSN: ESSN 1540-9538
DOI: 10.1084/JEM.20240896