Sodium in PDB 4lfh: Crystal Structure of 9C2 Tcr

The structure of Crystal Structure of 9C2 Tcr, PDB code: 4lfh was solved by A.P.Uldrich, J.Le Nours, D.G.Pellicci, S.Gras, J.Rossjohn, D.I.Godfrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.71 / 2.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	118.534, 118.534, 89.127, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.8

The binding sites of Sodium atom in the Crystal Structure of 9C2 Tcr (pdb code 4lfh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of 9C2 Tcr, PDB code: 4lfh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 9C2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 9C2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ G:Na302 b:35.8 occ:1.00 N G:TRP79 3.2 37.4 1.0 NH1 G:ARG78 3.5 36.6 1.0 OG1 G:THR75 3.6 52.8 1.0 NE1 G:TRP81 3.8 37.1 1.0 CD G:ARG78 3.8 34.2 1.0 O G:HOH458 3.8 43.7 1.0 CA G:TRP79 3.8 37.0 1.0 CG1 G:VAL55 3.9 37.3 1.0 CD1 G:TRP79 3.9 39.6 1.0 CA G:ARG78 4.2 37.5 1.0 C G:ARG78 4.2 42.1 1.0 CZ2 G:TRP81 4.3 36.6 1.0 CE2 G:TRP81 4.3 38.0 1.0 CZ G:ARG78 4.5 48.6 1.0 NE G:ARG78 4.6 36.3 1.0 CB G:THR75 4.7 49.0 1.0 CG G:TRP79 4.7 37.1 1.0 O G:ARG77 4.7 39.4 1.0 N G:SER80 4.7 36.8 1.0 CG G:ARG78 4.7 41.5 1.0 NE1 G:TRP79 4.8 39.9 1.0 CD1 G:TRP81 4.8 37.0 1.0 C G:TRP79 4.9 40.0 1.0 CB G:TRP79 4.9 36.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 9C2 Tcr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 9C2 Tcr within 5.0Å range: probe atom residue distance (Å) B Occ G:Na303 b:78.8 occ:1.00 ND2 G:ASN91 3.5 71.6 1.0 O G:ASN91 3.8 42.0 1.0 O G:HOH421 4.2 39.4 1.0 O G:HOH438 4.2 48.0 1.0 O G:HOH412 4.3 36.2 1.0 OD2 G:ASP92 4.5 42.5 1.0 C G:ASN91 4.6 43.5 1.0 CG G:ASN91 4.6 82.6 1.0 CD1 G:LEU40 4.7 37.5 1.0 OH G:TYR71 4.8 47.9 1.0 O G:HOH469 4.9 69.1 1.0 CB G:ASN91 4.9 53.2 1.0

A.P.Uldrich, J.Le Nours, D.G.Pellicci, N.A.Gherardin, K.G.Mcpherson, R.T.Lim, O.Patel, T.Beddoe, S.Gras, J.Rossjohn, D.I.Godfrey. CD1D-Lipid Antigen Recognition By the Gamma Delta Tcr. Nat.Immunol. V. 14 1137 2013.
ISSN: ISSN 1529-2908
PubMed: 24076636
DOI: 10.1038/NI.2713