Sodium in PDB 4nqc: Crystal Structure of Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil

The structure of Crystal Structure of Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil, PDB code: 4nqc was solved by R.W.Birkinshaw, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.42 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	218.760, 71.110, 144.280, 90.00, 104.87, 90.00
R / Rfree (%)	16.5 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil (pdb code 4nqc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil, PDB code: 4nqc:

Sodium binding site 1 out of 1 in the Crystal Structure of Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil


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 Tcr-Mhc Ternary Complex and Covalently Bound 5- (2-Oxopropylideneamino)-6-D-Ribitylaminouracil within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:40.6 occ:1.00 O H:HOH574 2.2 15.2 1.0 O H:TYR64 2.2 17.7 1.0 O H:HOH571 2.4 40.2 1.0 OH H:TYR47 2.5 32.0 1.0 O H:HOH575 2.5 37.4 1.0 O H:PRO61 2.9 24.7 1.0 C H:TYR64 3.5 19.8 1.0 CZ H:TYR47 3.6 25.9 1.0 C H:PRO61 3.8 25.0 1.0 CE1 H:TYR47 3.8 15.8 1.0 N H:TYR64 4.0 20.4 1.0 NZ H:LYS57 4.1 59.2 1.0 OD1 H:ASN65 4.1 46.3 1.0 O H:HOH547 4.2 33.7 1.0 CA H:TYR64 4.3 17.9 1.0 CA H:ASN62 4.4 25.1 1.0 N H:GLY63 4.4 24.6 1.0 CG H:ASN65 4.4 62.0 1.0 N H:ASN65 4.4 17.8 1.0 CB H:PRO61 4.5 23.5 1.0 N H:ASN62 4.5 23.8 1.0 CE H:LYS57 4.5 51.3 1.0 ND2 H:ASN65 4.6 62.0 1.0 CA H:PRO61 4.7 21.6 1.0 CA H:ASN65 4.7 18.6 1.0 CE2 H:TYR47 4.8 20.1 1.0 C H:ASN62 4.8 28.9 1.0 OD1 H:ASN62 5.0 29.3 1.0

A.J.Corbett, S.B.Eckle, R.W.Birkinshaw, L.Liu, O.Patel, J.Mahony, Z.Chen, R.Reantragoon, B.Meehan, H.Cao, N.A.Williamson, R.A.Strugnell, D.Van Sinderen, J.Y.Mak, D.P.Fairlie, L.Kjer-Nielsen, J.Rossjohn, J.Mccluskey. T-Cell Activation By Transitory Neo-Antigens Derived From Distinct Microbial Pathways. Nature V. 509 361 2014.
ISSN: ISSN 0028-0836
PubMed: 24695216
DOI: 10.1038/NATURE13160