Sodium in PDB 2aq2: Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant

The structure of Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant, PDB code: 2aq2 was solved by S.Cho, C.P.Swaminathan, J.Yang, M.C.Kerzic, R.Guan, M.C.Kieke, D.M.Kranz, R.A.Mariuzza, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.80
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	96.537, 96.537, 92.182, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 21.3

The structure of Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant (pdb code 2aq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant, PDB code: 2aq2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant


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 T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:39.3 occ:1.00 N B:ASN175 3.1 22.8 1.0 O B:HOH1070 3.2 34.3 1.0 N B:PHE174 3.5 20.6 1.0 CB B:GLU173 3.8 22.0 1.0 CB B:PHE174 3.8 20.6 1.0 OE1 A:GLU66 3.9 39.6 1.0 CA B:PHE174 3.9 20.7 1.0 C B:PHE174 4.0 21.8 1.0 CB B:ASN175 4.0 28.2 1.0 CA B:ASN175 4.0 25.3 1.0 NA B:NA1003 4.1 48.0 1.0 O B:HOH1145 4.2 67.5 1.0 C B:GLU173 4.3 20.3 1.0 N B:SER176 4.7 24.8 1.0 CA B:GLU173 4.7 20.4 1.0 OE1 B:GLU173 4.8 36.9 1.0 CD B:GLU173 4.8 33.0 1.0 CD2 B:PHE174 4.8 24.1 1.0 CG B:PHE174 4.9 22.6 1.0 CG B:GLU173 4.9 24.7 1.0 CD A:GLU66 4.9 36.5 1.0 C B:ASN175 4.9 25.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant


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 T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:48.0 occ:1.00 N B:PHE174 3.2 20.6 1.0 NZ B:LYS25 3.6 31.4 1.0 CB B:GLU173 3.8 22.0 1.0 CA B:GLU173 3.8 20.4 1.0 C B:GLU173 4.0 20.3 1.0 CB B:PHE174 4.0 20.6 1.0 OE1 A:GLU66 4.1 39.6 1.0 O B:HOH1066 4.1 39.5 1.0 NA B:NA1002 4.1 39.3 1.0 CA B:PHE174 4.2 20.7 1.0 CG B:GLU173 4.4 24.7 1.0 OE2 A:GLU66 4.5 38.8 1.0 CD A:GLU66 4.6 36.5 1.0 CE B:LYS25 4.8 25.7 1.0 CD B:LYS25 5.0 20.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of T-Cell Receptor V Beta Domain Variant Complexed with Superantigen SEC3 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1004 b:40.9 occ:1.00 O B:HOH1150 2.7 46.1 1.0 N B:LYS115 3.1 22.1 1.0 O B:HOH1112 3.3 36.8 1.0 OH B:TYR77 3.6 33.2 1.0 CG B:LYS115 3.6 30.5 1.0 CA B:THR114 3.7 20.1 1.0 C B:THR114 3.9 20.8 1.0 CE2 B:TYR77 3.9 28.5 1.0 CB B:LYS115 4.0 24.8 1.0 CA B:LYS115 4.1 24.5 1.0 CB B:THR114 4.2 20.5 1.0 CZ B:TYR77 4.3 30.0 1.0 CG2 B:THR114 4.5 19.6 1.0 O B:ILE113 4.6 19.9 1.0 CD B:LYS115 4.8 39.1 1.0 N B:THR114 4.9 19.7 1.0

S.Cho, C.P.Swaminathan, J.Yang, M.C.Kerzic, R.Guan, M.C.Kieke, D.M.Kranz, R.A.Mariuzza, E.J.Sundberg. Structural Basis of Affinity Maturation and Intramolecular Cooperativity in A Protein-Protein Interaction. Structure V. 13 1775 2005.
ISSN: ISSN 0969-2126
PubMed: 16338399
DOI: 10.1016/J.STR.2005.08.015