Zinc in PDB 1l0y: T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc

The structure of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc, PDB code: 1l0y was solved by H.Li, E.J.Sundberg, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.69 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.722, 83.734, 93.900, 90.00, 91.74, 90.00
R / Rfree (%)	22.1 / 26.2

The binding sites of Zinc atom in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc (pdb code 1l0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc, PDB code: 1l0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:54.3 occ:1.00 OE1 A:GLU158 1.9 38.3 1.0 NE2 A:HIS217 2.0 29.0 1.0 O A:HOH782 2.1 55.0 1.0 NE2 A:GLN215 2.3 32.0 1.0 CE1 A:HIS217 2.7 28.3 1.0 CD A:GLU158 2.8 38.8 1.0 OE2 A:GLU158 3.0 41.9 1.0 CD2 A:HIS217 3.1 28.0 1.0 CD A:GLN215 3.5 31.3 1.0 ND1 A:HIS217 3.9 29.1 1.0 CG A:GLN215 4.0 29.6 1.0 CG A:HIS217 4.1 29.5 1.0 CG A:GLU158 4.2 36.6 1.0 ND2 A:ASN10 4.2 26.9 1.0 OE1 A:GLN215 4.5 31.6 1.0 CB A:GLN215 4.7 26.1 1.0 CB A:GLU158 5.0 33.2 1.0

Zinc binding site 2 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:58.8 occ:1.00 NE2 B:HIS110 1.8 53.4 1.0 ND1 B:HIS106 1.9 53.2 1.0 OD2 B:ASP77 2.2 53.0 1.0 OE1 B:GLU33 2.3 57.6 1.0 CE1 B:HIS106 2.5 54.0 1.0 OD1 B:ASP77 2.5 50.5 1.0 CE1 B:HIS110 2.6 53.9 1.0 CG B:ASP77 2.7 49.2 1.0 CD2 B:HIS110 3.0 53.4 1.0 CG B:HIS106 3.2 53.1 1.0 CD B:GLU33 3.4 57.0 1.0 NE2 B:HIS106 3.7 54.5 1.0 ND1 B:HIS110 3.8 54.2 1.0 OE2 B:GLU33 3.8 58.4 1.0 CB B:HIS106 3.8 52.0 1.0 CG B:HIS110 4.0 53.1 1.0 CA B:HIS106 4.0 50.8 1.0 CD2 B:HIS106 4.1 53.3 1.0 CB B:ASP77 4.1 45.1 1.0 O B:HIS106 4.2 51.7 1.0 O B:HOH735 4.4 38.7 1.0 C B:HIS106 4.5 51.5 1.0 N B:ASN34 4.5 45.2 1.0 CG B:GLU33 4.6 53.5 1.0 CB B:GLU33 4.6 49.0 1.0 CA B:GLU33 4.8 45.9 1.0

Zinc binding site 3 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn706 b:66.8 occ:1.00 O B:HOH760 1.7 55.2 1.0 O B:HOH759 1.9 48.9 1.0 NE2 B:HIS10 2.1 45.1 1.0 OE2 B:GLU189 2.5 53.0 1.0 CE1 B:HIS10 3.1 43.4 1.0 CD2 B:HIS10 3.1 43.9 1.0 CD B:GLU189 3.6 51.5 1.0 CG B:GLU189 4.1 47.2 1.0 ND1 B:HIS10 4.1 43.1 1.0 CG B:HIS10 4.2 41.4 1.0 OE1 B:GLU189 4.7 54.2 1.0

Zinc binding site 4 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:49.0 occ:1.00 NE2 C:HIS217 2.0 29.9 1.0 OE1 C:GLU158 2.0 37.6 1.0 NE2 C:GLN215 2.2 30.0 1.0 CE1 C:HIS217 2.6 29.0 1.0 CD C:GLU158 2.7 38.3 1.0 OE2 C:GLU158 2.7 39.8 1.0 O C:HOH786 2.8 44.0 1.0 O C:HOH714 2.8 27.0 1.0 CD2 C:HIS217 3.2 30.3 1.0 CD C:GLN215 3.3 31.2 1.0 O C:HOH732 3.9 32.9 1.0 ND1 C:HIS217 3.9 30.9 1.0 CG C:GLN215 4.0 29.2 1.0 CG C:GLU158 4.2 36.1 1.0 OE1 C:GLN215 4.2 31.7 1.0 ND2 C:ASN10 4.2 24.5 1.0 CG C:HIS217 4.2 31.4 1.0 CB C:GLN215 4.4 25.7 1.0 CB C:GLU158 4.9 32.6 1.0

Zinc binding site 5 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn704 b:37.0 occ:1.00 OD2 D:ASP77 1.9 36.4 1.0 OE1 D:GLU33 1.9 30.4 1.0 NE2 D:HIS110 2.0 42.4 1.0 ND1 D:HIS106 2.2 42.7 1.0 OD1 D:ASP77 2.5 38.4 1.0 CG D:ASP77 2.5 38.0 1.0 CD D:GLU33 2.6 35.6 1.0 OE2 D:GLU33 2.7 37.9 1.0 CE1 D:HIS110 2.7 42.1 1.0 CE1 D:HIS106 3.0 41.4 1.0 CD2 D:HIS110 3.2 42.7 1.0 CG D:HIS106 3.3 42.7 1.0 CB D:HIS106 3.8 43.0 1.0 CB D:ASP77 3.9 36.6 1.0 ND1 D:HIS110 4.0 44.1 1.0 CA D:HIS106 4.0 43.8 1.0 CG D:GLU33 4.1 35.0 1.0 CG D:HIS110 4.2 43.4 1.0 NE2 D:HIS106 4.2 41.8 1.0 O D:HIS106 4.3 45.0 1.0 N D:ASN34 4.4 37.9 1.0 CD2 D:HIS106 4.4 42.2 1.0 O D:HOH731 4.5 26.7 1.0 C D:HIS106 4.5 45.4 1.0 CB D:GLU33 4.5 37.2 1.0 CA D:GLU33 4.7 37.5 1.0 CA D:ASP77 5.0 36.4 1.0

Zinc binding site 6 out of 6 in the T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of T Cell Receptor Beta Chain Complexed with Superantigen Spea Soaked with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn705 b:52.5 occ:1.00 O D:HOH785 1.8 50.3 1.0 O D:HOH788 2.0 54.2 1.0 NE2 D:HIS10 2.0 31.7 1.0 O D:HOH787 2.1 52.8 1.0 CE1 D:HIS10 2.8 31.7 1.0 OE2 D:GLU189 3.0 47.2 1.0 CD2 D:HIS10 3.1 30.3 1.0 ND1 D:HIS10 4.0 30.0 1.0 CD D:GLU189 4.0 45.8 1.0 O D:HOH709 4.2 16.4 1.0 CG D:HIS10 4.2 31.0 1.0 CG D:GLU189 4.3 40.6 1.0

E.J.Sundberg, H.Li, A.S.Llera, J.K.Mccormick, J.Tormo, P.M.Schlievert, K.Karjalainen, R.A.Mariuzza. Structures of Two Streptococcal Superantigens Bound to Tcr Beta Chains Reveal Diversity in the Architecture of T Cell Signaling Complexes. Structure V. 10 687 2002.
ISSN: ISSN 0969-2126
PubMed: 12015151
DOI: 10.1016/S0969-2126(02)00759-1