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Zinc in PDB 1ty2: Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J)

Protein crystallography data

The structure of Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J), PDB code: 1ty2 was solved by H.M.Baker, T.Proft, P.D.Webb, V.L.Arcus, J.D.Fraser, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.330, 46.330, 72.220, 90.00, 90.54, 90.00
R / Rfree (%) 21.8 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J) (pdb code 1ty2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J), PDB code: 1ty2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1ty2

Go back to Zinc Binding Sites List in 1ty2
Zinc binding site 1 out of 3 in the Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:51.5
occ:1.00
O A:HOH735 1.7 34.8 1.0
OD2 A:ASP205 2.1 30.8 1.0
NE2 A:HIS203 2.2 34.1 1.0
CG A:ASP205 2.9 29.9 1.0
CE1 A:HIS203 3.1 32.9 1.0
OD1 A:ASP205 3.1 30.7 1.0
CD2 A:HIS203 3.2 33.0 1.0
NE2 A:HIS169 3.3 56.7 1.0
CD2 A:HIS169 4.1 55.7 1.0
ND1 A:HIS203 4.2 34.9 1.0
CE1 A:HIS169 4.3 56.2 1.0
CG A:HIS203 4.3 34.8 1.0
CB A:ASP205 4.3 28.1 1.0
CB A:ALA163 4.5 36.7 1.0
ND2 A:ASN107 4.6 38.9 1.0
ND2 C:ASN96 4.9 74.9 1.0

Zinc binding site 2 out of 3 in 1ty2

Go back to Zinc Binding Sites List in 1ty2
Zinc binding site 2 out of 3 in the Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:55.4
occ:1.00
OD2 B:ASP205 2.0 31.6 1.0
NE2 B:HIS203 2.3 29.2 1.0
NE2 B:HIS169 2.5 42.9 1.0
CE1 B:HIS203 3.1 27.2 1.0
CG B:ASP205 3.2 27.4 1.0
CD2 B:HIS203 3.3 27.3 1.0
CE1 B:HIS169 3.4 45.6 1.0
CD2 B:HIS169 3.6 44.4 1.0
OD1 B:ASP205 3.8 26.4 1.0
ND1 B:HIS203 4.2 27.1 1.0
CB B:ASP205 4.3 25.5 1.0
CG B:HIS203 4.4 28.8 1.0
CB B:ALA163 4.6 27.2 1.0
ND1 B:HIS169 4.6 45.6 1.0
CG B:HIS169 4.7 44.4 1.0
OH B:TYR207 5.0 41.0 1.0

Zinc binding site 3 out of 3 in 1ty2

Go back to Zinc Binding Sites List in 1ty2
Zinc binding site 3 out of 3 in the Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Streptococcal Pyrogenic Exotoxin J (Spe-J) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:50.2
occ:1.00
O C:HOH716 1.6 25.4 1.0
NE2 C:HIS169 2.1 52.6 1.0
OD2 C:ASP205 2.1 35.4 1.0
NE2 C:HIS203 2.1 38.0 1.0
CD2 C:HIS169 2.7 53.1 1.0
CE1 C:HIS203 2.9 40.0 1.0
CG C:ASP205 2.9 34.1 1.0
OD1 C:ASP205 3.1 34.5 1.0
CD2 C:HIS203 3.2 38.1 1.0
CE1 C:HIS169 3.3 53.2 1.0
CB C:ALA163 3.9 41.7 1.0
CG C:HIS169 3.9 53.4 1.0
ND1 C:HIS203 4.0 39.1 1.0
CG C:HIS203 4.2 38.5 1.0
ND1 C:HIS169 4.2 53.9 1.0
CB C:ASP205 4.4 34.6 1.0

Reference:

H.M.Baker, T.Proft, P.D.Webb, V.L.Arcus, J.D.Fraser, E.N.Baker. Crystallographic and Mutational Data Show That the Streptococcal Pyrogenic Exotoxin J Can Use A Common Binding Surface For T-Cell Receptor Binding and Dimerization J.Biol.Chem. V. 279 38571 2004.
ISSN: ISSN 0021-9258
PubMed: 15247241
DOI: 10.1074/JBC.M406695200
Page generated: Mon Jan 25 16:14:25 2021

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