Zinc in PDB 1ha5: Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
Protein crystallography data
The structure of Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition., PDB code: 1ha5
was solved by
M.D.Baker,
D.M.Gutman,
A.C.Papageorgiou,
C.M.Collins,
K.R.Acharya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.60 /
2.82
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.946,
101.320,
82.019,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.4 /
28.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
(pdb code 1ha5). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition., PDB code: 1ha5:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 1ha5
Go back to
Zinc Binding Sites List in 1ha5
Zinc binding site 1 out
of 4 in the Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2221
b:50.8
occ:1.00
|
OE1
|
A:GLU1033
|
2.2
|
15.3
|
1.0
|
OD2
|
A:ASP1077
|
2.2
|
28.2
|
1.0
|
NE2
|
A:HIS1110
|
2.3
|
20.0
|
1.0
|
OD1
|
A:ASP1077
|
2.5
|
28.2
|
1.0
|
CG
|
A:ASP1077
|
2.6
|
28.2
|
1.0
|
CD2
|
A:HIS1106
|
2.7
|
45.0
|
1.0
|
CD
|
A:GLU1033
|
2.8
|
15.3
|
1.0
|
OE2
|
A:GLU1033
|
2.9
|
15.3
|
1.0
|
CG
|
A:HIS1106
|
3.0
|
45.0
|
1.0
|
NE2
|
A:HIS1106
|
3.0
|
45.0
|
1.0
|
CD2
|
A:HIS1110
|
3.0
|
20.0
|
1.0
|
CE1
|
A:HIS1110
|
3.4
|
20.0
|
1.0
|
ND1
|
A:HIS1106
|
3.4
|
45.0
|
1.0
|
CE1
|
A:HIS1106
|
3.5
|
45.0
|
1.0
|
CB
|
A:HIS1106
|
3.7
|
45.0
|
1.0
|
CA
|
A:HIS1106
|
3.9
|
28.1
|
1.0
|
O
|
A:HIS1106
|
4.1
|
28.1
|
1.0
|
CB
|
A:ASP1077
|
4.1
|
28.2
|
1.0
|
CG
|
A:HIS1110
|
4.2
|
20.0
|
1.0
|
CG
|
A:GLU1033
|
4.2
|
15.3
|
1.0
|
O
|
A:GLU1033
|
4.3
|
38.5
|
1.0
|
ND1
|
A:HIS1110
|
4.4
|
20.0
|
1.0
|
C
|
A:HIS1106
|
4.4
|
28.1
|
1.0
|
C
|
A:GLU1033
|
4.5
|
38.5
|
1.0
|
O
|
A:HOH2019
|
4.6
|
17.1
|
1.0
|
CB
|
A:GLU1033
|
4.6
|
15.3
|
1.0
|
CA
|
A:GLU1033
|
4.6
|
38.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 1ha5
Go back to
Zinc Binding Sites List in 1ha5
Zinc binding site 2 out
of 4 in the Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3221
b:50.8
occ:1.00
|
OE1
|
B:GLU2033
|
2.0
|
29.3
|
1.0
|
NE2
|
B:HIS2110
|
2.2
|
23.9
|
1.0
|
ND1
|
B:HIS2106
|
2.3
|
50.2
|
1.0
|
OD2
|
B:ASP2077
|
2.4
|
24.7
|
1.0
|
OD1
|
B:ASP2077
|
2.5
|
24.7
|
1.0
|
CG
|
B:ASP2077
|
2.7
|
24.7
|
1.0
|
CE1
|
B:HIS2110
|
3.0
|
23.9
|
1.0
|
CE1
|
B:HIS2106
|
3.1
|
50.2
|
1.0
|
CD
|
B:GLU2033
|
3.2
|
29.3
|
1.0
|
CG
|
B:HIS2106
|
3.3
|
50.2
|
1.0
|
CD2
|
B:HIS2110
|
3.4
|
23.9
|
1.0
|
CB
|
B:HIS2106
|
3.7
|
50.2
|
1.0
|
OE2
|
B:GLU2033
|
3.8
|
29.3
|
1.0
|
CA
|
B:HIS2106
|
3.9
|
23.7
|
1.0
|
O
|
B:HIS2106
|
4.0
|
23.7
|
1.0
|
O
|
B:GLU2033
|
4.0
|
53.5
|
1.0
|
ND1
|
B:HIS2110
|
4.2
|
23.9
|
1.0
|
O
|
B:HOH3016
|
4.2
|
22.5
|
1.0
|
CB
|
B:ASP2077
|
4.3
|
24.7
|
1.0
|
CG
|
B:GLU2033
|
4.3
|
29.3
|
1.0
|
NE2
|
B:HIS2106
|
4.3
|
50.2
|
1.0
|
C
|
B:GLU2033
|
4.3
|
53.5
|
1.0
|
CD2
|
B:HIS2106
|
4.4
|
50.2
|
1.0
|
CB
|
B:GLU2033
|
4.4
|
29.3
|
1.0
|
C
|
B:HIS2106
|
4.4
|
23.7
|
1.0
|
CA
|
B:GLU2033
|
4.4
|
53.5
|
1.0
|
CG
|
B:HIS2110
|
4.4
|
23.9
|
1.0
|
O
|
B:HOH3012
|
4.6
|
37.5
|
1.0
|
N
|
B:ASN2034
|
5.0
|
44.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 1ha5
Go back to
Zinc Binding Sites List in 1ha5
Zinc binding site 3 out
of 4 in the Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn4221
b:50.8
occ:1.00
|
OE1
|
C:GLU3033
|
2.1
|
19.6
|
1.0
|
NE2
|
C:HIS3110
|
2.1
|
26.8
|
1.0
|
ND1
|
C:HIS3106
|
2.2
|
9.8
|
1.0
|
OD2
|
C:ASP3077
|
2.3
|
16.7
|
1.0
|
OD1
|
C:ASP3077
|
2.6
|
16.7
|
1.0
|
CG
|
C:ASP3077
|
2.8
|
16.7
|
1.0
|
CE1
|
C:HIS3110
|
2.8
|
26.8
|
1.0
|
CE1
|
C:HIS3106
|
3.1
|
9.8
|
1.0
|
CD2
|
C:HIS3110
|
3.2
|
26.8
|
1.0
|
CG
|
C:HIS3106
|
3.3
|
9.8
|
1.0
|
CD
|
C:GLU3033
|
3.3
|
19.6
|
1.0
|
CB
|
C:HIS3106
|
3.7
|
9.8
|
1.0
|
CA
|
C:HIS3106
|
3.8
|
35.3
|
1.0
|
ND1
|
C:HIS3110
|
4.0
|
26.8
|
1.0
|
O
|
C:HIS3106
|
4.0
|
35.3
|
1.0
|
OE2
|
C:GLU3033
|
4.0
|
19.6
|
1.0
|
CG
|
C:HIS3110
|
4.2
|
26.8
|
1.0
|
NE2
|
C:HIS3106
|
4.2
|
9.8
|
1.0
|
CB
|
C:ASP3077
|
4.3
|
16.7
|
1.0
|
C
|
C:HIS3106
|
4.3
|
35.3
|
1.0
|
CG
|
C:GLU3033
|
4.3
|
19.6
|
1.0
|
CD2
|
C:HIS3106
|
4.4
|
9.8
|
1.0
|
CB
|
C:GLU3033
|
4.5
|
19.6
|
1.0
|
CA
|
C:GLU3033
|
4.6
|
38.9
|
1.0
|
O
|
C:HOH2030
|
4.6
|
32.5
|
1.0
|
C
|
C:GLU3033
|
4.7
|
38.9
|
1.0
|
O
|
C:GLU3033
|
4.9
|
38.9
|
1.0
|
N
|
C:ASN3034
|
4.9
|
12.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 1ha5
Go back to
Zinc Binding Sites List in 1ha5
Zinc binding site 4 out
of 4 in the Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structural Features of A Zinc-Binding Site in the Superantigen Streptococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn5221
b:50.8
occ:1.00
|
OD1
|
D:ASP4077
|
2.2
|
59.7
|
1.0
|
ND1
|
D:HIS4106
|
2.2
|
30.8
|
1.0
|
OE1
|
D:GLU4033
|
2.3
|
55.4
|
1.0
|
NE2
|
D:HIS4110
|
2.5
|
47.1
|
1.0
|
CG
|
D:ASP4077
|
2.6
|
59.7
|
1.0
|
OD2
|
D:ASP4077
|
2.6
|
59.7
|
1.0
|
CE1
|
D:HIS4106
|
2.8
|
30.8
|
1.0
|
CE1
|
D:HIS4110
|
2.8
|
47.1
|
1.0
|
CD
|
D:GLU4033
|
3.0
|
55.4
|
1.0
|
CG
|
D:HIS4106
|
3.3
|
30.8
|
1.0
|
OE2
|
D:GLU4033
|
3.5
|
55.4
|
1.0
|
CD2
|
D:HIS4110
|
3.8
|
47.1
|
1.0
|
CB
|
D:ASP4077
|
3.8
|
59.7
|
1.0
|
NE2
|
D:HIS4106
|
3.9
|
30.8
|
1.0
|
CB
|
D:HIS4106
|
3.9
|
30.8
|
1.0
|
CA
|
D:GLU4033
|
3.9
|
42.1
|
1.0
|
CB
|
D:GLU4033
|
3.9
|
55.4
|
1.0
|
C
|
D:GLU4033
|
4.0
|
42.1
|
1.0
|
CG
|
D:GLU4033
|
4.1
|
55.4
|
1.0
|
O
|
D:GLU4033
|
4.1
|
42.1
|
1.0
|
CD2
|
D:HIS4106
|
4.1
|
30.8
|
1.0
|
ND1
|
D:HIS4110
|
4.1
|
47.1
|
1.0
|
CA
|
D:HIS4106
|
4.3
|
31.0
|
1.0
|
O
|
D:HIS4106
|
4.5
|
31.0
|
1.0
|
N
|
D:ASN4034
|
4.6
|
28.1
|
1.0
|
CG
|
D:HIS4110
|
4.6
|
47.1
|
1.0
|
CA
|
D:ASP4077
|
4.7
|
52.1
|
1.0
|
C
|
D:HIS4106
|
4.9
|
31.0
|
1.0
|
|
Reference:
M.D.Baker,
D.M.Gutman,
A.C.Papageorgiou,
C.M.Collins,
K.R.Acharya.
Structural Features of A Zinc Binding Site in the Superantigen Strepococcal Pyrogenic Exotoxin A (SPEA1): Implications For Mhc Class II Recognition. Protein Sci. V. 10 1268 2001.
ISSN: ISSN 0961-8368
PubMed: 11369867
DOI: 10.1110/PS.330101
Page generated: Sun Oct 13 02:05:12 2024
|