Arsenic in PDB 1nlx: Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Protein crystallography data
The structure of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc, PDB code: 1nlx
was solved by
A.A.Fedorov,
T.Ball,
E.V.Fedorov,
S.Vrtala,
R.Valenta,
S.C.Almo,
S.K.Burley,
New York Sgx Research Center For Structural Genomics(Nysgxrc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.809,
110.335,
159.420,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.3 /
27.2
|
Other elements in 1nlx:
The structure of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc also contains other interesting chemical elements:
Arsenic Binding Sites:
The binding sites of Arsenic atom in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
(pdb code 1nlx). This binding sites where shown within
5.0 Angstroms radius around Arsenic atom.
In total 7 binding sites of Arsenic where determined in the
Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc, PDB code: 1nlx:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
7;
Arsenic binding site 1 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 1 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 1 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:As7001
b:61.8
occ:1.00
|
ZN
|
N:ZN6014
|
3.5
|
26.5
|
1.0
|
ZN
|
A:ZN6001
|
3.6
|
28.9
|
1.0
|
OE2
|
A:GLU493
|
3.8
|
30.0
|
1.0
|
CD2
|
A:LEU489
|
3.9
|
42.0
|
1.0
|
OE2
|
N:GLU3093
|
4.0
|
16.9
|
1.0
|
CD2
|
N:LEU3089
|
4.0
|
43.4
|
1.0
|
CG
|
A:LEU489
|
4.3
|
43.1
|
1.0
|
NE2
|
N:HIS3090
|
4.3
|
23.3
|
1.0
|
NE2
|
A:HIS490
|
4.4
|
23.1
|
1.0
|
CD
|
A:GLU493
|
4.5
|
30.2
|
1.0
|
CG
|
N:LEU3089
|
4.5
|
45.1
|
1.0
|
OE1
|
A:GLU493
|
4.5
|
31.0
|
1.0
|
CE1
|
N:HIS3090
|
4.5
|
22.5
|
1.0
|
CE1
|
A:HIS490
|
4.6
|
23.1
|
1.0
|
CD
|
N:GLU3093
|
4.7
|
16.7
|
1.0
|
CD1
|
A:LEU489
|
4.7
|
42.4
|
1.0
|
OE1
|
N:GLU3093
|
4.8
|
17.1
|
1.0
|
CD2
|
N:HIS3090
|
5.0
|
23.1
|
1.0
|
CD1
|
N:LEU3089
|
5.0
|
44.4
|
1.0
|
|
Arsenic binding site 2 out
of 7 in 1nlx
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Arsenic Binding Sites List in 1nlx
Arsenic binding site 2 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 2 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:As7002
b:68.9
occ:1.00
|
ZN
|
B:ZN6002
|
3.6
|
29.2
|
1.0
|
OE2
|
B:GLU693
|
3.7
|
31.2
|
1.0
|
CD2
|
B:LEU689
|
3.9
|
38.9
|
1.0
|
CG
|
B:LEU689
|
4.3
|
39.7
|
1.0
|
NE2
|
B:HIS690
|
4.4
|
18.3
|
1.0
|
CD
|
B:GLU693
|
4.4
|
31.8
|
1.0
|
OE1
|
B:GLU693
|
4.5
|
32.4
|
1.0
|
CE1
|
B:HIS690
|
4.6
|
18.8
|
1.0
|
CD1
|
B:LEU689
|
4.8
|
40.2
|
1.0
|
|
Arsenic binding site 3 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 3 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 3 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As7003
b:60.1
occ:1.00
|
ZN
|
C:ZN6003
|
3.5
|
27.6
|
1.0
|
CD2
|
C:LEU889
|
3.8
|
55.0
|
1.0
|
OE2
|
C:GLU893
|
3.9
|
25.8
|
1.0
|
CG
|
C:LEU889
|
4.3
|
52.2
|
1.0
|
NE2
|
C:HIS890
|
4.4
|
20.1
|
1.0
|
CE1
|
C:HIS890
|
4.6
|
19.6
|
1.0
|
CD
|
C:GLU893
|
4.6
|
26.6
|
1.0
|
OE1
|
C:GLU893
|
4.7
|
29.2
|
1.0
|
CD1
|
C:LEU889
|
4.8
|
51.5
|
1.0
|
|
Arsenic binding site 4 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 4 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 4 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As7004
b:66.2
occ:1.00
|
ZN
|
D:ZN6004
|
3.5
|
28.0
|
1.0
|
ZN
|
F:ZN6006
|
3.6
|
26.4
|
1.0
|
OE2
|
F:GLU1493
|
3.8
|
18.5
|
1.0
|
OE2
|
D:GLU1093
|
3.8
|
17.8
|
1.0
|
CD2
|
F:LEU1489
|
4.0
|
40.6
|
1.0
|
CD2
|
D:LEU1089
|
4.1
|
33.9
|
1.0
|
NE2
|
F:HIS1490
|
4.2
|
28.9
|
1.0
|
NE2
|
D:HIS1090
|
4.3
|
25.4
|
1.0
|
CG
|
F:LEU1489
|
4.5
|
39.5
|
1.0
|
CE1
|
F:HIS1490
|
4.5
|
27.3
|
1.0
|
CE1
|
D:HIS1090
|
4.5
|
25.2
|
1.0
|
CG
|
D:LEU1089
|
4.5
|
34.1
|
1.0
|
CD
|
F:GLU1493
|
4.5
|
20.1
|
1.0
|
CD
|
D:GLU1093
|
4.6
|
21.3
|
1.0
|
OE1
|
F:GLU1493
|
4.6
|
22.1
|
1.0
|
OE1
|
D:GLU1093
|
4.7
|
23.8
|
1.0
|
CD2
|
F:HIS1490
|
4.9
|
28.0
|
1.0
|
CD2
|
D:HIS1090
|
4.9
|
25.1
|
1.0
|
CD1
|
F:LEU1489
|
5.0
|
39.8
|
1.0
|
CD1
|
D:LEU1089
|
5.0
|
32.9
|
1.0
|
|
Arsenic binding site 5 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 5 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 5 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:As7005
b:57.2
occ:1.00
|
ZN
|
L:ZN6012
|
3.3
|
26.4
|
1.0
|
ZN
|
E:ZN6005
|
3.6
|
25.5
|
1.0
|
OE2
|
L:GLU2693
|
3.6
|
8.8
|
1.0
|
OE2
|
E:GLU1293
|
3.7
|
31.4
|
1.0
|
CD2
|
E:LEU1289
|
4.0
|
43.5
|
1.0
|
CD2
|
L:LEU2689
|
4.0
|
33.4
|
1.0
|
NE2
|
L:HIS2690
|
4.3
|
21.2
|
1.0
|
CG
|
E:LEU1289
|
4.4
|
42.8
|
1.0
|
CG
|
L:LEU2689
|
4.4
|
33.4
|
1.0
|
CD
|
L:GLU2693
|
4.4
|
11.5
|
1.0
|
CD
|
E:GLU1293
|
4.5
|
31.0
|
1.0
|
NE2
|
E:HIS1290
|
4.5
|
19.3
|
1.0
|
CE1
|
L:HIS2690
|
4.5
|
19.3
|
1.0
|
OE1
|
E:GLU1293
|
4.5
|
34.2
|
1.0
|
OE1
|
L:GLU2693
|
4.6
|
11.0
|
1.0
|
CE1
|
E:HIS1290
|
4.7
|
19.0
|
1.0
|
CD1
|
E:LEU1289
|
4.8
|
43.1
|
1.0
|
CD1
|
L:LEU2689
|
4.8
|
31.8
|
1.0
|
CD2
|
L:HIS2690
|
4.9
|
20.6
|
1.0
|
|
Arsenic binding site 6 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 6 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 6 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:As7007
b:63.4
occ:1.00
|
ZN
|
K:ZN6011
|
3.3
|
28.8
|
1.0
|
OE2
|
G:GLU1693
|
3.6
|
27.9
|
1.0
|
ZN
|
G:ZN6007
|
3.7
|
24.4
|
1.0
|
OE2
|
K:GLU2493
|
3.7
|
26.1
|
1.0
|
CD2
|
G:LEU1689
|
4.0
|
38.1
|
1.0
|
CD2
|
K:LEU2489
|
4.1
|
24.0
|
1.0
|
NE2
|
K:HIS2490
|
4.3
|
16.5
|
1.0
|
CD
|
G:GLU1693
|
4.3
|
29.2
|
1.0
|
CG
|
G:LEU1689
|
4.4
|
35.0
|
1.0
|
OE1
|
G:GLU1693
|
4.4
|
27.8
|
1.0
|
CG
|
K:LEU2489
|
4.4
|
23.7
|
1.0
|
NE2
|
G:HIS1690
|
4.5
|
32.2
|
1.0
|
CE1
|
K:HIS2490
|
4.5
|
17.2
|
1.0
|
CD
|
K:GLU2493
|
4.5
|
27.5
|
1.0
|
OE1
|
K:GLU2493
|
4.7
|
29.3
|
1.0
|
CE1
|
G:HIS1690
|
4.7
|
30.5
|
1.0
|
CD1
|
G:LEU1689
|
4.8
|
36.3
|
1.0
|
CD2
|
K:HIS2490
|
4.9
|
16.3
|
1.0
|
CD1
|
K:LEU2489
|
4.9
|
21.1
|
1.0
|
|
Arsenic binding site 7 out
of 7 in 1nlx
Go back to
Arsenic Binding Sites List in 1nlx
Arsenic binding site 7 out
of 7 in the Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc
Mono view
Stereo pair view
|
A full contact list of Arsenic with other atoms in the As binding
site number 7 of Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:As7009
b:57.0
occ:1.00
|
ZN
|
I:ZN6009
|
3.3
|
25.7
|
1.0
|
OE2
|
M:GLU2893
|
3.5
|
22.6
|
1.0
|
ZN
|
M:ZN6013
|
3.6
|
32.1
|
1.0
|
OE2
|
I:GLU2093
|
3.6
|
26.3
|
1.0
|
CD2
|
I:LEU2089
|
4.0
|
28.6
|
1.0
|
CD2
|
M:LEU2889
|
4.1
|
32.2
|
1.0
|
NE2
|
I:HIS2090
|
4.2
|
24.5
|
1.0
|
CD
|
M:GLU2893
|
4.3
|
25.1
|
1.0
|
CD
|
I:GLU2093
|
4.4
|
27.5
|
1.0
|
CG
|
I:LEU2089
|
4.4
|
28.1
|
1.0
|
OE1
|
M:GLU2893
|
4.5
|
25.4
|
1.0
|
CE1
|
I:HIS2090
|
4.5
|
24.8
|
1.0
|
CG
|
M:LEU2889
|
4.5
|
30.6
|
1.0
|
OE1
|
I:GLU2093
|
4.5
|
29.3
|
1.0
|
NE2
|
M:HIS2890
|
4.5
|
25.5
|
1.0
|
CE1
|
M:HIS2890
|
4.8
|
22.9
|
1.0
|
CD2
|
I:HIS2090
|
4.8
|
23.4
|
1.0
|
CD1
|
I:LEU2089
|
4.8
|
25.5
|
1.0
|
CD1
|
M:LEU2889
|
4.9
|
32.1
|
1.0
|
|
Reference:
A.A.Fedorov,
T.Ball,
E.V.Fedorov,
S.Vrtala,
R.Valenta,
S.C.Almo.
Crystal Structure Oh Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc To Be Published.
Page generated: Wed Jul 10 11:08:24 2024
|