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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:

Zinc (Zn) 28 atoms

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

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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 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

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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

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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

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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

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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: Tue Oct 27 16:46:56 2020

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