Zinc in PDB 1nlx: Crystal Structure of Phl P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc

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

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

(As)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 28 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 28 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 Zinc with other atoms in the Zn 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 A:Zn5001 b:29.1 occ:1.00 NE2 B:HIS677 2.1 26.5 1.0 OD2 A:ASP476 2.5 39.3 1.0 CD2 B:HIS677 2.9 26.0 1.0 CG A:ASP476 3.0 37.4 1.0 OD1 A:ASP476 3.1 36.5 1.0 CE1 B:HIS677 3.1 25.7 1.0 OD2 B:ASP676 3.4 33.3 1.0 OD1 B:ASN673 3.5 42.0 1.0 CG B:HIS677 4.1 24.5 1.0 ND1 B:HIS677 4.2 26.0 1.0 CG B:ASN673 4.2 42.9 1.0 CB A:ASP476 4.3 35.8 1.0 ZN B:ZN5002 4.6 29.6 1.0 CB B:ASN673 4.6 41.8 1.0 CG B:ASP676 4.6 30.8 1.0 O B:ASN673 4.8 26.4 1.0 OD1 A:ASN473 4.9 40.9 1.0 CA B:ASN673 5.0 26.3 1.0

Zinc binding site 2 out of 28 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 Zinc with other atoms in the Zn 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:Zn5002 b:29.6 occ:1.00 OE2 N:GLU3103 2.1 45.5 1.0 NE2 A:HIS477 2.1 34.7 1.0 OD2 B:ASP676 2.5 33.3 1.0 CD N:GLU3103 2.7 45.5 1.0 OE1 N:GLU3103 2.7 43.9 1.0 CD2 A:HIS477 2.9 35.1 1.0 OD1 B:ASP676 2.9 28.6 1.0 CG B:ASP676 3.0 30.8 1.0 CE1 A:HIS477 3.1 34.1 1.0 OD2 A:ASP476 3.5 39.3 1.0 OD1 A:ASN473 3.6 40.9 1.0 CG A:HIS477 4.1 33.6 1.0 ND1 A:HIS477 4.2 33.3 1.0 CG N:GLU3103 4.2 44.5 1.0 CB B:ASP676 4.3 30.7 1.0 CG A:ASN473 4.3 42.3 1.0 ZN A:ZN5001 4.6 29.1 1.0 CB A:ASN473 4.6 40.5 1.0 CG A:ASP476 4.7 37.4 1.0 O A:ASN473 4.9 28.3 1.0

Zinc binding site 3 out of 28 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 Zinc with other atoms in the Zn 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:Zn5003 b:32.8 occ:1.00 OE2 F:GLU1503 2.1 30.3 1.0 NE2 D:HIS1077 2.1 33.2 1.0 OD2 C:ASP876 2.6 43.6 1.0 CD F:GLU1503 2.8 29.5 1.0 OE1 F:GLU1503 2.9 28.4 1.0 CD2 D:HIS1077 2.9 33.3 1.0 CG C:ASP876 3.1 39.4 1.0 CE1 D:HIS1077 3.1 33.1 1.0 OD1 C:ASP876 3.2 39.4 1.0 OD2 D:ASP1076 3.4 35.8 1.0 OD1 D:ASN1073 3.5 36.0 1.0 CG D:HIS1077 4.1 33.6 1.0 ND1 D:HIS1077 4.2 32.1 1.0 CG F:GLU1503 4.2 27.4 1.0 CG D:ASN1073 4.3 34.1 1.0 CB C:ASP876 4.3 36.9 1.0 CG D:ASP1076 4.6 30.9 1.0 CB D:ASN1073 4.6 33.4 1.0 ZN D:ZN5004 4.7 25.0 1.0 OD1 C:ASN873 4.7 27.0 1.0 O D:ASN1073 4.8 13.9 1.0

Zinc binding site 4 out of 28 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 Zinc with other atoms in the Zn 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:Zn5004 b:25.0 occ:1.00 NE2 C:HIS877 2.1 16.6 1.0 OD2 D:ASP1076 2.5 35.8 1.0 OD1 D:ASP1076 2.8 27.0 1.0 CG D:ASP1076 2.8 30.9 1.0 CD2 C:HIS877 2.9 18.5 1.0 CE1 C:HIS877 3.1 19.9 1.0 OD1 C:ASN873 3.5 27.0 1.0 OD2 C:ASP876 3.6 43.6 1.0 CG C:HIS877 4.1 19.4 1.0 ND1 C:HIS877 4.2 21.0 1.0 CB D:ASP1076 4.2 31.4 1.0 CG C:ASN873 4.3 24.6 1.0 CB C:ASN873 4.6 23.4 1.0 ZN C:ZN5003 4.7 32.8 1.0 CE1 D:TYR1072 4.7 66.5 1.0 CG C:ASP876 4.8 39.4 1.0 O C:ASN873 4.9 27.5 1.0

Zinc binding site 5 out of 28 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 Zinc with other atoms in the Zn 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 E:Zn5005 b:30.1 occ:1.00 OE2 D:GLU1103 2.1 30.7 1.0 NE2 F:HIS1477 2.1 24.9 1.0 OD2 E:ASP1276 2.6 40.8 1.0 CD D:GLU1103 2.8 31.1 1.0 OE1 D:GLU1103 2.8 29.9 1.0 CD2 F:HIS1477 2.9 25.4 1.0 CG E:ASP1276 3.1 38.2 1.0 CE1 F:HIS1477 3.1 25.0 1.0 OD1 E:ASP1276 3.2 38.6 1.0 OD2 F:ASP1476 3.4 31.2 1.0 OD1 F:ASN1473 3.5 29.0 1.0 CG F:HIS1477 4.1 25.7 1.0 ND1 F:HIS1477 4.2 25.2 1.0 CG D:GLU1103 4.2 30.3 1.0 CG F:ASN1473 4.3 29.9 1.0 CB E:ASP1276 4.3 35.6 1.0 CG F:ASP1476 4.6 27.2 1.0 CB F:ASN1473 4.6 30.4 1.0 ZN F:ZN5006 4.6 23.4 1.0 OD1 E:ASN1273 4.7 23.0 1.0 O F:ASN1473 4.9 18.2 1.0

Zinc binding site 6 out of 28 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 Zinc with other atoms in the Zn 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 F:Zn5006 b:23.4 occ:1.00 OE2 L:GLU2703 2.0 28.1 1.0 NE2 E:HIS1277 2.1 17.4 1.0 OD2 F:ASP1476 2.5 31.2 1.0 CD L:GLU2703 2.7 27.3 1.0 OE1 L:GLU2703 2.8 27.9 1.0 OD1 F:ASP1476 2.8 23.1 1.0 CG F:ASP1476 2.9 27.2 1.0 CD2 E:HIS1277 2.9 18.5 1.0 CE1 E:HIS1277 3.2 20.3 1.0 OD1 E:ASN1273 3.5 23.0 1.0 OD2 E:ASP1276 3.6 40.8 1.0 CG E:HIS1277 4.1 18.4 1.0 CG L:GLU2703 4.1 27.4 1.0 CG E:ASN1273 4.2 23.0 1.0 ND1 E:HIS1277 4.2 20.7 1.0 CB F:ASP1476 4.2 27.9 1.0 CB E:ASN1273 4.5 21.6 1.0 ZN E:ZN5005 4.6 30.1 1.0 CG E:ASP1276 4.7 38.2 1.0 O E:ASN1273 4.8 25.2 1.0 CE1 F:TYR1472 4.9 65.6 1.0 CA E:ASN1273 5.0 24.2 1.0

Zinc binding site 7 out of 28 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 Zinc with other atoms in the Zn 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 G:Zn5007 b:25.2 occ:1.00 NE2 H:HIS1877 2.1 34.7 1.0 OD2 G:ASP1676 2.5 32.3 1.0 OD1 G:ASP1676 2.9 29.3 1.0 CG G:ASP1676 2.9 31.6 1.0 CD2 H:HIS1877 3.0 35.8 1.0 CE1 H:HIS1877 3.1 35.4 1.0 OD2 H:ASP1876 3.6 66.2 1.0 OD1 H:ASN1873 3.6 19.6 1.0 CG H:HIS1877 4.1 35.8 1.0 ND1 H:HIS1877 4.2 37.1 1.0 CB G:ASP1676 4.2 31.2 1.0 CG H:ASN1873 4.3 21.0 1.0 ZN H:ZN5008 4.6 29.3 1.0 CB H:ASN1873 4.7 20.2 1.0 CG H:ASP1876 4.7 64.5 1.0 O H:ASN1873 4.9 24.6 1.0

Zinc binding site 8 out of 28 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 Zinc with other atoms in the Zn binding site number 8 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 H:Zn5008 b:29.3 occ:1.00 OE2 K:GLU2503 2.0 25.5 1.0 NE2 G:HIS1677 2.2 29.8 1.0 OD2 H:ASP1876 2.5 66.2 1.0 CD K:GLU2503 2.8 25.8 1.0 OE1 K:GLU2503 2.9 27.5 1.0 CG H:ASP1876 3.0 64.5 1.0 CD2 G:HIS1677 3.0 29.5 1.0 OD1 H:ASP1876 3.1 64.7 1.0 CE1 G:HIS1677 3.2 30.1 1.0 OD2 G:ASP1676 3.5 32.3 1.0 OD1 G:ASN1673 3.5 21.7 1.0 CG K:GLU2503 4.2 23.2 1.0 CG G:HIS1677 4.2 29.3 1.0 ND1 G:HIS1677 4.2 29.4 1.0 CB H:ASP1876 4.2 62.2 1.0 CG G:ASN1673 4.3 23.8 1.0 ZN G:ZN5007 4.6 25.2 1.0 CB G:ASN1673 4.6 24.9 1.0 CG G:ASP1676 4.7 31.6 1.0 OD1 H:ASN1873 4.8 19.6 1.0 O G:ASN1673 4.9 28.8 1.0

Zinc binding site 9 out of 28 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 Zinc with other atoms in the Zn binding site number 9 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:Zn5009 b:23.2 occ:1.00 NE2 J:HIS2277 2.0 19.4 1.0 OD2 I:ASP2076 2.5 21.4 1.0 CD2 J:HIS2277 2.8 19.6 1.0 CG I:ASP2076 3.1 15.9 1.0 CE1 J:HIS2277 3.1 19.7 1.0 OD1 I:ASP2076 3.2 13.4 1.0 OD2 J:ASP2276 3.4 26.8 1.0 OD1 J:ASN2273 3.5 16.2 1.0 CG J:HIS2277 4.0 18.1 1.0 ND1 J:HIS2277 4.1 19.6 1.0 CG J:ASN2273 4.2 18.1 1.0 CB I:ASP2076 4.3 18.4 1.0 ZN J:ZN5010 4.5 22.6 1.0 CB J:ASN2273 4.6 21.0 1.0 CG J:ASP2276 4.6 22.9 1.0 O J:ASN2273 4.8 19.8 1.0 OD1 I:ASN2073 4.9 26.4 1.0 CA J:ASN2273 5.0 21.6 1.0

Zinc binding site 10 out of 28 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 Zinc with other atoms in the Zn binding site number 10 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 J:Zn5010 b:22.6 occ:1.00 OE2 M:GLU2903 2.0 35.7 1.0 NE2 I:HIS2077 2.1 22.4 1.0 OD2 J:ASP2276 2.4 26.8 1.0 CD M:GLU2903 2.7 35.9 1.0 OE1 M:GLU2903 2.8 35.5 1.0 CG J:ASP2276 2.9 22.9 1.0 OD1 J:ASP2276 2.9 20.8 1.0 CD2 I:HIS2077 2.9 21.1 1.0 CE1 I:HIS2077 3.1 23.5 1.0 OD2 I:ASP2076 3.5 21.4 1.0 OD1 I:ASN2073 3.6 26.4 1.0 CG I:HIS2077 4.1 20.4 1.0 ND1 I:HIS2077 4.1 22.7 1.0 CG M:GLU2903 4.2 35.2 1.0 CB J:ASP2276 4.2 22.6 1.0 CG I:ASN2073 4.3 27.9 1.0 ZN I:ZN5009 4.5 23.2 1.0 CB I:ASN2073 4.6 26.7 1.0 CG I:ASP2076 4.7 15.9 1.0 O I:ASN2073 4.8 15.2 1.0 OD1 J:ASN2273 5.0 16.2 1.0

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.