Zinc in PDB 8db4: Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1

The structure of Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1, PDB code: 8db4 was solved by J.Min, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.75 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.796, 92.177, 96.18, 95.04, 106.03, 108.87
R / Rfree (%)	21.1 / 24.6

The binding sites of Zinc atom in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 (pdb code 8db4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1, PDB code: 8db4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:51.4 occ:1.00 O A:HOH452 1.8 46.7 1.0 OD2 A:ASP73 2.0 47.2 1.0 OE2 I:GLU56 2.0 56.5 1.0 NE2 A:HIS80 2.2 38.9 1.0 OE1 I:GLU56 2.7 55.3 1.0 CD I:GLU56 2.7 50.7 1.0 CG A:ASP73 2.8 48.6 1.0 OD1 A:ASP73 2.9 51.0 1.0 O A:HOH425 3.1 41.8 1.0 CD2 A:HIS80 3.2 43.8 1.0 CE1 A:HIS80 3.2 35.4 1.0 NH2 A:ARG19 3.8 55.9 1.0 NH1 A:ARG19 4.0 36.7 1.0 CG2 A:THR78 4.1 35.8 1.0 CG I:GLU56 4.2 52.4 1.0 CB A:ASP73 4.2 44.1 1.0 CZ A:ARG19 4.3 53.8 1.0 ND1 A:HIS80 4.3 39.2 1.0 CG A:HIS80 4.3 33.8 1.0 CB A:THR78 4.4 47.4 1.0 CD A:LYS76 4.5 57.5 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:67.2 occ:1.00 OD2 B:ASP153 1.9 50.4 1.0 ND1 B:HIS191 2.2 67.5 1.0 O B:HOH437 2.3 60.3 1.0 CG B:ASP153 2.9 54.1 1.0 CE1 B:HIS191 3.0 59.9 1.0 CG B:HIS191 3.4 59.7 1.0 CB B:ASP153 3.4 48.1 1.0 CB B:HIS191 3.8 56.8 1.0 CA B:HIS191 4.0 57.0 1.0 OD1 B:ASP153 4.1 54.2 1.0 NE2 B:HIS191 4.2 67.1 1.0 CD2 B:HIS191 4.4 61.6 1.0 O B:LYS190 4.4 62.5 1.0 CA B:ASP153 4.8 63.4 1.0 N B:HIS191 4.8 60.0 1.0 C B:LYS190 4.9 61.6 1.0 O B:VAL152 5.0 57.4 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:66.7 occ:1.00 OD1 D:ASP185 2.1 74.6 1.0 NE2 D:HIS189 2.3 66.1 1.0 CE1 D:HIS189 2.8 67.4 1.0 CG D:ASP185 2.9 71.5 1.0 OD2 D:ASP185 3.2 70.2 1.0 CD2 D:HIS189 3.6 62.0 1.0 ND1 D:HIS189 4.1 61.3 1.0 O D:ASP185 4.3 65.3 1.0 CB D:ASP185 4.3 66.4 1.0 CG D:HIS189 4.5 63.3 1.0 CA D:ASP185 4.7 62.3 1.0 CE D:LYS188 4.8 64.9 1.0 C D:ASP185 4.8 62.9 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:88.2 occ:0.57 OD1 D:ASN138 2.3 59.2 1.0 OD1 D:ASN137 2.3 68.4 1.0 NE2 C:HIS172 2.4 70.4 1.0 O D:HOH418 2.5 61.1 1.0 CG D:ASN138 3.0 66.8 1.0 CG D:ASN137 3.0 64.5 1.0 CD2 C:HIS172 3.0 72.1 1.0 ND2 D:ASN137 3.1 66.9 1.0 ND2 D:ASN138 3.3 66.0 1.0 CE1 C:HIS172 3.5 73.7 1.0 CG2 C:THR191 4.1 81.6 1.0 O C:GLY170 4.2 79.0 1.0 CB D:ASN138 4.2 58.2 1.0 CG C:HIS172 4.3 66.9 1.0 CA C:GLY170 4.4 83.1 1.0 CB D:ASN137 4.5 59.3 1.0 ND1 C:HIS172 4.5 72.8 1.0 C C:GLY170 4.6 82.9 1.0 OG D:SER174 4.6 64.0 1.0 CB C:THR191 4.6 77.5 1.0 N D:ASN138 4.8 60.5 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:111.3 occ:0.91 ND1 E:HIS48 2.3 72.7 1.0 CB E:SER85 3.0 90.2 1.0 CG E:HIS48 3.2 66.4 1.0 OG E:SER85 3.2 93.7 1.0 CE1 E:HIS48 3.3 69.4 1.0 CB E:HIS48 3.4 60.6 1.0 CA E:HIS48 3.5 60.1 1.0 ND1 E:HIS87 4.0 86.4 1.0 N E:GLN88 4.0 71.0 1.0 CB E:GLN88 4.1 71.2 1.0 O E:HIS48 4.2 58.4 1.0 C E:HIS48 4.3 55.2 1.0 CD2 E:HIS48 4.3 68.5 1.0 NE2 E:HIS48 4.4 62.3 1.0 CA E:SER85 4.5 91.0 1.0 CB E:HIS87 4.5 76.7 1.0 CA E:GLN88 4.5 64.3 1.0 N E:HIS87 4.6 76.5 1.0 N E:HIS48 4.6 58.7 1.0 CG E:HIS87 4.7 78.9 1.0 C E:HIS87 4.7 65.2 1.0 CA E:HIS87 4.8 67.3 1.0 C E:SER85 4.9 90.2 1.0 CE1 E:HIS87 5.0 88.5 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:104.1 occ:1.00 ND1 F:HIS48 2.4 84.3 1.0 CE1 F:HIS48 3.3 86.0 1.0 CG F:HIS48 3.4 79.2 1.0 CA F:HIS48 3.6 64.3 1.0 CB F:HIS48 3.7 58.3 1.0 O F:HIS48 4.0 63.9 1.0 C F:HIS48 4.3 60.9 1.0 NE2 F:HIS48 4.4 78.2 1.0 CB F:HIS87 4.4 59.7 1.0 CD2 F:HIS48 4.5 68.7 1.0 N F:GLN88 4.6 75.7 1.0 CB F:GLN88 4.6 69.4 1.0 N F:HIS48 4.7 62.1 1.0 CB F:GLN51 4.8 75.6 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:63.3 occ:1.00 OD2 H:ASP153 2.0 58.4 1.0 ND1 H:HIS191 2.4 70.0 1.0 O H:HOH411 2.6 59.6 1.0 CG H:ASP153 3.0 58.5 1.0 CE1 H:HIS191 3.3 67.2 1.0 CB H:ASP153 3.4 49.5 1.0 CG H:HIS191 3.5 64.3 1.0 CB H:HIS191 3.8 58.8 1.0 CA H:HIS191 3.9 62.5 1.0 OD1 H:ASP153 4.1 63.0 1.0 O H:LYS190 4.3 72.5 1.0 NE2 H:HIS191 4.5 70.8 1.0 CD2 H:HIS191 4.6 68.1 1.0 N H:HIS191 4.8 62.0 1.0 CA H:ASP153 4.8 62.8 1.0 O H:VAL152 4.9 57.1 1.0 C H:LYS190 4.9 69.5 1.0 N H:LYS192 4.9 60.3 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:57.4 occ:1.00 OD1 J:ASP185 2.1 46.4 1.0 NE2 J:HIS189 2.4 58.3 1.0 O J:HOH439 2.5 61.0 1.0 CG J:ASP185 2.8 59.6 1.0 OD2 J:ASP185 3.0 49.9 1.0 CE1 J:HIS189 3.2 62.3 1.0 CD2 J:HIS189 3.4 53.9 1.0 CB J:ASP185 4.3 51.6 1.0 O J:ASP185 4.3 56.0 1.0 ND1 J:HIS189 4.3 52.5 1.0 CG J:HIS189 4.4 54.7 1.0 CA J:ASP185 4.8 51.8 1.0 C J:ASP185 4.8 54.8 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1


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 the Peanut Allergen Ara H 2 Bound By Two Neutralizing Antibodies 22S1 and 13T1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn302 b:71.5 occ:0.45 NE2 I:HIS172 2.2 61.1 1.0 OD1 J:ASN138 2.3 56.1 1.0 CD2 I:HIS172 2.7 45.0 1.0 CG J:ASN138 3.0 46.9 1.0 ND2 J:ASN137 3.0 55.4 1.0 OD1 J:ASN137 3.0 62.9 1.0 ND2 J:ASN138 3.1 63.2 1.0 CG J:ASN137 3.4 52.4 1.0 CE1 I:HIS172 3.4 60.6 1.0 O I:GLY170 3.9 62.0 1.0 CG I:HIS172 4.0 55.8 1.0 OG1 I:THR191 4.3 55.3 1.0 OG J:SER174 4.3 39.8 1.0 ND1 I:HIS172 4.3 58.2 1.0 CB J:ASN138 4.4 38.1 1.0 C I:GLY170 4.4 64.3 1.0 CA I:GLY170 4.5 59.4 1.0 CB J:ASN137 4.8 45.9 1.0 O J:HOH431 4.9 44.0 1.0 N J:ASN138 4.9 41.1 1.0

N.A.Lahood, J.Min, T.Keswani, C.M.Richardson, K.Amoako, J.Zhou, O.Marini-Rapoport, H.Bernard, S.Hazebrouck, W.G.Shreffler, J.C.Love, A.Pomes, L.C.Pedersen, G.A.Mueller, S.U.Patil. Immunotherapy-Induced Neutralizing Antibodies Disrupt Allergen Binding and Sustain Allergen Tolerance in Peanut Allergy. J.Clin.Invest. V. 133 2023.
ISSN: ISSN 0021-9738
PubMed: 36647835
DOI: 10.1172/JCI164501