Zinc in PDB 3liz: Crystal Structure of Bla G 2 Complexed with Fab 4C3

The structure of Crystal Structure of Bla G 2 Complexed with Fab 4C3, PDB code: 3liz was solved by M.Li, A.Gustchina, J.Glesner, S.Wunschmann, A.Pomes, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.49 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.213, 105.285, 109.154, 90.00, 132.58, 90.00
R / Rfree (%)	17.7 / 20.2

The structure of Crystal Structure of Bla G 2 Complexed with Fab 4C3 also contains other interesting chemical elements:

Cadmium

(Cd)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Bla G 2 Complexed with Fab 4C3 (pdb code 3liz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Bla G 2 Complexed with Fab 4C3, PDB code: 3liz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn333 b:22.7 occ:1.00 OD1 A:ASP303 2.0 25.1 1.0 NE2 A:HIS161 2.0 14.3 1.0 OD1 A:ASP307 2.0 21.0 1.0 ND1 A:HIS155 2.1 21.7 1.0 CG A:ASP303 2.8 23.3 1.0 CG A:ASP307 2.8 23.2 1.0 CD2 A:HIS161 2.9 17.8 1.0 OD2 A:ASP303 2.9 25.6 1.0 OD2 A:ASP307 2.9 24.7 1.0 CE1 A:HIS155 3.0 20.6 1.0 CE1 A:HIS161 3.1 24.4 1.0 CG A:HIS155 3.2 20.4 1.0 CB A:HIS155 3.6 21.5 1.0 OH A:TYR14 3.9 24.0 1.0 CG A:HIS161 4.1 21.6 1.0 ND1 A:HIS161 4.1 18.9 1.0 NE2 A:HIS155 4.2 20.9 1.0 CB A:ASP307 4.2 22.6 1.0 CB A:ASP303 4.2 22.7 1.0 O A:ASP303 4.3 24.1 1.0 CD2 A:HIS155 4.3 19.8 1.0 N A:ALA156 4.4 23.4 1.0 NE A:ARG157 4.5 30.5 1.0 CE1 A:TYR14 4.5 20.3 1.0 C A:HIS155 4.5 22.6 1.0 CZ A:TYR14 4.6 24.8 1.0 C A:ASP303 4.7 23.7 1.0 CA A:ASP307 4.7 22.2 1.0 CG A:ARG157 4.7 29.1 1.0 CA A:HIS155 4.7 21.4 1.0 CA A:ASP303 4.8 23.2 1.0 N A:ASP307 4.8 22.1 1.0 NH2 A:ARG157 4.9 29.1 1.0 C A:ALA156 4.9 25.2 1.0 O A:ALA156 4.9 23.8 1.0 CA A:ALA156 5.0 23.7 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn334 b:32.1 occ:0.60 OD1 A:ASP248 1.9 39.1 0.5 O A:HOH443 2.1 45.5 1.0 O A:HOH877 2.2 37.3 0.5 OG A:SER250 2.2 33.2 1.0 OE2 L:GLU93 2.5 34.6 0.6 CG A:ASP248 2.6 36.4 0.5 OD2 A:ASP248 2.6 37.0 0.5 OE1 L:GLU93 2.7 35.1 0.6 CD L:GLU93 3.0 34.2 0.6 CB A:SER250 3.3 31.7 1.0 OD2 A:ASP248 3.7 39.7 0.5 CB A:ASP248 3.9 35.5 0.5 O A:HOH452 3.9 55.1 1.0 CG A:ASP248 3.9 36.6 0.5 CB A:ASP248 4.0 35.3 0.5 O L:HOH235 4.1 27.6 1.0 O L:HOH412 4.3 42.3 1.0 N A:SER250 4.4 31.4 1.0 O L:HOH445 4.4 36.9 1.0 CA A:SER250 4.5 31.1 1.0 CG L:GLU93 4.5 34.6 1.0 O A:HOH108 4.6 42.8 1.0 O L:ASP92 4.7 28.1 1.0 NZ A:LYS251 4.7 32.0 1.0 OD1 A:ASP248 4.8 37.5 0.5 ZN L:ZN212 4.9 53.9 0.6

Zinc binding site 3 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn335 b:35.8 occ:0.49 O A:HOH450 2.0 21.8 1.0 OD1 A:ASP100 2.3 36.2 1.0 O A:HOH648 2.8 51.3 1.0 OD2 A:ASP100 3.0 37.7 1.0 CG A:ASP100 3.0 31.1 1.0 O A:HOH849 3.2 55.2 1.0 OE2 A:GLU86 4.0 44.1 1.0 O A:HOH629 4.0 40.9 1.0 CD1 A:ILE67 4.3 33.0 1.0 CB A:ASP100 4.5 26.7 1.0 O A:GLN98 4.6 31.7 1.0 CG2 A:ILE67 4.7 30.0 1.0 O A:HOH529 4.8 57.3 1.0 O A:HOH583 4.9 57.7 1.0 CD A:GLU86 4.9 42.0 1.0 CB A:GLU86 5.0 27.5 1.0 CG A:GLU86 5.0 33.4 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn336 b:95.3 occ:0.97 ND1 A:HIS298 2.7 31.8 0.5 CG A:HIS298 3.2 30.9 0.5 CB A:HIS298 3.2 31.5 1.0 OD1 A:ASP297 3.3 51.1 1.0 OD2 A:ASP297 3.4 49.8 1.0 NZ A:LYS191 3.4 43.5 1.0 CG A:ASP297 3.5 44.9 1.0 CE1 A:HIS298 3.7 31.9 0.5 O A:HOH524 3.8 59.5 1.0 CE A:LYS191 3.9 39.8 1.0 N A:HIS298 4.0 33.2 1.0 CD A:LYS191 4.2 35.1 1.0 NE2 A:GLN211 4.2 32.9 1.0 CA A:HIS298 4.2 30.5 1.0 CD2 A:HIS298 4.3 31.2 0.5 C A:ASP297 4.4 35.4 1.0 NE2 A:HIS298 4.5 32.1 0.5 O A:HOH528 4.6 67.2 1.0 CB A:ASP297 4.6 38.9 1.0 CB A:GLN211 4.6 27.3 1.0 O A:HOH486 4.6 34.8 1.0 CD A:GLN211 4.7 33.1 1.0 O A:ASP297 4.8 36.5 1.0 N A:ASP297 4.8 36.3 1.0 CA A:ASP297 4.8 37.5 1.0 OG A:SER292 4.8 53.5 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn337 b:69.0 occ:0.99 SG A:CYS289 2.7 44.1 1.0 O A:HOH559 2.7 42.8 1.0 ND1 A:HIS291 2.9 58.7 1.0 CB A:CYS289 3.7 40.2 1.0 CG A:HIS291 3.8 56.1 1.0 CE1 A:HIS291 3.9 59.8 1.0 CA A:CYS289 3.9 40.1 1.0 CB A:HIS291 4.0 53.5 1.0 N A:GLY290 4.0 44.5 1.0 N A:HIS291 4.1 50.9 1.0 O A:HOH790 4.2 78.2 1.0 C A:CYS289 4.4 41.8 1.0 CA A:HIS291 4.6 52.8 1.0 O A:HOH590 4.9 93.2 1.0 O A:HOH873 4.9 58.7 1.0 NE2 A:HIS291 5.0 59.9 1.0 CD2 A:HIS291 5.0 58.3 1.0 CA A:GLY290 5.0 47.0 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn212 b:53.9 occ:0.60 O L:HOH445 1.6 36.9 1.0 OD2 L:ASP92 2.3 29.9 1.0 O L:HOH446 2.4 44.6 1.0 O L:HOH410 2.4 44.4 1.0 OD1 L:ASP92 2.4 30.0 1.0 O A:HOH108 2.4 42.8 1.0 CG L:ASP92 2.7 29.8 1.0 O A:HOH877 3.2 37.3 0.5 OE2 L:GLU93 3.4 34.6 0.6 OD2 A:ASP248 3.6 39.7 0.5 NZ A:LYS251 3.6 32.0 1.0 O L:HOH760 4.0 51.4 1.0 OD1 A:ASP248 4.1 39.1 0.5 CB L:ASP92 4.2 27.5 1.0 CD L:GLU93 4.4 34.2 0.6 O L:ASP92 4.4 28.1 1.0 CB L:ASN30 4.4 30.1 1.0 O L:HOH726 4.5 95.3 1.0 O A:HOH791 4.5 71.9 1.0 CG L:GLU93 4.7 34.6 1.0 CG A:ASP248 4.8 36.6 0.5 C L:ASP92 4.8 28.8 1.0 ND2 L:ASN30 4.9 36.0 1.0 CA L:ASP92 4.9 28.3 1.0 ZN A:ZN334 4.9 32.1 0.6 CE A:LYS251 4.9 32.0 1.0 O L:ASP28 5.0 31.7 1.0 O L:ILE29 5.0 27.3 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Bla G 2 Complexed with Fab 4C3


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 Bla G 2 Complexed with Fab 4C3 within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn213 b:58.8 occ:0.96 O L:HOH214 2.3 28.1 1.0 NE2 H:HIS170 2.5 43.3 1.0 ND2 L:ASN138 2.7 35.9 1.0 O H:HOH451 2.7 48.5 1.0 OD1 L:ASN138 2.8 38.2 1.0 CG L:ASN138 3.1 33.6 1.0 CE1 H:HIS170 3.2 43.1 1.0 CD2 H:HIS170 3.5 41.8 1.0 CA H:GLY168 4.2 48.0 1.0 ND1 H:HIS170 4.3 40.8 1.0 CG H:HIS170 4.5 40.1 1.0 OD2 L:ASP170 4.5 38.5 1.0 O L:HOH239 4.5 37.1 1.0 C H:GLY168 4.6 46.6 1.0 OD2 L:ASP167 4.6 44.0 1.0 CB L:ASN138 4.7 31.1 1.0 O H:GLY168 4.9 46.5 1.0 O H:HOH263 4.9 37.6 1.0 CG L:ASP167 5.0 40.5 1.0

J.Glesner, S.Wunschmann, M.Li, A.Gustchina, A.Wlodawer, M.Himly, M.D.Chapman, A.Pomes. Mechanisms of Allergen-Antibody Interaction of Cockroach Allergen Bla G 2 with Monoclonal Antibodies That Inhibit Ige Antibody Binding. Plos One V. 6 22223 2011.
ISSN: ESSN 1932-6203
PubMed: 21789239
DOI: 10.1371/JOURNAL.PONE.0022223