Zinc in PDB 3hzy: Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo

The structure of Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo, PDB code: 3hzy was solved by C.L.Brooks, S.Muller-Loennies, S.N.Borisova, L.Brade, P.Kosma, T.Hirama, C.R.Mackenzie, H.Brade, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.945, 81.966, 128.242, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.1

The structure of Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo (pdb code 3hzy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo, PDB code: 3hzy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo


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 S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn218 b:47.5 occ:1.00 OD2 A:ASP150 2.0 28.8 1.0 ND1 A:HIS188 2.1 35.5 1.0 O A:HOH287 2.5 30.6 1.0 CE1 A:HIS188 2.9 33.3 1.0 CG A:ASP150 3.1 30.6 1.0 CG A:HIS188 3.1 28.7 1.0 CB A:ASP150 3.5 29.1 1.0 CB A:HIS188 3.6 29.1 1.0 O A:ARG187 3.8 35.5 1.0 O A:HOH344 3.8 36.0 1.0 CA A:HIS188 3.8 31.3 1.0 NE2 A:HIS188 4.0 29.1 1.0 OD1 A:ASP150 4.2 32.5 1.0 CD2 A:HIS188 4.2 29.5 1.0 C A:ARG187 4.5 35.0 1.0 N A:HIS188 4.6 32.7 1.0 N A:ASN189 5.0 30.4 1.0 O A:HOH386 5.0 40.4 1.0 C A:HIS188 5.0 34.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo


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 S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:45.3 occ:1.00 OH B:TYR100D 2.3 38.9 1.0 OE2 A:GLU55 2.4 34.9 1.0 O A:HOH223 2.6 43.7 1.0 O A:HOH289 2.8 27.8 1.0 MG B:MG220 3.2 25.9 1.0 CD A:GLU55 3.2 36.2 1.0 CZ B:TYR100D 3.3 40.0 1.0 OE1 A:GLU55 3.4 39.1 1.0 CE1 B:TYR100D 3.7 41.9 1.0 CB A:SER56 4.0 41.9 1.0 N A:SER56 4.1 31.9 1.0 CE2 B:TYR100D 4.3 37.1 1.0 OH A:TYR49 4.5 37.2 1.0 CG A:GLU55 4.6 31.4 1.0 CA A:SER56 4.7 36.6 1.0 CE1 A:TYR49 4.7 32.0 1.0 CA A:GLU55 4.9 32.1 1.0 CD1 B:TYR100D 5.0 37.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo


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 S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn215 b:42.7 occ:1.00 NE2 A:HIS188 2.0 29.1 1.0 O A:HOH281 2.3 38.1 1.0 CE1 A:HIS188 2.6 33.3 1.0 OE2 A:GLU184 2.9 27.8 1.0 CD2 A:HIS188 3.2 29.5 1.0 OE1 A:GLU184 3.3 31.8 1.0 CD A:GLU184 3.5 32.0 1.0 ND1 A:HIS188 3.8 35.5 1.0 NH1 A:ARG154 4.0 49.5 1.0 NH2 A:ARG154 4.0 48.3 1.0 CG A:HIS188 4.1 28.7 1.0 CZ A:ARG154 4.4 48.9 1.0 O A:HOH386 4.7 40.4 1.0 CD A:ARG187 4.7 29.2 1.0 CB A:ARG187 4.9 29.8 1.0 CG A:GLU184 4.9 25.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo


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 S73-2 Antibody in Complex with Antigen Kdo(2.4)Kdo(2.4)Kdo within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn215 b:51.0 occ:1.00 OE2 B:GLU58 2.3 32.2 1.0 CD B:GLU58 3.0 32.8 1.0 OE1 B:GLU58 3.1 30.3 1.0 NH2 B:ARG52 4.1 24.5 1.0 NH1 B:ARG52 4.4 29.2 1.0 CG B:GLU58 4.5 27.5 1.0 O B:HOH359 4.6 40.8 1.0 CZ B:ARG52 4.7 29.6 1.0

C.L.Brooks, S.Muller-Loennies, S.N.Borisova, L.Brade, P.Kosma, T.Hirama, C.R.Mackenzie, H.Brade, S.V.Evans. Antibodies Raised Against Chlamydial Lipopolysaccharide Antigens Reveal Convergence in Germline Gene Usage and Differential Epitope Recognition Biochemistry V. 49 570 2010.
ISSN: ISSN 0006-2960
PubMed: 20000757
DOI: 10.1021/BI9011308