Zinc in PDB 3giz: Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab

The structure of Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab, PDB code: 3giz was solved by J.Du, H.Yang, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.330, 55.944, 79.780, 90.00, 122.17, 90.00
R / Rfree (%)	19.5 / 25

The binding sites of Zinc atom in the Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab (pdb code 3giz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab, PDB code: 3giz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab


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 Fab Fragment of Anti-CD20 Antibody Ofatumumab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn212 b:28.3 occ:0.50 OE1 L:GLU79 2.1 36.0 1.0 OE1 L:GLU81 2.4 20.4 1.0 OE2 L:GLU81 2.6 20.7 1.0 CD L:GLU81 2.8 20.9 1.0 CD L:GLU79 3.2 31.4 1.0 CB L:GLU79 3.8 25.8 1.0 CG L:GLU79 3.8 27.4 1.0 CG L:GLU81 4.1 23.1 1.0 OE2 L:GLU79 4.2 28.6 1.0 CD L:PRO80 4.5 24.5 1.0 O L:HOH225 4.7 27.6 1.0 CA L:GLU79 4.9 25.4 1.0 NH2 L:ARG61 4.9 21.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab


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 Fab Fragment of Anti-CD20 Antibody Ofatumumab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn213 b:28.9 occ:1.00 ND2 L:ASN137 2.0 20.2 1.0 NE2 H:HIS173 2.1 21.3 1.0 OD1 L:ASN138 2.2 28.3 1.0 CD2 H:HIS173 2.9 21.0 1.0 CG L:ASN137 3.1 21.5 1.0 CG L:ASN138 3.2 24.8 1.0 CE1 H:HIS173 3.3 21.5 1.0 OD1 L:ASN137 3.5 21.2 1.0 ND2 L:ASN138 3.8 26.4 1.0 OG L:SER174 3.9 18.0 1.0 CG H:HIS173 4.1 22.0 1.0 O H:GLY171 4.2 24.1 1.0 CB L:ASN138 4.3 23.2 1.0 ND1 H:HIS173 4.3 21.1 1.0 CB L:ASN137 4.4 22.2 1.0 OG1 H:THR192 4.4 25.8 1.0 N L:ASN138 4.4 22.5 1.0 O L:HOH218 4.5 22.9 1.0 CA H:GLY171 4.7 26.0 1.0 C H:GLY171 4.7 24.9 1.0 CA L:ASN137 4.8 21.8 1.0 CA L:ASN138 4.9 22.6 1.0 O H:HOH267 4.9 29.7 1.0 C L:ASN137 4.9 22.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Fab Fragment of Anti-CD20 Antibody Ofatumumab


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 Fab Fragment of Anti-CD20 Antibody Ofatumumab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn214 b:34.6 occ:1.00 O L:GLU1 2.2 28.4 1.0 N L:GLU1 2.2 28.2 1.0 C L:GLU1 2.9 27.7 1.0 CA L:GLU1 3.1 28.0 1.0 O L:HOH216 4.1 20.8 1.0 CB L:GLU1 4.2 28.0 1.0 N L:ILE2 4.2 26.7 1.0 CG L:GLU1 4.4 30.4 1.0 O L:HOH325 4.5 34.5 1.0 OE1 L:GLU1 4.5 34.2 1.0 CD L:GLU1 4.8 32.4 1.0 CA L:ILE2 4.9 25.8 1.0 NE2 L:GLN27 4.9 23.8 1.0

J.Du, H.Yang, Y.Guo, J.Ding. Structure of the Fab Fragment of Therapeutic Antibody Ofatumumab Provides Insights Into the Recognition Mechanism with CD20 Mol.Immunol. V. 46 2419 2009.
ISSN: ISSN 0161-5890
PubMed: 19427037
DOI: 10.1016/J.MOLIMM.2009.04.009