Atomistry » Zinc » PDB 2vh5-2vqw » 3giz
Atomistry »
  Zinc »
    PDB 2vh5-2vqw »
      3giz »

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

Protein crystallography data

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

Zinc Binding Sites:

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 3giz

Go back to Zinc Binding Sites List in 3giz
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 3giz

Go back to Zinc Binding Sites List in 3giz
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 3giz

Go back to Zinc Binding Sites List in 3giz
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

Reference:

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
Page generated: Sat Sep 26 10:16:33 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy