Zinc in PDB 1dvf: Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex

The structure of Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex, PDB code: 1dvf was solved by B.C.Braden, B.A.Fields, X.Ysern, W.Dall'acqua, F.A.Goldbaum, R.J.Poljak, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.800, 79.400, 51.500, 90.00, 100.20, 90.00
R / Rfree (%)	19.4 / 24.9

The binding sites of Zinc atom in the Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex (pdb code 1dvf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex, PDB code: 1dvf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1158 b:42.1 occ:1.00 OD2 B:ASP100 1.8 28.9 1.0 NE2 D:HIS33 2.1 28.4 1.0 OD2 D:ASP52 2.2 26.5 1.0 O B:HOH1011 2.7 35.9 1.0 CG B:ASP100 2.9 28.8 1.0 CE1 D:HIS33 3.0 36.0 1.0 CD2 D:HIS33 3.2 33.3 1.0 CG D:ASP52 3.2 29.9 1.0 OD1 B:ASP100 3.5 33.9 1.0 CB D:ASP52 3.7 23.6 1.0 O B:HOH1111 3.8 57.2 1.0 NH1 B:ARG102 4.1 29.9 1.0 ND1 D:HIS33 4.2 32.1 1.0 CB B:ASP100 4.2 26.6 1.0 CG D:HIS33 4.3 28.8 1.0 OD1 D:ASP52 4.3 36.9 1.0 ND2 D:ASN54 4.4 30.4 1.0 O D:HOH1003 4.8 28.6 1.0 O D:HOH1006 4.8 38.1 1.0 O D:HOH1044 4.8 59.5 1.0 CA D:ASP52 4.9 25.4 1.0 NH2 B:ARG102 4.9 35.6 1.0 OD1 D:ASN54 5.0 31.8 1.0

Zinc binding site 2 out of 3 in the Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1160 b:55.3 occ:0.50 OD2 B:ASP88 2.1 56.5 1.0 ND1 B:HIS86 2.1 49.6 1.0 CG B:ASP88 2.8 58.4 1.0 OD1 B:ASP88 2.8 65.4 1.0 CE1 B:HIS86 3.1 54.8 1.0 CG B:HIS86 3.2 52.3 1.0 CB B:HIS86 3.5 52.1 1.0 NE2 B:HIS86 4.3 56.1 1.0 CB B:ASP88 4.3 52.8 1.0 CD2 B:HIS86 4.3 56.3 1.0

Zinc binding site 3 out of 3 in the Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Idiotopic Antibody D1.3 Fv Fragment-Antiidiotopic Antibody E5.2 Fv Fragment Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1159 b:43.2 occ:0.50 O C:ASP1 2.0 37.8 1.0 N C:ASP1 2.4 37.9 1.0 OE1 C:GLN3 2.6 70.1 1.0 C C:ASP1 2.7 35.0 1.0 CA C:ASP1 2.8 42.4 1.0 OD2 C:ASP1 3.1 52.0 1.0 CB C:ASP1 3.2 42.7 1.0 CG C:ASP1 3.3 49.5 1.0 CD C:GLN3 3.9 60.9 1.0 N C:ILE2 4.0 26.1 1.0 OD1 C:ASP1 4.2 56.2 1.0 NE2 C:GLN3 4.7 62.4 1.0 O C:HOH1038 4.7 45.7 1.0 CA C:ILE2 4.8 23.7 1.0 CG C:GLN3 4.9 49.3 1.0

B.C.Braden, B.A.Fields, X.Ysern, W.Dall'acqua, F.A.Goldbaum, R.J.Poljak, R.A.Mariuzza. Crystal Structure of An Fv-Fv Idiotope-Anti-Idiotope Complex at 1.9 A Resolution. J.Mol.Biol. V. 264 137 1996.
ISSN: ISSN 0022-2836
PubMed: 8950273
DOI: 10.1006/JMBI.1996.0629