Zinc in PDB 5nsg: Fc Dede Homodimer Variant

The structure of Fc Dede Homodimer Variant, PDB code: 5nsg was solved by C.De Nardis, L.J.A.Hendriks, E.Poirier, T.Arvinte, P.Gros, A.B.H.Bakker, J.De Kruif, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.82 / 2.22
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.000, 147.010, 76.370, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.3

The binding sites of Zinc atom in the Fc Dede Homodimer Variant (pdb code 5nsg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Fc Dede Homodimer Variant, PDB code: 5nsg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Fc Dede Homodimer Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Fc Dede Homodimer Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:54.9 occ:0.62 OE2 A:GLU318 2.0 73.5 1.0 OE1 A:GLU318 2.4 76.6 1.0 CD A:GLU318 2.5 67.9 1.0 CG A:GLU318 4.0 60.0 1.0 CG2 A:THR335 4.2 31.7 1.0 CB A:GLU318 4.8 42.0 1.0 CB A:THR335 4.9 32.0 1.0

Zinc binding site 2 out of 3 in the Fc Dede Homodimer Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Fc Dede Homodimer Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1009 b:34.5 occ:1.00 C A:ACT1011 1.8 47.4 1.0 O A:ACT1011 2.0 55.4 1.0 H3 A:ACT1011 2.0 61.4 1.0 NE2 A:HIS435 2.0 27.0 1.0 NE2 A:HIS310 2.0 27.6 1.0 O A:HOH1171 2.1 30.5 1.0 CH3 A:ACT1011 2.3 51.1 1.0 OXT A:ACT1011 2.4 59.4 1.0 H1 A:ACT1011 2.9 61.4 1.0 CD2 A:HIS435 2.9 24.4 1.0 CE1 A:HIS310 2.9 30.9 1.0 CE1 A:HIS435 3.1 24.2 1.0 CD2 A:HIS310 3.1 29.4 1.0 H2 A:ACT1011 3.2 61.4 1.0 CD1 A:LEU314 3.7 24.2 1.0 ND1 A:HIS310 4.1 28.0 1.0 CG A:HIS435 4.1 24.9 1.0 ND1 A:HIS435 4.2 24.0 1.0 CG A:HIS310 4.2 29.1 1.0 CG2 A:ILE253 4.5 40.1 1.0

Zinc binding site 3 out of 3 in the Fc Dede Homodimer Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Fc Dede Homodimer Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1010 b:0.9 occ:1.00 CD2 A:HIS268 2.3 87.2 1.0 CG A:HIS268 2.3 88.8 1.0 NE2 A:HIS268 2.7 86.6 1.0 ND1 A:HIS268 2.7 90.9 1.0 CE1 A:HIS268 2.9 89.3 1.0 CB A:HIS268 3.1 86.6 1.0 CA A:HIS268 4.5 80.5 1.0 O A:SER298 4.5 65.8 1.0 N A:HIS268 4.9 74.8 1.0

C.De Nardis, L.J.A.Hendriks, E.Poirier, T.Arvinte, P.Gros, A.B.H.Bakker, J.De Kruif. A New Approach For Generating Bispecific Antibodies Based on A Common Light Chain Format and the Stable Architecture of Human Immunoglobulin G1. J. Biol. Chem. V. 292 14706 2017.
ISSN: ESSN 1083-351X
PubMed: 28655766
DOI: 10.1074/JBC.M117.793497