Zinc in PDB 7om5: Anti-Egfr Nanobody EGB4

The structure of Anti-Egfr Nanobody EGB4, PDB code: 7om5 was solved by M.R.Zeronian, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.69 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.539, 71.576, 53.204, 90, 91.48, 90
R / Rfree (%)	17.7 / 20.5

The binding sites of Zinc atom in the Anti-Egfr Nanobody EGB4 (pdb code 7om5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Anti-Egfr Nanobody EGB4, PDB code: 7om5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Anti-Egfr Nanobody EGB4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anti-Egfr Nanobody EGB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:12.4 occ:1.00 OD2 A:ASP110 1.9 14.8 1.0 OD2 A:ASP98 2.0 9.2 1.0 CG A:ASP98 2.7 10.8 1.0 OD1 A:ASP98 2.7 12.0 1.0 CG A:ASP110 2.9 15.1 1.0 CB A:ASP110 3.4 15.0 1.0 O A:ASP108 3.9 19.7 1.0 N A:ASP110 4.0 12.2 1.0 OD1 A:ASP110 4.1 18.5 1.0 CB A:ASP98 4.1 10.6 1.0 CA A:ASP110 4.4 12.9 1.0 C A:ASP108 4.6 17.0 1.0 C A:TYR109 4.8 12.0 1.0 CD1 A:TRP100 4.8 15.2 0.5 CE3 A:TRP100 4.8 15.9 0.5 CA A:TYR109 4.9 13.3 1.0 CA A:ASP98 4.9 10.4 1.0 CB A:TRP100 5.0 14.3 0.5

Zinc binding site 2 out of 2 in the Anti-Egfr Nanobody EGB4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anti-Egfr Nanobody EGB4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:10.8 occ:1.00 OD1 B:ASP98 2.0 8.7 1.0 OD2 B:ASP110 2.3 14.1 1.0 CG B:ASP98 2.6 8.4 1.0 OD2 B:ASP98 2.7 9.7 1.0 CG B:ASP110 3.3 18.6 1.0 CB B:ASP110 3.7 16.3 1.0 O B:ASP108 3.9 12.2 1.0 N B:ASP110 4.0 12.1 1.0 CB B:ASP98 4.1 8.4 1.0 OD1 B:ASP110 4.3 28.6 1.0 CA B:ASP110 4.4 13.6 1.0 CB B:TRP100 4.5 13.2 1.0 C B:ASP108 4.5 11.9 1.0 C B:TYR109 4.7 10.9 1.0 CA B:TYR109 4.8 11.3 1.0 CD1 B:TRP100 4.9 14.8 1.0 CA B:ASP98 4.9 8.6 1.0

M.R.Zeronian, S.Doulkeridou, P.M.P.Van Bergen En Henegouwen, B.J.C.Janssen. Structural Insights Into the Non-Inhibitory Mechanism of the Anti-Egfr EGB4 Nanobody. Bmc Mol Cell Biol V. 23 12 2022.
ISSN: ESSN 2661-8850
PubMed: 35232398
DOI: 10.1186/S12860-022-00412-X