Zinc in PDB 8ijs: Anti-Vegf Nanobody Mutant

The structure of Anti-Vegf Nanobody Mutant, PDB code: 8ijs was solved by F.Qian, S.Q.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.17 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.915, 53.205, 65.376, 90, 90, 90
R / Rfree (%)	20.1 / 22

The binding sites of Zinc atom in the Anti-Vegf Nanobody Mutant (pdb code 8ijs). 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-Vegf Nanobody Mutant, PDB code: 8ijs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Anti-Vegf Nanobody Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Anti-Vegf Nanobody Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:58.4 occ:1.00 OD2 A:ASP60 1.9 58.5 1.0 O A:HOH340 2.2 57.8 1.0 O A:HOH319 2.8 37.5 1.0 CG A:ASP60 3.0 48.1 1.0 CB A:ASP60 3.5 39.8 1.0 NZ A:LYS58 4.1 60.5 1.0 OD1 A:ASP60 4.1 62.2 1.0 O A:HOH323 4.2 50.8 1.0 N A:ASP60 4.3 36.8 1.0 CD A:LYS58 4.5 71.5 1.0 CA A:ASP60 4.5 40.9 1.0 CE A:LYS58 4.7 57.7 1.0

Zinc binding site 2 out of 2 in the Anti-Vegf Nanobody Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Anti-Vegf Nanobody Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:87.8 occ:1.00 OD2 A:ASP73 2.2 79.8 1.0 CG A:ASP73 3.1 65.1 1.0 OD1 A:ASP73 3.3 76.5 1.0 NZ A:LYS76 3.8 85.3 1.0 CB A:ASP73 4.5 60.1 1.0

S.Zhu, S.Fan, T.Tang, J.Huang, H.Zhou, C.Huang, Y.Chen, F.Qian. Polymorphic Nanobody Crystals As Long-Acting Intravitreal Therapy For Wet Age-Related Macular Degeneration. Bioeng Transl Med V. 8 10523 2023.
ISSN: ISSN 2380-6761
PubMed: 38023710
DOI: 10.1002/BTM2.10523