Zinc in PDB 9kud: Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2

The structure of Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2, PDB code: 9kud was solved by J.Lan, C.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.38 / 3.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.674, 129.157, 138.062, 90, 90, 90
R / Rfree (%)	22.5 / 28.1

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2 (pdb code 9kud). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2, PDB code: 9kud:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2


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 Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:30.0 occ:1.00 NE2 A:HIS374 1.9 13.5 1.0 NE2 A:HIS378 2.1 23.5 1.0 OE1 A:GLU402 2.1 13.9 1.0 CD A:GLU402 2.8 14.2 1.0 OE2 A:GLU402 2.8 12.2 1.0 CD2 A:HIS374 2.8 20.9 1.0 CE1 A:HIS374 3.0 17.8 1.0 OE2 A:GLU375 3.0 35.1 1.0 CD2 A:HIS378 3.0 25.2 1.0 CE1 A:HIS378 3.1 21.4 1.0 CD A:GLU375 3.8 28.4 1.0 CG A:HIS374 4.0 18.2 1.0 OE1 A:GLU375 4.0 30.9 1.0 ND1 A:HIS374 4.0 19.4 1.0 ND1 A:HIS378 4.2 21.2 1.0 CG A:HIS378 4.2 22.9 1.0 CG A:GLU402 4.2 29.0 1.0 OH A:TYR515 4.5 27.3 1.0 CE1 A:TYR515 4.6 17.8 1.0 CA A:GLU402 4.8 29.4 1.0 CB A:GLU402 4.8 17.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2


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 Sars-Cov-2 Jn.1 Variant Rbd Complexed with Squirrel ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:30.0 occ:1.00 NE2 B:HIS378 1.9 24.7 1.0 NE2 B:HIS374 2.2 22.8 1.0 OE1 B:GLU402 2.7 6.7 1.0 CE1 B:HIS378 2.8 25.6 1.0 CD2 B:HIS378 3.1 34.6 1.0 CD2 B:HIS374 3.1 26.7 1.0 CE1 B:HIS374 3.2 24.4 1.0 CD B:GLU402 3.7 13.2 1.0 ND1 B:HIS378 3.9 22.5 1.0 CG B:HIS378 4.1 25.7 1.0 OE2 B:GLU402 4.2 22.0 1.0 CG B:HIS374 4.3 28.0 1.0 ND1 B:HIS374 4.3 26.0 1.0 OE2 B:GLU375 4.3 23.2 1.0 OH B:TYR515 4.4 24.4 1.0 CE1 B:TYR515 4.6 15.0 1.0 CB B:GLU402 4.7 19.7 1.0 CA B:GLU402 4.7 28.7 1.0 CG B:GLU402 4.8 11.1 1.0 CD B:GLU375 4.8 23.3 1.0 OE1 B:GLU375 4.9 25.6 1.0

C.Wang, X.Nan, Y.Deng, S.Fan, J.Lan. Cross-Species Recognition of Squirrel ACE2 By the Receptor Binding Domains of Sars-Cov-2, RATG13, Pcov-Gd and Pcov-Gx Structure 2025.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2025.07.003