Zinc in PDB 9n1f: Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex

All present enzymatic activity of Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex:
2.3.2.23; 2.3.2.27;

The structure of Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex, PDB code: 9n1f was solved by A.Paluda, A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.00 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.735, 100.415, 142.076, 90, 90, 90
R / Rfree (%)	22.9 / 27.9

The binding sites of Zinc atom in the Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex (pdb code 9n1f). 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 the ARK2C-UBC13~Ub-MMS2 Complex, PDB code: 9n1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex


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 the ARK2C-UBC13~Ub-MMS2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:49.3 occ:1.00 ND1 A:HIS314 2.0 53.2 1.0 SG A:CYS334 2.3 44.3 1.0 SG A:CYS312 2.3 44.9 1.0 SG A:CYS331 2.3 45.7 1.0 CE1 A:HIS314 3.0 51.1 1.0 CG A:HIS314 3.0 54.0 1.0 CB A:CYS331 3.1 48.2 1.0 CB A:CYS312 3.3 54.6 1.0 CB A:HIS314 3.4 56.1 1.0 CB A:CYS334 3.4 46.5 1.0 N A:CYS334 3.8 49.9 1.0 NE2 A:HIS314 4.1 55.2 1.0 CD2 A:HIS314 4.1 52.1 1.0 CA A:CYS334 4.2 47.6 1.0 CB A:ILE333 4.4 46.5 1.0 N A:HIS314 4.6 51.1 1.0 CA A:CYS331 4.6 49.1 1.0 CA A:HIS314 4.6 49.6 1.0 CA A:CYS312 4.6 58.7 1.0 C A:ILE333 4.7 50.2 1.0 N A:ILE333 4.8 45.7 1.0 C A:CYS334 4.9 44.0 1.0 CA A:ILE333 4.9 43.2 1.0 C A:CYS312 4.9 54.5 1.0 N A:ARG335 4.9 53.6 1.0 O A:CYS312 5.0 56.2 1.0 CG2 A:ILE333 5.0 42.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the ARK2C-UBC13~Ub-MMS2 Complex


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 the ARK2C-UBC13~Ub-MMS2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:56.0 occ:1.00 ND1 A:HIS317 2.1 64.1 1.0 SG A:CYS297 2.3 54.0 1.0 SG A:CYS294 2.3 51.1 1.0 SG A:CYS320 2.3 55.1 1.0 CB A:CYS294 3.0 49.6 1.0 CG A:HIS317 3.0 59.3 1.0 CE1 A:HIS317 3.1 60.3 1.0 CB A:HIS317 3.3 57.0 1.0 CB A:CYS297 3.3 54.0 1.0 CB A:CYS320 3.3 53.5 1.0 N A:CYS297 3.8 52.5 1.0 CA A:CYS297 4.2 49.9 1.0 CD2 A:HIS317 4.2 61.6 1.0 NE2 A:HIS317 4.2 61.8 1.0 N A:HIS317 4.2 55.2 1.0 CA A:HIS317 4.3 54.5 1.0 CA A:CYS294 4.5 51.6 1.0 CA A:CYS320 4.7 59.5 1.0 CB A:ILE296 4.8 48.9 1.0 O A:CYS294 4.8 54.6 1.0 C A:ILE296 4.8 53.3 1.0 C A:CYS294 4.9 42.4 1.0 C A:CYS297 4.9 50.9 1.0

C.Rossig, A.Paluda, R.Chen, A.J.Middleton, C.L.Day. Arkadia and ARK2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes. J.Mol.Biol. 69259 2025.
ISSN: ESSN 1089-8638
PubMed: 40451499
DOI: 10.1016/J.JMB.2025.169259