Zinc in PDB 5d0i: Structure of Ring Finger Protein 165

The structure of Structure of Ring Finger Protein 165, PDB code: 5d0i was solved by J.D.Wright, C.L.Day, P.D.Mace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.37 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.220, 76.220, 103.260, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20

The binding sites of Zinc atom in the Structure of Ring Finger Protein 165 (pdb code 5d0i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Ring Finger Protein 165, PDB code: 5d0i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Ring Finger Protein 165


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ring Finger Protein 165 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:36.6 occ:0.90 ND1 A:HIS314 2.0 44.4 1.0 SG A:CYS331 2.3 36.7 1.0 SG A:CYS334 2.3 41.6 1.0 SG A:CYS312 2.3 39.3 1.0 CE1 A:HIS314 2.9 53.2 1.0 CB A:CYS331 3.0 39.2 1.0 CG A:HIS314 3.0 38.0 1.0 CB A:CYS312 3.2 40.3 1.0 CB A:HIS314 3.5 34.9 1.0 CB A:CYS334 3.5 40.6 1.0 N A:CYS334 3.8 40.0 1.0 NE2 A:HIS314 4.1 48.6 1.0 CD2 A:HIS314 4.1 39.5 1.0 CA A:CYS334 4.2 40.4 1.0 CA A:CYS331 4.5 36.9 1.0 N A:HIS314 4.5 36.7 1.0 CB A:ILE333 4.5 34.1 1.0 O A:HOH526 4.5 44.2 1.0 CA A:CYS312 4.5 40.6 1.0 CA A:HIS314 4.6 37.2 1.0 C A:CYS312 4.7 44.8 1.0 O A:CYS312 4.7 46.2 1.0 C A:ILE333 4.8 46.2 1.0 C A:CYS334 4.9 39.8 1.0 N A:ILE333 5.0 32.9 1.0

Zinc binding site 2 out of 4 in the Structure of Ring Finger Protein 165


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ring Finger Protein 165 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.1 occ:1.00 ND1 A:HIS317 2.1 26.3 1.0 SG A:CYS320 2.3 27.1 1.0 SG A:CYS297 2.3 28.7 1.0 SG A:CYS294 2.4 28.3 1.0 CB A:CYS294 3.0 27.3 1.0 CE1 A:HIS317 3.0 30.3 1.0 CG A:HIS317 3.1 25.0 1.0 CB A:CYS297 3.2 28.2 1.0 CB A:CYS320 3.3 27.6 1.0 CB A:HIS317 3.4 26.7 1.0 N A:CYS297 3.8 28.2 1.0 CA A:CYS297 4.1 22.9 1.0 NE2 A:HIS317 4.2 36.1 1.0 CD2 A:HIS317 4.2 28.3 1.0 N A:HIS317 4.2 31.4 1.0 CA A:HIS317 4.4 28.3 1.0 CA A:CYS294 4.5 28.1 1.0 O A:HOH536 4.6 22.3 0.6 OG A:SER299 4.7 54.6 1.0 CA A:CYS320 4.7 27.1 1.0 CB A:ILE296 4.8 25.6 1.0 C A:ILE296 4.9 26.2 1.0 C A:CYS294 4.9 35.4 1.0 O A:CYS294 4.9 30.2 1.0 C A:CYS297 4.9 29.2 1.0 N A:CYS320 5.0 25.2 1.0

Zinc binding site 3 out of 4 in the Structure of Ring Finger Protein 165


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ring Finger Protein 165 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:46.3 occ:1.00 ND1 B:HIS314 2.0 52.6 1.0 SG B:CYS312 2.2 40.6 1.0 SG B:CYS331 2.2 40.8 1.0 SG B:CYS334 2.4 49.4 1.0 CE1 B:HIS314 3.0 59.8 1.0 CB B:CYS331 3.0 41.8 1.0 CG B:HIS314 3.1 50.8 1.0 CB B:CYS312 3.3 43.3 1.0 CB B:CYS334 3.4 47.0 1.0 CB B:HIS314 3.5 44.9 1.0 N B:CYS334 3.8 53.2 1.0 NE2 B:HIS314 4.1 56.9 1.0 CA B:CYS334 4.1 56.0 1.0 CD2 B:HIS314 4.2 54.3 1.0 CA B:CYS331 4.5 36.4 1.0 N B:HIS314 4.5 45.2 1.0 CA B:CYS312 4.5 49.6 1.0 CB B:ILE333 4.6 47.7 1.0 O B:CYS312 4.6 50.7 1.0 CA B:HIS314 4.6 50.3 1.0 C B:CYS312 4.6 48.8 1.0 C B:CYS334 4.8 54.5 1.0 C B:ILE333 4.8 55.4 1.0 N B:ILE333 4.9 46.4 1.0 N B:ARG335 5.0 52.8 1.0

Zinc binding site 4 out of 4 in the Structure of Ring Finger Protein 165


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ring Finger Protein 165 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:36.0 occ:1.00 ND1 B:HIS317 2.1 37.5 1.0 SG B:CYS294 2.3 35.6 1.0 SG B:CYS320 2.3 32.0 1.0 SG B:CYS297 2.3 40.0 1.0 CB B:CYS294 2.9 37.4 1.0 CE1 B:HIS317 3.0 39.0 1.0 CG B:HIS317 3.1 35.9 1.0 CB B:CYS320 3.3 29.6 1.0 CB B:CYS297 3.3 34.0 1.0 CB B:HIS317 3.4 33.9 1.0 N B:CYS297 3.8 36.4 1.0 N B:HIS317 4.1 33.8 1.0 O B:HOH524 4.1 46.1 1.0 CA B:CYS297 4.1 33.9 1.0 NE2 B:HIS317 4.2 40.2 1.0 CD2 B:HIS317 4.2 37.5 1.0 CA B:HIS317 4.3 35.4 1.0 CA B:CYS294 4.3 40.2 1.0 CB B:ILE296 4.6 31.7 1.0 O B:HOH526 4.7 39.8 1.0 CA B:CYS320 4.7 26.9 1.0 O B:CYS294 4.8 51.0 1.0 C B:CYS294 4.8 47.0 1.0 C B:ILE296 4.8 46.0 1.0 C B:CYS297 4.9 42.8 1.0 N B:ILE296 5.0 38.3 1.0

J.D.Wright, P.D.Mace, C.L.Day. Secondary Ubiquitin-Ring Docking Enhances Arkadia and ARK2C E3 Ligase Activity. Nat.Struct.Mol.Biol. V. 23 45 2016.
ISSN: ESSN 1545-9985
PubMed: 26656854
DOI: 10.1038/NSMB.3142