Zinc in PDB 4ap4: RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex

All present enzymatic activity of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex:
6.3.2.19;

The structure of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex, PDB code: 4ap4 was solved by A.Plechanovova, R.T.Hay, M.H.Tatham, E.Jaffray, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.82 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.480, 65.090, 189.650, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.2

The binding sites of Zinc atom in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex (pdb code 4ap4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex, PDB code: 4ap4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn800 b:40.6 occ:1.00 SG A:CYS166 2.3 47.1 1.0 SG A:CYS139 2.4 54.9 1.0 SG A:CYS163 2.4 48.1 1.0 SG A:CYS136 2.4 40.8 1.0 CB A:CYS166 3.1 44.9 1.0 CB A:CYS136 3.1 42.5 1.0 CB A:CYS163 3.3 45.1 1.0 CB A:CYS139 3.4 54.2 1.0 N A:CYS139 3.7 48.2 1.0 NH1 A:ARG151 3.8 52.9 1.0 N A:CYS163 4.0 38.5 1.0 CA A:CYS139 4.1 51.8 1.0 CA A:CYS163 4.2 41.5 1.0 CA A:CYS166 4.3 46.3 1.0 N A:CYS166 4.3 47.9 1.0 CA A:CYS136 4.6 41.5 1.0 CB A:ILE138 4.7 42.4 1.0 O A:CYS163 4.7 37.6 1.0 C A:CYS163 4.7 40.7 1.0 C A:ILE138 4.8 46.3 1.0 N A:MET140 5.0 52.2 1.0 C A:CYS139 5.0 53.2 1.0 N A:ILE138 5.0 41.6 1.0 C A:CYS136 5.0 40.3 1.0

Zinc binding site 2 out of 4 in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:32.8 occ:1.00 ND1 A:HIS160 2.1 30.2 1.0 SG A:CYS180 2.3 32.5 1.0 SG A:CYS177 2.4 32.2 1.0 SG A:CYS158 2.4 34.9 1.0 CE1 A:HIS160 2.8 31.0 1.0 CB A:CYS177 3.0 32.4 1.0 CG A:HIS160 3.2 28.5 1.0 CB A:CYS158 3.4 34.5 1.0 CB A:CYS180 3.5 31.6 1.0 CB A:HIS160 3.7 27.9 1.0 N A:CYS180 3.8 29.7 1.0 OG1 A:THR156 4.0 31.7 1.0 NE2 A:HIS160 4.0 31.4 1.0 CA A:CYS180 4.2 30.8 1.0 CD2 A:HIS160 4.2 30.1 1.0 CA A:CYS158 4.5 34.5 1.0 CA A:CYS177 4.5 32.6 1.0 C A:CYS158 4.5 34.1 1.0 O A:CYS158 4.6 34.4 1.0 NZ A:LYS182 4.6 51.2 1.0 C A:THR179 4.7 29.1 1.0 CB A:THR179 4.7 30.2 1.0 C A:CYS180 4.8 32.1 1.0 N A:HIS160 4.8 29.0 1.0 CB A:THR156 4.8 31.8 1.0 N A:ARG181 4.9 31.9 1.0 CA A:HIS160 4.9 28.7 1.0 N A:THR179 4.9 29.3 1.0

Zinc binding site 3 out of 4 in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:30.4 occ:1.00 SG A:CYS231 2.3 33.4 1.0 SG A:CYS204 2.4 34.5 1.0 SG A:CYS201 2.4 34.1 1.0 SG A:CYS228 2.4 37.6 1.0 CB A:CYS231 3.0 32.8 1.0 CB A:CYS204 3.1 33.3 1.0 CB A:CYS201 3.1 32.9 1.0 CB A:CYS228 3.3 37.4 1.0 N A:CYS204 3.5 30.4 1.0 CA A:CYS204 3.9 32.1 1.0 NH1 A:ARG216 4.0 39.0 1.0 N A:CYS228 4.1 33.4 1.0 CA A:CYS231 4.2 33.7 1.0 CA A:CYS228 4.2 35.8 1.0 N A:CYS231 4.3 33.8 1.0 O A:HOH2024 4.4 37.5 1.0 CA A:CYS201 4.6 33.5 1.0 O A:CYS228 4.6 34.0 1.0 C A:ILE203 4.6 29.9 1.0 CB A:ILE203 4.7 29.4 1.0 C A:CYS228 4.7 35.5 1.0 C A:CYS204 4.9 33.5 1.0 N A:MET205 4.9 34.8 1.0 C A:CYS201 4.9 32.6 1.0 O A:CYS201 5.0 33.4 1.0 N A:ILE203 5.0 29.3 1.0 CA A:ILE203 5.0 28.8 1.0

Zinc binding site 4 out of 4 in the RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RNF4 - UBCH5A - Ubiquitin Heterotrimeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:29.4 occ:1.00 ND1 A:HIS225 2.1 29.7 1.0 SG A:CYS242 2.3 30.2 1.0 SG A:CYS223 2.3 32.4 1.0 SG A:CYS245 2.4 28.0 1.0 CE1 A:HIS225 2.9 31.0 1.0 CB A:CYS242 3.1 30.0 1.0 CG A:HIS225 3.2 29.5 1.0 CB A:CYS245 3.3 27.4 1.0 CB A:CYS223 3.4 32.2 1.0 CB A:HIS225 3.7 29.8 1.0 N A:CYS245 3.8 26.2 1.0 OG1 A:THR221 3.9 29.9 1.0 NE2 A:HIS225 4.1 31.2 1.0 CA A:CYS245 4.1 26.3 1.0 CD2 A:HIS225 4.2 30.5 1.0 O A:CYS223 4.5 31.1 1.0 CA A:CYS223 4.5 32.1 1.0 C A:CYS223 4.5 31.3 1.0 CA A:CYS242 4.6 29.2 1.0 CB A:THR244 4.6 26.2 1.0 C A:CYS245 4.7 26.9 1.0 C A:THR244 4.7 25.6 1.0 CB A:LYS247 4.8 35.4 1.0 CB A:THR221 4.8 31.6 1.0 N A:HIS225 4.8 29.2 1.0 N A:ARG246 4.9 26.2 1.0 CA A:HIS225 4.9 29.3 1.0 N A:LYS247 5.0 32.2 1.0

A.Plechanovova, E.Jaffray, M.H.Tatham, J.H.Naismith, R.T.Hay. Structure of A Ring E3 Ligase and Ubiquitin-Loaded E2 Primed For Catalysis Nature V. 489 115 2012.
ISSN: ISSN 0028-0836
PubMed: 22842904
DOI: 10.1038/NATURE11376