Zinc in PDB 5ait: A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink)

All present enzymatic activity of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink):
6.3.2.19;

The structure of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink), PDB code: 5ait was solved by E.Branigan, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.19 / 3.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.580, 77.580, 328.840, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 28.6

The binding sites of Zinc atom in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink) (pdb code 5ait). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink), PDB code: 5ait:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1260 b:0.9 occ:1.00 SG A:CYS139 2.2 0.3 1.0 SG A:CYS166 2.3 0.5 1.0 SG A:CYS163 2.3 0.5 1.0 SG A:CYS136 2.3 0.0 1.0 CB A:CYS139 3.2 0.7 1.0 CB A:CYS166 3.2 0.3 1.0 CB A:CYS136 3.3 0.2 1.0 CB A:CYS163 3.4 0.1 1.0 N A:CYS139 3.5 97.5 1.0 NH1 A:ARG151 3.7 0.2 1.0 CA A:CYS139 3.9 99.0 1.0 N A:CYS163 4.2 0.7 1.0 CA A:CYS163 4.3 0.8 1.0 O A:CYS136 4.3 0.7 1.0 O A:CYS163 4.4 0.8 1.0 CB A:ILE138 4.5 0.7 1.0 CA A:CYS166 4.6 0.6 1.0 CA A:CYS136 4.6 0.6 1.0 C A:ILE138 4.6 0.1 1.0 N A:MET140 4.6 0.5 1.0 C A:CYS139 4.6 0.5 1.0 C A:CYS136 4.7 0.2 1.0 N A:CYS166 4.7 0.9 1.0 C A:CYS163 4.7 0.9 1.0 CG2 A:ILE138 4.9 93.4 1.0 CZ A:ARG151 4.9 0.2 1.0 CA A:ILE138 4.9 0.5 1.0

Zinc binding site 2 out of 4 in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1261 b:0.8 occ:1.00 ND1 A:HIS160 2.1 0.4 1.0 SG A:CYS177 2.2 1.0 1.0 SG A:CYS180 2.3 0.7 1.0 SG A:CYS158 2.3 0.2 1.0 CE1 A:HIS160 2.7 0.3 1.0 CG A:HIS160 2.9 0.5 1.0 CB A:CYS177 3.0 0.2 1.0 CB A:CYS180 3.4 0.7 1.0 CB A:CYS158 3.4 0.6 1.0 CB A:HIS160 3.5 92.9 1.0 NE2 A:HIS160 3.6 0.7 1.0 N A:CYS180 3.6 0.8 1.0 CD2 A:HIS160 3.7 0.2 1.0 CA A:CYS180 4.0 0.4 1.0 OG1 A:THR156 4.3 0.5 1.0 O A:CYS158 4.4 0.7 1.0 CA A:CYS177 4.5 0.2 1.0 CB A:LYS182 4.5 0.4 1.0 C A:CYS158 4.5 0.3 1.0 C A:THR179 4.5 0.5 1.0 CB A:THR179 4.5 90.6 1.0 N A:HIS160 4.5 93.5 1.0 CA A:CYS158 4.6 0.6 1.0 CA A:HIS160 4.7 90.0 1.0 C A:CYS180 4.7 0.9 1.0 N A:ARG181 4.8 0.4 1.0 N A:THR179 4.8 92.2 1.0 CA A:THR179 4.8 95.8 1.0 N A:LYS182 4.9 0.6 1.0 C A:CYS177 5.0 98.3 1.0 CG2 A:THR156 5.0 0.8 1.0

Zinc binding site 3 out of 4 in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1262 b:0.8 occ:1.00 SG A:CYS204 2.2 0.1 1.0 SG A:CYS231 2.3 0.8 1.0 SG A:CYS228 2.3 0.1 1.0 SG A:CYS201 2.3 91.6 1.0 CB A:CYS204 3.2 1.0 1.0 CB A:CYS228 3.2 0.7 1.0 CB A:CYS231 3.2 0.9 1.0 CB A:CYS201 3.3 0.1 1.0 N A:CYS204 3.5 0.1 1.0 CA A:CYS204 4.0 0.6 1.0 N A:CYS228 4.1 0.4 1.0 CA A:CYS228 4.2 0.8 1.0 N A:CYS231 4.3 0.9 1.0 CB A:ILE203 4.3 0.6 1.0 CA A:CYS231 4.4 0.3 1.0 O A:CYS228 4.5 0.8 1.0 C A:ILE203 4.6 0.4 1.0 C A:CYS228 4.7 0.7 1.0 CA A:CYS201 4.7 1.0 1.0 O A:CYS201 4.8 0.7 1.0 CA A:ILE203 4.9 0.4 1.0 CG2 A:ILE203 4.9 91.6 1.0 C A:CYS201 4.9 0.3 1.0 N A:ILE203 4.9 0.7 1.0 C A:CYS204 5.0 0.4 1.0

Zinc binding site 4 out of 4 in the A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Complex of of RNF4-Ring Domain, UBEV2, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1263 b:0.1 occ:1.00 ND1 A:HIS225 2.1 0.3 1.0 SG A:CYS245 2.3 0.5 1.0 SG A:CYS242 2.3 0.8 1.0 SG A:CYS223 2.4 0.2 1.0 CG A:HIS225 2.8 96.5 1.0 CE1 A:HIS225 2.8 0.3 1.0 CB A:HIS225 3.3 0.8 1.0 CB A:CYS245 3.4 0.1 1.0 CB A:CYS242 3.4 0.8 1.0 CB A:CYS223 3.4 0.3 1.0 NE2 A:HIS225 3.6 0.9 1.0 CD2 A:HIS225 3.6 91.3 1.0 N A:CYS245 3.9 0.0 1.0 CA A:CYS245 4.2 0.3 1.0 OG1 A:THR221 4.4 0.5 1.0 CB A:THR244 4.6 1.0 1.0 CA A:CYS223 4.6 0.2 1.0 CA A:HIS225 4.7 1.0 1.0 O A:CYS223 4.7 0.0 1.0 C A:CYS223 4.7 0.4 1.0 N A:HIS225 4.8 0.5 1.0 CA A:CYS242 4.8 0.4 1.0 C A:THR244 4.8 0.3 1.0 CG2 A:THR244 4.9 0.5 1.0 N A:ARG246 4.9 0.5 1.0

E.Branigan, A.Plechanovova, E.Jaffray, J.H.Naismith, R.T.Hay. Structural Basis For the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains Nat.Struct.Mol.Biol. V. 22 597 2015.
ISSN: ISSN 1545-9993
PubMed: 26148049
DOI: 10.1038/NSMB.3052