Zinc in PDB 5ywr: Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13)

All present enzymatic activity of Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13):
2.3.2.23; 2.3.2.27;

The structure of Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13), PDB code: 5ywr was solved by A.P.Behera, P.Naskar, A.B.Datta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.42 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.430, 59.548, 94.792, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.4

The binding sites of Zinc atom in the Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13) (pdb code 5ywr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13), PDB code: 5ywr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13)


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 Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.3 occ:1.00 ND1 B:HIS207 2.1 10.6 1.0 SG B:CYS187 2.3 12.2 1.0 SG B:CYS210 2.3 12.2 1.0 SG B:CYS184 2.3 11.9 1.0 CB B:CYS184 3.1 13.8 1.0 CE1 B:HIS207 3.1 11.0 1.0 CG B:HIS207 3.1 12.5 1.0 CB B:CYS187 3.3 11.2 1.0 CB B:CYS210 3.4 12.4 1.0 CB B:HIS207 3.4 10.7 1.0 N B:CYS187 3.8 11.4 1.0 N B:HIS207 4.0 9.6 1.0 CA B:CYS187 4.1 12.0 1.0 NE2 B:HIS207 4.2 14.5 1.0 CD2 B:HIS207 4.3 13.2 1.0 CA B:HIS207 4.4 11.9 1.0 CA B:CYS184 4.5 13.5 1.0 CB B:ILE186 4.7 10.8 1.0 CA B:CYS210 4.7 9.7 1.0 C B:ILE186 4.9 13.5 1.0 C B:CYS184 4.9 11.8 1.0 C B:CYS187 5.0 12.4 1.0 O B:CYS184 5.0 13.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13)


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 Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:16.3 occ:1.00 NE2 B:HIS160 2.1 14.8 1.0 SG B:CYS164 2.3 16.8 1.0 SG B:CYS148 2.3 16.4 1.0 SG B:CYS145 2.3 15.4 1.0 CD2 B:HIS160 3.0 15.6 1.0 CE1 B:HIS160 3.1 18.4 1.0 CB B:CYS145 3.1 15.4 1.0 CB B:CYS148 3.3 14.7 1.0 CB B:CYS164 3.4 14.6 1.0 N B:CYS148 3.7 14.2 1.0 CA B:CYS148 4.0 14.8 1.0 O B:HOH548 4.1 38.3 1.0 ND1 B:HIS160 4.1 20.8 1.0 CG B:HIS160 4.1 17.0 1.0 O B:HOH507 4.2 27.9 1.0 CB B:ILE147 4.5 13.2 1.0 CA B:CYS145 4.6 14.9 1.0 C B:ILE147 4.6 12.6 1.0 C B:CYS148 4.7 14.1 1.0 O B:HIS160 4.7 17.2 1.0 CA B:CYS164 4.8 15.1 1.0 N B:SER149 4.9 16.8 1.0 CA B:ILE147 4.9 12.7 1.0 N B:ILE147 4.9 15.5 1.0 O B:HOH554 4.9 22.7 1.0 C B:CYS145 5.0 15.7 1.0 CG2 B:ILE147 5.0 14.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ring E3 Ligase ZNRF1 in Complex with UBE2N (UBC13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:16.2 occ:1.00 ND1 B:HIS224 2.0 18.5 1.0 SG B:CYS202 2.2 17.8 1.0 SG B:CYS221 2.3 14.7 1.0 SG B:CYS204 2.3 17.2 1.0 CE1 B:HIS224 2.9 22.3 1.0 CG B:HIS224 3.1 18.0 1.0 CB B:CYS204 3.2 14.7 1.0 CB B:CYS202 3.2 19.2 1.0 CB B:CYS221 3.4 15.3 1.0 CB B:HIS224 3.6 19.5 1.0 N B:HIS224 4.0 17.8 1.0 NE2 B:HIS224 4.0 27.8 1.0 CB B:GLU223 4.0 16.4 0.6 CB B:GLU223 4.1 16.4 0.4 CD2 B:HIS224 4.2 26.1 1.0 N B:CYS204 4.2 17.2 1.0 CA B:CYS204 4.3 14.6 1.0 CA B:HIS224 4.4 22.1 1.0 C B:GLU223 4.4 17.6 0.6 CA B:CYS202 4.5 20.8 1.0 O B:HOH447 4.5 24.6 1.0 C B:GLU223 4.5 16.1 0.4 OH B:TYR206 4.6 16.5 1.0 C B:CYS202 4.6 18.9 1.0 O B:CYS202 4.6 24.0 1.0 CA B:GLU223 4.6 17.4 0.6 O B:HOH535 4.7 25.4 1.0 CA B:GLU223 4.7 14.4 0.4 N B:GLU223 4.7 11.8 0.6 N B:GLU223 4.7 17.5 0.4 CA B:CYS221 4.8 13.7 1.0 CG B:GLU223 4.8 15.8 0.6

A.P.Behera, P.Naskar, S.Agarwal, P.A.Banka, A.Poddar, A.B.Datta. Structural Insights Into the Nanomolar Affinity of Ring E3 Ligase ZNRF1 For UBE2N and Its Functional Implications. Biochem. J. V. 475 1569 2018.
ISSN: ESSN 1470-8728
PubMed: 29626159
DOI: 10.1042/BCJ20170909