Zinc in PDB 5tdd: Human Ubr-Box From UBR2 in Complex with Hifs Peptide

The structure of Human Ubr-Box From UBR2 in Complex with Hifs Peptide, PDB code: 5tdd was solved by J.Munoz-Escobar, G.Kozlov, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.73 / 1.55
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	29.313, 29.313, 74.151, 90.00, 90.00, 90.00
R / Rfree (%)	10.6 / 15.2

The binding sites of Zinc atom in the Human Ubr-Box From UBR2 in Complex with Hifs Peptide (pdb code 5tdd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human Ubr-Box From UBR2 in Complex with Hifs Peptide, PDB code: 5tdd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human Ubr-Box From UBR2 in Complex with Hifs Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Ubr-Box From UBR2 in Complex with Hifs Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:11.3 occ:1.00 SG A:CYS99 2.3 13.2 1.0 SG A:CYS149 2.3 11.1 1.0 SG A:CYS124 2.4 12.7 1.0 SG A:CYS127 2.4 11.8 1.0 HB2 A:CYS127 3.1 14.2 1.0 HB2 A:CYS99 3.1 18.8 1.0 CB A:CYS99 3.1 15.6 1.0 HB3 A:CYS99 3.2 18.8 1.0 H A:CYS124 3.2 13.3 1.0 HB3 A:CYS149 3.2 13.7 1.0 CB A:CYS149 3.2 11.4 1.0 HB2 A:CYS149 3.2 13.7 1.0 CB A:CYS127 3.4 11.8 1.0 HB3 A:CYS124 3.4 14.4 1.0 CB A:CYS124 3.5 12.0 1.0 HB3 A:CYS151 3.7 15.1 1.0 HB2 A:CYS151 3.7 15.1 1.0 HE1 A:HIS166 3.7 21.5 1.0 HB3 A:ARG101 3.9 19.5 1.0 H A:CYS127 3.9 14.7 1.0 HB3 A:CYS127 3.9 14.2 1.0 N A:CYS124 3.9 11.1 1.0 CB A:CYS151 4.2 12.6 1.0 O A:HOH311 4.2 39.3 1.0 HB2 A:CYS124 4.3 14.4 1.0 CA A:CYS124 4.3 11.6 1.0 H A:ARG101 4.3 17.1 1.0 HB2 A:ARG101 4.3 19.5 1.0 H A:CYS151 4.4 14.1 1.0 ZN A:ZN202 4.4 12.7 1.0 CE1 A:HIS166 4.5 17.9 1.0 N A:CYS127 4.5 12.2 1.0 HD3 A:ARG101 4.5 24.3 1.0 CA A:CYS127 4.5 11.1 1.0 CB A:ARG101 4.6 16.2 1.0 HA A:LEU123 4.6 13.4 1.0 CA A:CYS99 4.6 15.9 1.0 CA A:CYS149 4.7 10.6 1.0 HB3 A:LEU123 4.8 12.9 1.0 HA A:CYS99 4.9 19.1 1.0 HB3 A:GLU126 4.9 20.1 1.0 O A:CYS124 4.9 10.3 1.0 ND1 A:HIS166 4.9 16.9 1.0 HA A:CYS127 4.9 13.3 1.0 C A:CYS124 4.9 11.0 1.0 HA A:CYS149 5.0 12.7 1.0

Zinc binding site 2 out of 3 in the Human Ubr-Box From UBR2 in Complex with Hifs Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Ubr-Box From UBR2 in Complex with Hifs Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:12.7 occ:1.00 ND1 A:HIS166 2.1 16.9 1.0 SG A:CYS163 2.3 12.5 1.0 SG A:CYS151 2.3 15.4 1.0 SG A:CYS127 2.4 11.8 1.0 HB3 A:CYS127 2.9 14.2 1.0 CE1 A:HIS166 2.9 17.9 1.0 HB2 A:HIS166 3.0 20.8 1.0 HE1 A:HIS166 3.1 21.5 1.0 HB3 A:CYS151 3.1 15.1 1.0 CG A:HIS166 3.1 17.2 1.0 CB A:CYS127 3.2 11.8 1.0 CB A:CYS151 3.2 12.6 1.0 HB3 A:CYS163 3.2 18.2 1.0 H A:CYS163 3.4 15.8 1.0 HB2 A:CYS151 3.4 15.1 1.0 CB A:CYS163 3.4 15.2 1.0 HB2 A:CYS99 3.4 18.8 1.0 HA A:CYS127 3.5 13.3 1.0 CB A:HIS166 3.6 17.3 1.0 HB3 A:LYS165 3.8 24.3 1.0 H A:HIS166 3.9 21.5 1.0 CA A:CYS127 3.9 11.1 1.0 HB2 A:CYS127 4.0 14.2 1.0 N A:CYS163 4.1 13.2 1.0 NE2 A:HIS166 4.1 20.5 1.0 HB2 A:CYS163 4.1 18.2 1.0 CD2 A:HIS166 4.2 18.8 1.0 HB3 A:HIS166 4.2 20.8 1.0 CA A:CYS163 4.3 13.8 1.0 N A:HIS166 4.3 17.9 1.0 CB A:CYS99 4.4 15.6 1.0 ZN A:ZN201 4.4 11.3 1.0 CA A:CYS151 4.6 10.9 1.0 CA A:HIS166 4.6 17.0 1.0 H A:LYS165 4.7 21.2 1.0 HB3 A:CYS99 4.7 18.8 1.0 CB A:LYS165 4.8 20.2 1.0 HA A:TYR162 4.8 21.1 1.0 HE2 A:HIS166 4.9 24.6 1.0 C A:CYS163 4.9 14.1 1.0 HD22 A:LEU123 4.9 17.8 1.0 N A:CYS127 4.9 12.2 1.0 HD3 A:LYS165 4.9 38.1 1.0 HA A:CYS151 4.9 13.1 1.0 C A:CYS127 4.9 12.2 1.0

Zinc binding site 3 out of 3 in the Human Ubr-Box From UBR2 in Complex with Hifs Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Ubr-Box From UBR2 in Complex with Hifs Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:14.4 occ:1.00 ND1 A:HIS136 2.1 13.4 1.0 ND1 A:HIS133 2.1 13.9 1.0 SG A:CYS112 2.3 13.9 1.0 SG A:CYS115 2.3 16.6 1.0 HB2 A:CYS115 2.9 19.6 1.0 CE1 A:HIS133 2.9 15.3 1.0 CE1 A:HIS136 3.0 16.5 1.0 HE1 A:HIS133 3.0 18.3 1.0 HE1 A:HIS136 3.1 19.8 1.0 CG A:HIS136 3.1 14.7 1.0 CG A:HIS133 3.2 14.0 1.0 CB A:CYS115 3.2 16.4 1.0 HA A:HIS133 3.2 17.0 1.0 HB2 A:HIS136 3.3 17.9 1.0 HB3 A:HIS133 3.3 15.8 1.0 CB A:CYS112 3.3 15.1 1.0 HB2 A:ASP114 3.3 21.4 1.0 HB3 A:CYS112 3.4 18.1 1.0 HB2 A:CYS112 3.4 18.1 1.0 HB3 A:HIS136 3.5 17.9 1.0 CB A:HIS136 3.5 14.9 1.0 H A:CYS115 3.6 18.3 1.0 CB A:HIS133 3.6 13.2 1.0 CA A:HIS133 3.9 14.2 1.0 HB3 A:CYS115 3.9 19.6 1.0 N A:CYS115 3.9 15.2 1.0 HG23 A:ILE132 4.0 22.3 1.0 NE2 A:HIS133 4.1 15.2 1.0 NE2 A:HIS136 4.1 16.3 1.0 CA A:CYS115 4.2 16.6 1.0 CD2 A:HIS136 4.2 16.0 1.0 CD2 A:HIS133 4.2 14.0 1.0 CB A:ASP114 4.3 17.9 1.0 H A:ASP114 4.5 20.1 1.0 HB2 A:HIS133 4.6 15.8 1.0 N A:HIS133 4.6 14.3 1.0 HB3 A:ASP114 4.6 21.4 1.0 C A:ASP114 4.7 17.4 1.0 CA A:CYS112 4.7 12.6 1.0 HA A:CYS115 4.7 19.9 1.0 CG2 A:ILE132 4.8 18.6 1.0 HE2 A:HIS133 4.8 18.3 1.0 HG3 A:GLU159 4.9 46.7 1.0 HE2 A:HIS136 4.9 19.5 1.0 CA A:ASP114 4.9 18.7 1.0 H A:HIS133 4.9 17.1 1.0 HA A:CYS112 4.9 15.1 1.0 OD1 A:ASP114 5.0 22.3 1.0 HG22 A:ILE132 5.0 22.3 1.0

J.Munoz-Escobar, E.Matta-Camacho, C.Cho, G.Kozlov, K.Gehring. Bound Waters Mediate Binding of Diverse Substrates to A Ubiquitin Ligase. Structure V. 25 719 2017.
ISSN: ISSN 1878-4186
PubMed: 28392261
DOI: 10.1016/J.STR.2017.03.004