Zinc in PDB 5tda: Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron

The structure of Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron, PDB code: 5tda 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)	17.03 / 0.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.702, 37.158, 57.474, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 12.8

The binding sites of Zinc atom in the Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron (pdb code 5tda). 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 the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron, PDB code: 5tda:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron


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 the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:5.5 occ:1.00 SG A:CYS99 2.3 6.3 1.0 SG A:CYS149 2.3 5.3 1.0 SG A:CYS124 2.3 5.8 1.0 SG A:CYS127 2.4 5.5 1.0 HB2 A:CYS127 3.0 6.5 1.0 CB A:CYS149 3.2 5.4 1.0 HB2 A:CYS149 3.2 6.5 1.0 HB3 A:CYS149 3.2 6.5 1.0 H A:CYS124 3.3 7.1 0.9 HB2 A:CYS99 3.3 7.8 1.0 CB A:CYS99 3.3 6.5 1.0 CB A:CYS127 3.3 5.4 1.0 HB3 A:CYS124 3.4 7.5 1.0 HB3 A:CYS99 3.4 7.8 1.0 HD3 A:ARG101 3.4 12.1 0.8 CB A:CYS124 3.5 6.2 1.0 HB3 A:CYS151 3.7 7.1 1.0 HB2 A:CYS151 3.7 7.1 1.0 HB2 A:ARG101 3.7 10.0 0.8 H A:CYS127 3.8 6.9 1.0 HB3 A:CYS127 3.9 6.5 1.0 HB3 A:ARG101 4.0 10.5 0.2 N A:CYS124 4.0 5.9 1.0 HB2 A:ARG101 4.1 10.5 0.2 HE1 A:HIS166 4.1 9.2 1.0 CB A:CYS151 4.2 5.9 1.0 HB2 A:CYS124 4.3 7.5 1.0 CA A:CYS124 4.3 6.0 1.0 H A:ARG101 4.3 9.1 0.2 H A:ARG101 4.3 8.1 0.8 HD2 A:ARG101 4.3 12.3 0.2 N A:CYS127 4.4 5.8 1.0 CD A:ARG101 4.4 10.1 0.8 H A:CYS151 4.4 6.5 1.0 ZN A:ZN202 4.4 5.7 1.0 HB3 A:GLU126 4.5 8.8 1.0 CA A:CYS127 4.5 5.6 1.0 CB A:ARG101 4.5 8.8 0.2 O A:HOH342 4.6 13.7 0.9 CA A:CYS149 4.6 5.2 1.0 CB A:ARG101 4.6 8.3 0.8 HE A:ARG101 4.6 12.8 0.2 CA A:CYS99 4.7 6.9 1.0 HA A:LEU123 4.7 7.3 1.0 HG3 A:ARG101 4.7 11.3 0.8 CE1 A:HIS166 4.8 7.7 1.0 CG A:ARG101 4.8 9.4 0.8 HA A:CYS99 4.9 8.3 1.0 HA A:CYS127 4.9 6.7 1.0 C A:CYS124 4.9 6.0 1.0 NE A:ARG101 4.9 10.7 0.2 HA A:CYS149 4.9 6.3 1.0 O A:CYS124 4.9 6.1 1.0 HB3 A:LEU123 4.9 7.8 1.0 HD22 A:LEU123 4.9 8.5 1.0 NE A:ARG101 5.0 11.3 0.8 HD2 A:ARG101 5.0 12.1 0.8

Zinc binding site 2 out of 3 in the Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron


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 the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:5.7 occ:1.00 ND1 A:HIS166 2.1 6.8 1.0 SG A:CYS151 2.3 6.3 1.0 SG A:CYS163 2.3 6.1 1.0 SG A:CYS127 2.3 5.5 1.0 HB2 A:HIS166 2.9 9.5 1.0 CE1 A:HIS166 3.0 7.7 1.0 HB3 A:CYS127 3.0 6.5 1.0 HE1 A:HIS166 3.1 9.2 1.0 CG A:HIS166 3.1 7.7 1.0 CB A:CYS127 3.2 5.4 1.0 CB A:CYS151 3.2 5.9 1.0 H A:CYS163 3.3 10.2 0.4 HB2 A:CYS151 3.3 7.1 1.0 HB3 A:CYS163 3.3 8.2 1.0 H A:CYS163 3.3 10.2 0.6 HB2 A:CYS99 3.3 7.8 1.0 HB3 A:CYS151 3.3 7.1 1.0 CB A:CYS163 3.4 6.9 1.0 HA A:CYS127 3.5 6.7 1.0 CB A:HIS166 3.5 7.9 1.0 CA A:CYS127 3.9 5.6 1.0 H A:HIS166 4.0 10.3 1.0 N A:CYS163 4.0 8.5 1.0 HB2 A:CYS127 4.1 6.5 1.0 HB2 A:LYS165 4.1 15.4 1.0 NE2 A:HIS166 4.1 8.8 1.0 HB3 A:HIS166 4.1 9.5 1.0 HB2 A:CYS163 4.2 8.2 1.0 O A:HOH344 4.2 8.1 0.9 CD2 A:HIS166 4.2 8.8 1.0 CB A:CYS99 4.2 6.5 1.0 O A:HOH374 4.3 24.7 0.5 CA A:CYS163 4.3 7.6 1.0 ZN A:ZN201 4.4 5.5 1.0 N A:HIS166 4.4 8.6 1.0 HB3 A:CYS99 4.5 7.8 1.0 CA A:HIS166 4.6 8.6 1.0 CA A:CYS151 4.7 5.7 1.0 HA A:TYR162 4.7 10.2 0.4 HB2 A:TYR162 4.7 10.9 0.4 N A:CYS127 4.8 5.8 1.0 HA A:TYR162 4.8 10.6 0.6 H A:LYS165 4.8 11.6 1.0 C A:CYS163 4.9 7.9 1.0 HE2 A:HIS166 4.9 10.6 1.0 H A:CYS99 4.9 9.3 1.0 HA A:CYS151 4.9 6.8 1.0 O A:CYS163 5.0 8.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron


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 the Ubr-Box Domain From UBR2 in Complex with Rlws N-Degron within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:5.9 occ:1.00 ND1 A:HIS136 2.1 6.5 1.0 ND1 A:HIS133 2.1 6.0 1.0 SG A:CYS112 2.3 6.1 1.0 SG A:CYS115 2.3 6.4 1.0 HB2 A:CYS115 2.8 7.5 1.0 CE1 A:HIS133 2.9 6.2 1.0 CE1 A:HIS136 3.0 7.2 1.0 HE1 A:HIS133 3.0 7.4 1.0 HE1 A:HIS136 3.1 8.6 1.0 CB A:CYS115 3.1 6.2 1.0 CG A:HIS136 3.1 7.0 1.0 CG A:HIS133 3.2 6.0 1.0 HA A:HIS133 3.2 7.3 1.0 HB2 A:HIS136 3.3 8.3 1.0 HB3 A:HIS133 3.4 7.3 1.0 CB A:CYS112 3.4 6.5 1.0 HB2 A:ASP114 3.4 10.0 1.0 HB2 A:CYS112 3.4 7.8 1.0 HB3 A:CYS112 3.5 7.8 1.0 HB3 A:HIS136 3.5 8.3 1.0 CB A:HIS136 3.6 6.9 1.0 H A:CYS115 3.6 7.2 0.9 CB A:HIS133 3.6 6.1 1.0 HB3 A:CYS115 3.8 7.5 1.0 HG22 A:ILE132 3.9 8.2 0.7 CA A:HIS133 3.9 6.1 1.0 N A:CYS115 3.9 6.0 1.0 NE2 A:HIS136 4.1 7.8 1.0 NE2 A:HIS133 4.1 6.3 1.0 CA A:CYS115 4.2 5.9 1.0 CD2 A:HIS136 4.2 7.7 1.0 CD2 A:HIS133 4.2 6.0 1.0 O A:HOH350 4.3 32.0 1.0 CB A:ASP114 4.3 8.4 1.0 O A:HOH378 4.4 15.8 0.8 HG13 A:ILE132 4.5 10.3 0.3 H A:ASP114 4.5 9.0 1.0 HB2 A:HIS133 4.6 7.3 1.0 HB3 A:ASP114 4.6 10.0 1.0 N A:HIS133 4.6 6.3 1.0 HA A:CYS115 4.7 7.1 1.0 C A:ASP114 4.7 6.7 1.0 CA A:CYS112 4.7 6.6 1.0 CG2 A:ILE132 4.8 6.8 0.7 HB3 A:GLU159 4.8 9.0 0.6 HD12 A:ILE132 4.8 10.8 0.3 HE2 A:HIS133 4.9 7.5 1.0 HE2 A:HIS136 4.9 9.4 1.0 HA A:CYS112 4.9 7.9 1.0 HD11 A:ILE132 4.9 10.8 0.3 H A:HIS133 4.9 7.6 1.0 CA A:ASP114 4.9 7.4 1.0 HG21 A:ILE132 5.0 8.2 0.7 HG23 A:ILE132 5.0 8.2 0.7

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