Zinc in PDB 5tdb: Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide

The structure of Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide, PDB code: 5tdb 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)	15.46 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.573, 37.168, 29.746, 90.00, 109.50, 90.00
R / Rfree (%)	12.5 / 13.4

The binding sites of Zinc atom in the Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide (pdb code 5tdb). 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 Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide, PDB code: 5tdb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide


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 Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:9.8 occ:1.00 SG A:CYS99 2.3 11.5 1.0 SG A:CYS149 2.3 9.8 1.0 SG A:CYS124 2.3 9.7 1.0 SG A:CYS127 2.4 10.0 1.0 HB2 A:CYS127 3.0 11.8 1.0 CB A:CYS149 3.2 10.8 1.0 H A:CYS124 3.2 12.5 1.0 HB3 A:CYS149 3.2 12.9 1.0 HB2 A:CYS149 3.2 12.9 1.0 CB A:CYS99 3.2 14.2 1.0 HB2 A:CYS99 3.3 17.1 1.0 HB3 A:CYS99 3.3 17.1 1.0 CB A:CYS127 3.3 9.8 1.0 HB3 A:CYS124 3.3 12.9 1.0 CB A:CYS124 3.5 10.7 1.0 HB3 A:CYS151 3.6 14.3 1.0 H A:CYS127 3.7 11.9 1.0 HB2 A:CYS151 3.8 14.3 1.0 HB3 A:CYS127 3.9 11.8 1.0 HB3 A:ARG101 3.9 15.4 1.0 N A:CYS124 4.0 10.4 1.0 HE1 A:HIS166 4.1 16.8 1.0 H A:ARG101 4.2 14.7 1.0 CB A:CYS151 4.2 11.9 1.0 HB2 A:ARG101 4.2 15.4 1.0 O A:HOH303 4.2 29.5 1.0 HB2 A:CYS124 4.2 12.9 1.0 CA A:CYS124 4.3 10.2 1.0 N A:CYS127 4.3 9.9 1.0 HE A:ARG101 4.4 18.8 1.0 H A:CYS151 4.4 12.3 1.0 ZN A:ZN202 4.4 11.1 1.0 CA A:CYS127 4.5 10.0 1.0 HB3 A:GLU126 4.5 14.3 1.0 CB A:ARG101 4.5 12.8 1.0 CA A:CYS99 4.6 17.1 1.0 CA A:CYS149 4.7 10.4 1.0 HA A:LEU123 4.7 13.7 1.0 CE1 A:HIS166 4.7 14.0 1.0 HA A:CYS127 4.9 12.0 1.0 C A:CYS124 4.9 10.4 1.0 HA A:CYS99 4.9 20.5 1.0 NE A:ARG101 4.9 15.6 1.0 H A:GLY100 4.9 18.0 1.0 HD22 A:LEU123 4.9 16.4 1.0 O A:CYS124 4.9 10.2 1.0 HA A:CYS149 5.0 12.4 1.0 N A:ARG101 5.0 12.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide


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 Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:11.1 occ:1.00 ND1 A:HIS166 2.1 13.3 1.0 SG A:CYS151 2.3 14.2 1.0 SG A:CYS163 2.3 11.6 1.0 SG A:CYS127 2.4 10.0 1.0 HB2 A:HIS166 2.9 17.9 1.0 CE1 A:HIS166 3.0 14.0 1.0 HB3 A:CYS127 3.0 11.8 1.0 CG A:HIS166 3.1 13.6 1.0 HE1 A:HIS166 3.1 16.8 1.0 CB A:CYS151 3.2 11.9 1.0 HB3 A:CYS163 3.2 15.0 1.0 HB2 A:CYS151 3.2 14.3 1.0 CB A:CYS127 3.2 9.8 1.0 HB3 A:CYS151 3.3 14.3 1.0 H A:CYS163 3.3 17.1 1.0 HB2 A:CYS99 3.4 17.1 1.0 CB A:CYS163 3.4 12.5 1.0 HA A:CYS127 3.5 12.0 1.0 CB A:HIS166 3.5 14.9 1.0 H A:HIS166 3.9 18.4 1.0 CA A:CYS127 3.9 10.0 1.0 HB2 A:CYS127 4.1 11.8 1.0 N A:CYS163 4.1 14.2 1.0 HB3 A:LYS165 4.1 23.9 1.0 NE2 A:HIS166 4.1 16.6 1.0 HB2 A:CYS163 4.1 15.0 1.0 HB3 A:HIS166 4.2 17.9 1.0 CD2 A:HIS166 4.2 16.6 1.0 CA A:CYS163 4.3 13.5 1.0 CB A:CYS99 4.3 14.2 1.0 N A:HIS166 4.4 15.3 1.0 ZN A:ZN201 4.4 9.8 1.0 HB3 A:CYS99 4.5 17.1 1.0 CA A:HIS166 4.6 15.2 1.0 CA A:CYS151 4.7 10.8 1.0 H A:LYS165 4.8 18.4 1.0 N A:CYS127 4.8 9.9 1.0 HA A:TYR162 4.8 18.1 1.0 C A:CYS163 4.9 14.1 1.0 HE2 A:HIS166 4.9 19.9 1.0 HA A:CYS151 4.9 13.0 1.0 HD2 A:LYS165 5.0 32.9 1.0 H A:CYS127 5.0 11.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide


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 Human Ubr-Box Domain From UBR2 in Complex with Asymmetrically Double Methylated Arginine Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:13.8 occ:1.00 ND1 A:HIS136 2.0 14.7 1.0 ND1 A:HIS133 2.1 12.8 1.0 SG A:CYS112 2.3 13.9 1.0 SG A:CYS115 2.3 15.7 1.0 HB2 A:CYS115 2.9 18.8 1.0 CE1 A:HIS136 2.9 15.1 1.0 CE1 A:HIS133 3.0 13.0 1.0 HE1 A:HIS133 3.1 15.6 1.0 HE1 A:HIS136 3.1 18.1 1.0 CG A:HIS136 3.1 14.9 1.0 CB A:CYS115 3.2 15.7 1.0 HA A:HIS133 3.2 15.2 1.0 CG A:HIS133 3.2 12.5 1.0 HB2 A:HIS136 3.3 18.9 1.0 HB3 A:HIS133 3.3 14.9 1.0 CB A:CYS112 3.4 14.4 1.0 HB2 A:ASP114 3.4 20.5 1.0 HB3 A:CYS112 3.4 17.3 1.0 HB2 A:CYS112 3.4 17.3 1.0 HB3 A:HIS136 3.5 18.9 1.0 CB A:HIS136 3.5 15.8 1.0 H A:CYS115 3.6 18.9 1.0 CB A:HIS133 3.6 12.4 1.0 HB3 A:CYS115 3.9 18.8 1.0 CA A:HIS133 3.9 12.7 1.0 N A:CYS115 3.9 15.8 1.0 HG13 A:ILE132 3.9 19.8 1.0 NE2 A:HIS136 4.1 16.8 1.0 NE2 A:HIS133 4.1 13.0 1.0 CA A:CYS115 4.2 15.5 1.0 CD2 A:HIS136 4.2 16.8 1.0 CD2 A:HIS133 4.3 12.8 1.0 CB A:ASP114 4.3 17.1 1.0 HD11 A:ILE132 4.4 23.5 1.0 H A:ASP114 4.4 19.3 1.0 HB3 A:ASP114 4.6 20.5 1.0 HB2 A:HIS133 4.6 14.9 1.0 HD12 A:ILE132 4.6 23.5 1.0 N A:HIS133 4.6 12.9 1.0 C A:ASP114 4.6 17.1 1.0 HA A:CYS115 4.7 18.6 1.0 CA A:CYS112 4.7 15.2 1.0 CG1 A:ILE132 4.8 16.5 1.0 CD1 A:ILE132 4.8 19.6 1.0 HE2 A:HIS136 4.9 20.1 1.0 CA A:ASP114 4.9 17.1 1.0 HE2 A:HIS133 4.9 15.6 1.0 H A:HIS133 4.9 15.5 1.0 HA A:CYS112 4.9 18.2 1.0 N A:ASP114 5.0 16.1 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