Zinc in PDB 7yrb: Ubr Box of Human UBR6

The structure of Ubr Box of Human UBR6, PDB code: 7yrb was solved by B.Kim, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.848, 39.359, 45.248, 90, 90, 90
R / Rfree (%)	16.6 / 19.9

The binding sites of Zinc atom in the Ubr Box of Human UBR6 (pdb code 7yrb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ubr Box of Human UBR6, PDB code: 7yrb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ubr Box of Human UBR6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ubr Box of Human UBR6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:22.7 occ:1.00 SG A:CYS899 2.3 25.6 1.0 SG A:CYS890 2.4 21.8 1.0 SG A:CYS868 2.4 20.5 1.0 SG A:CYS872 2.4 23.2 1.0 HB3 A:CYS868 3.0 27.0 1.0 HA A:CYS899 3.1 39.9 1.0 HB3 A:CYS890 3.1 26.1 1.0 CB A:CYS868 3.2 22.5 1.0 CB A:CYS899 3.3 34.5 1.0 HB2 A:CYS899 3.3 41.4 1.0 CB A:CYS890 3.3 21.7 1.0 HB2 A:CYS872 3.4 27.4 1.0 CB A:CYS872 3.4 22.8 1.0 HB3 A:CYS872 3.5 27.4 1.0 HA A:CYS868 3.6 23.7 1.0 CA A:CYS899 3.6 33.3 1.0 H A:THR900 3.7 32.4 1.0 H A:LEU901 3.8 39.2 1.0 HD12 A:LEU901 3.8 33.1 1.0 HB2 A:LEU901 3.8 34.4 1.0 CA A:CYS868 4.0 19.7 1.0 HB2 A:CYS890 4.0 26.1 1.0 HB2 A:CYS868 4.0 27.0 1.0 HB3 A:CYS899 4.1 41.4 1.0 N A:THR900 4.2 27.0 1.0 C A:CYS890 4.2 25.5 1.0 N A:GLY891 4.3 21.6 1.0 C A:CYS899 4.3 32.6 1.0 ZN A:ZN1002 4.4 19.5 1.0 H A:GLY891 4.4 26.0 1.0 CA A:CYS890 4.4 17.7 1.0 HE2 A:HIS873 4.4 24.6 1.0 HA2 A:GLY891 4.4 31.7 1.0 HB2 A:CYS835 4.4 32.9 1.0 N A:LEU901 4.6 32.6 1.0 HG A:LEU901 4.6 36.2 1.0 O A:CYS890 4.6 25.4 1.0 H A:CYS872 4.6 26.7 1.0 CB A:LEU901 4.7 28.7 1.0 CD1 A:LEU901 4.7 27.6 1.0 HA A:CYS890 4.8 21.3 1.0 CA A:CYS872 4.8 23.0 1.0 CA A:GLY891 4.8 26.4 1.0 N A:CYS899 4.9 38.1 1.0 C A:CYS868 4.9 20.4 1.0 HD2 A:HIS873 4.9 25.7 1.0 O A:CYS868 4.9 21.9 1.0 CG A:LEU901 4.9 30.2 1.0 SG A:CYS835 5.0 21.7 1.0

Zinc binding site 2 out of 3 in the Ubr Box of Human UBR6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ubr Box of Human UBR6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:19.5 occ:1.00 SG A:CYS835 2.3 21.7 1.0 SG A:CYS888 2.3 18.7 1.0 SG A:CYS865 2.4 19.0 1.0 SG A:CYS868 2.4 20.5 1.0 HB2 A:CYS868 3.0 27.0 1.0 CB A:CYS888 3.2 19.4 1.0 HB3 A:CYS888 3.2 23.3 1.0 HB2 A:CYS888 3.2 23.3 1.0 H A:CYS865 3.2 19.8 1.0 HB2 A:CYS835 3.3 32.9 1.0 CB A:CYS868 3.3 22.5 1.0 CB A:CYS835 3.3 27.4 1.0 HB3 A:CYS865 3.3 21.2 1.0 HA A:CYS835 3.4 26.0 1.0 CB A:CYS865 3.5 17.7 1.0 H A:GLY891 3.5 26.0 1.0 HB3 A:CYS890 3.5 26.1 1.0 H A:LEU836 3.5 24.2 1.0 H A:CYS868 3.8 22.0 1.0 CA A:CYS835 3.8 21.7 1.0 HB3 A:CYS868 3.9 27.0 1.0 N A:CYS865 4.0 16.5 1.0 H A:TYR837 4.0 29.8 1.0 N A:LEU836 4.1 20.2 1.0 HB3 A:CYS835 4.2 32.9 1.0 N A:GLY891 4.2 21.6 1.0 HA3 A:GLY891 4.2 31.7 1.0 HB2 A:CYS865 4.2 21.2 1.0 CA A:CYS865 4.3 19.0 1.0 HG23 A:ILE864 4.3 23.2 1.0 C A:CYS835 4.4 21.8 1.0 ZN A:ZN1001 4.4 22.7 1.0 N A:CYS868 4.4 18.3 1.0 CA A:CYS868 4.4 19.7 1.0 CB A:CYS890 4.5 21.7 1.0 HD12 A:LEU901 4.6 33.1 1.0 HB2 A:TYR837 4.6 31.1 1.0 CA A:CYS888 4.6 19.0 1.0 CA A:GLY891 4.7 26.4 1.0 HB2 A:LEU836 4.7 25.7 1.0 HA A:CYS868 4.8 23.7 1.0 H A:CYS890 4.8 23.5 1.0 HG22 A:ILE864 4.8 23.2 1.0 HA A:ILE864 4.8 20.5 1.0 N A:TYR837 4.8 24.8 1.0 HB2 A:CYS890 4.8 26.1 1.0 C A:CYS865 4.9 18.2 1.0 O A:CYS865 4.9 18.0 1.0 HA A:CYS888 4.9 22.8 1.0 HA2 A:GLY891 5.0 31.7 1.0

Zinc binding site 3 out of 3 in the Ubr Box of Human UBR6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ubr Box of Human UBR6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:21.7 occ:1.00 ND1 A:HIS876 2.0 22.6 1.0 ND1 A:HIS873 2.1 18.6 1.0 SG A:CYS853 2.3 20.6 1.0 SG A:CYS856 2.3 30.2 1.0 CE1 A:HIS876 2.9 26.0 1.0 HB2 A:CYS856 3.0 40.0 1.0 CE1 A:HIS873 3.0 24.7 1.0 HE1 A:HIS876 3.0 31.2 1.0 HE1 A:HIS873 3.1 29.6 1.0 HB3 A:HIS873 3.1 23.3 1.0 CG A:HIS876 3.1 18.6 1.0 CG A:HIS873 3.2 18.7 1.0 CB A:CYS856 3.2 33.3 1.0 HB3 A:HIS876 3.3 26.5 1.0 HB A:THR855 3.3 29.7 1.0 CB A:CYS853 3.4 19.6 1.0 HB3 A:CYS853 3.4 23.5 1.0 HB2 A:CYS853 3.5 23.5 1.0 H A:CYS856 3.6 33.5 1.0 CB A:HIS876 3.6 22.1 1.0 HB2 A:HIS876 3.6 26.5 1.0 CB A:HIS873 3.6 19.4 1.0 HA A:HIS873 3.8 23.5 1.0 N A:CYS856 3.9 27.9 1.0 HB3 A:CYS856 4.0 40.0 1.0 NE2 A:HIS876 4.1 24.2 1.0 NE2 A:HIS873 4.2 20.5 1.0 CA A:CYS856 4.2 31.1 1.0 CD2 A:HIS876 4.2 24.4 1.0 CD2 A:HIS873 4.3 21.4 1.0 CB A:THR855 4.3 24.7 1.0 CA A:HIS873 4.3 19.6 1.0 HG22 A:THR855 4.4 34.6 1.0 HB2 A:HIS873 4.4 23.3 1.0 H A:THR855 4.6 26.7 1.0 HA A:CYS856 4.6 37.3 1.0 HG12 A:VAL878 4.6 25.7 1.0 C A:THR855 4.7 29.1 1.0 CA A:CYS853 4.7 18.7 1.0 HE2 A:HIS876 4.8 29.0 1.0 HD13 A:LEU895 4.8 37.0 1.0 HD21 A:ASN897 4.8 62.8 1.0 CG2 A:THR855 4.8 28.8 1.0 CA A:THR855 4.9 26.5 1.0 O A:CYS872 4.9 26.7 1.0 HE2 A:HIS873 4.9 24.6 1.0 HA A:CYS853 4.9 22.4 1.0

B.Kim, B.H.Kim, H.K.Song. Crystal Structure of Ubr Box From Human UBR6 To Be Published.