Zinc in PDB 8j9r: Crystal Structure of Ubr Box of Yifs-UBR4

All present enzymatic activity of Crystal Structure of Ubr Box of Yifs-UBR4:
2.3.2.27;

The structure of Crystal Structure of Ubr Box of Yifs-UBR4, PDB code: 8j9r was solved by D.-E.Jeong, S.-J.Kim, H.-C.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.70 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.58, 38.28, 55.4, 90, 90, 90
R / Rfree (%)	23.4 / 28.7

The binding sites of Zinc atom in the Crystal Structure of Ubr Box of Yifs-UBR4 (pdb code 8j9r). 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 Ubr Box of Yifs-UBR4, PDB code: 8j9r:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Ubr Box of Yifs-UBR4


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 Ubr Box of Yifs-UBR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:12.8 occ:0.00 SG A:CYS1698 2.3 10.8 1.0 SG A:CYS1716 2.3 11.3 1.0 SG A:CYS1694 2.3 8.6 1.0 SG A:CYS1724 2.4 11.0 1.0 HB3 A:CYS1694 3.0 20.8 1.0 HB3 A:CYS1716 3.0 13.5 1.0 HB2 A:CYS1724 3.1 22.9 1.0 HB2 A:CYS1698 3.2 22.2 1.0 CB A:CYS1694 3.2 17.3 1.0 CB A:CYS1724 3.2 19.1 1.0 HA A:CYS1724 3.2 15.1 1.0 CB A:CYS1698 3.3 18.4 1.0 CB A:CYS1716 3.3 11.2 1.0 HB3 A:CYS1698 3.4 22.2 1.0 H A:LEU1725 3.5 13.2 1.0 HA A:CYS1694 3.5 12.5 1.0 HB3 A:ALA1726 3.6 25.5 1.0 H A:ALA1726 3.7 19.1 1.0 CA A:CYS1724 3.7 12.5 1.0 HB2 A:CYS1716 3.9 13.5 1.0 CA A:CYS1694 4.0 10.4 1.0 HB2 A:CYS1694 4.0 20.8 1.0 N A:LEU1725 4.1 11.0 1.0 HB3 A:CYS1724 4.1 22.9 1.0 C A:CYS1716 4.1 9.2 1.0 N A:GLY1717 4.2 6.7 1.0 H A:GLY1717 4.2 8.1 1.0 HB2 A:CYS1662 4.2 17.2 1.0 CA A:CYS1716 4.3 13.6 1.0 HA2 A:GLY1717 4.3 16.9 1.0 ZN A:ZN1802 4.3 10.7 0.0 C A:CYS1724 4.3 11.3 1.0 N A:ALA1726 4.4 15.9 1.0 H A:CYS1698 4.4 16.8 1.0 CB A:ALA1726 4.5 21.2 1.0 HD2 A:HIS1699 4.5 17.7 1.0 O A:HOH1920 4.5 34.3 1.0 HE2 A:HIS1699 4.5 15.7 1.0 O A:CYS1716 4.6 15.3 1.0 CA A:CYS1698 4.7 15.9 1.0 HB2 A:ALA1726 4.7 25.5 1.0 HA A:CYS1716 4.7 16.4 1.0 CA A:GLY1717 4.8 14.1 1.0 N A:CYS1694 4.9 8.4 1.0 SG A:CYS1662 5.0 9.8 1.0 C A:CYS1694 5.0 12.9 1.0 N A:CYS1698 5.0 14.0 1.0 N A:CYS1724 5.0 21.3 1.0 H A:CYS1694 5.0 10.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Ubr Box of Yifs-UBR4


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 Ubr Box of Yifs-UBR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:10.7 occ:0.00 SG A:CYS1691 2.3 9.6 1.0 SG A:CYS1662 2.3 9.8 1.0 SG A:CYS1694 2.3 8.6 1.0 SG A:CYS1714 2.3 9.5 1.0 HB2 A:CYS1694 3.0 20.8 1.0 H A:CYS1691 3.1 10.8 1.0 HB2 A:CYS1662 3.1 17.2 1.0 CB A:CYS1714 3.2 16.2 1.0 CB A:CYS1662 3.2 14.3 1.0 HB2 A:CYS1714 3.2 19.5 1.0 HB3 A:CYS1714 3.3 19.5 1.0 CB A:CYS1694 3.3 17.3 1.0 HB3 A:CYS1691 3.3 14.1 1.0 HA A:CYS1662 3.3 11.6 1.0 H A:GLY1717 3.4 8.1 1.0 CB A:CYS1691 3.4 11.7 1.0 H A:CYS1694 3.5 10.1 1.0 HB3 A:CYS1716 3.5 13.5 1.0 H A:THR1663 3.5 13.1 1.0 CA A:CYS1662 3.7 9.6 1.0 HB3 A:CYS1694 3.9 20.8 1.0 N A:CYS1691 3.9 9.0 1.0 H A:PHE1664 3.9 15.4 1.0 N A:THR1663 4.1 10.9 1.0 HB3 A:CYS1662 4.1 17.2 1.0 N A:GLY1717 4.1 6.7 1.0 N A:CYS1694 4.2 8.4 1.0 HB2 A:CYS1691 4.2 14.1 1.0 HA3 A:GLY1717 4.2 16.9 1.0 CA A:CYS1691 4.2 4.4 1.0 C A:CYS1662 4.3 8.7 1.0 CA A:CYS1694 4.3 10.4 1.0 ZN A:ZN1801 4.3 12.8 0.0 HB A:VAL1693 4.4 14.8 1.0 CB A:CYS1716 4.5 11.2 1.0 HB A:VAL1690 4.6 14.0 1.0 HB2 A:PHE1664 4.6 14.9 1.0 HA A:VAL1690 4.7 16.8 1.0 CA A:GLY1717 4.7 14.1 1.0 CA A:CYS1714 4.7 13.3 1.0 H A:CYS1716 4.7 12.4 1.0 OG1 A:THR1663 4.7 12.6 1.0 HA A:CYS1694 4.7 12.5 1.0 N A:PHE1664 4.8 12.8 1.0 C A:CYS1691 4.8 9.7 1.0 HG1 A:THR1663 4.9 15.1 1.0 HB3 A:ALA1726 4.9 25.5 1.0 HB2 A:CYS1716 4.9 13.5 1.0 O A:CYS1691 4.9 11.2 1.0 HA A:CYS1714 4.9 16.0 1.0 HA2 A:GLY1717 5.0 16.9 1.0 SG A:CYS1724 5.0 11.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Ubr Box of Yifs-UBR4


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 Ubr Box of Yifs-UBR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:16.0 occ:0.00 ND1 A:HIS1699 2.0 12.5 1.0 ND1 A:HIS1702 2.1 12.6 1.0 SG A:CYS1682 2.2 16.3 1.0 SG A:CYS1679 2.3 13.4 1.0 CE1 A:HIS1699 2.8 17.9 1.0 HE1 A:HIS1699 2.8 21.6 1.0 CE1 A:HIS1702 2.8 15.2 1.0 HE1 A:HIS1702 2.9 18.3 1.0 HB2 A:CYS1682 3.1 20.5 1.0 CG A:HIS1702 3.2 18.6 1.0 CG A:HIS1699 3.2 17.1 1.0 CB A:CYS1682 3.3 17.1 1.0 H A:CYS1682 3.3 17.4 1.0 HB3 A:HIS1699 3.4 15.2 1.0 HB A:THR1681 3.4 23.3 1.0 CB A:CYS1679 3.4 16.5 1.0 HB3 A:HIS1702 3.4 18.9 1.0 HB3 A:CYS1679 3.4 19.9 1.0 HB2 A:CYS1679 3.5 19.9 1.0 HB2 A:HIS1702 3.7 18.9 1.0 CB A:HIS1702 3.7 15.7 1.0 CB A:HIS1699 3.8 12.6 1.0 N A:CYS1682 3.8 14.5 1.0 HA A:HIS1699 3.9 13.9 1.0 NE2 A:HIS1699 4.0 13.0 1.0 HB3 A:CYS1682 4.0 20.5 1.0 NE2 A:HIS1702 4.0 19.3 1.0 CA A:CYS1682 4.2 14.5 1.0 CD2 A:HIS1702 4.2 20.9 1.0 CD2 A:HIS1699 4.2 14.7 1.0 HG22 A:THR1681 4.3 24.7 1.0 CB A:THR1681 4.3 19.4 1.0 O A:HOH1974 4.4 38.3 1.0 CA A:HIS1699 4.4 11.6 1.0 HA A:CYS1682 4.6 17.5 1.0 HB2 A:HIS1699 4.6 15.2 1.0 C A:THR1681 4.7 15.9 1.0 HE2 A:HIS1699 4.7 15.7 1.0 CA A:CYS1679 4.7 16.1 1.0 H A:THR1681 4.7 20.7 1.0 HG22 A:ILE1704 4.7 21.2 1.0 HE2 A:HIS1702 4.8 23.2 1.0 CG2 A:THR1681 4.8 20.5 1.0 HA A:CYS1679 4.9 19.4 1.0 CA A:THR1681 4.9 17.9 1.0

D.E.Jeong, H.S.Lee, B.Ku, C.H.Kim, S.J.Kim, H.C.Shin. Insights Into the Recognition Mechanism in the Ubr Box of UBR4 For Its Specific Substrates. Commun Biol V. 6 1214 2023.
ISSN: ESSN 2399-3642
PubMed: 38030679
DOI: 10.1038/S42003-023-05602-7