Zinc in PDB 9q88: High-Resolution Structure of RNF38 Ring Domain

All present enzymatic activity of High-Resolution Structure of RNF38 Ring Domain:
2.3.2.27;

The structure of High-Resolution Structure of RNF38 Ring Domain, PDB code: 9q88 was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.62 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.82, 39.309, 53.208, 90, 90, 90
R / Rfree (%)	15.1 / 16.8

The binding sites of Zinc atom in the High-Resolution Structure of RNF38 Ring Domain (pdb code 9q88). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the High-Resolution Structure of RNF38 Ring Domain, PDB code: 9q88:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the High-Resolution Structure of RNF38 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Structure of RNF38 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:9.7 occ:1.00 ND1 A:HIS436 2.1 10.0 1.0 SG A:CYS439 2.3 11.3 1.0 SG A:CYS416 2.3 9.5 1.0 SG A:CYS413 2.3 8.7 1.0 HB2 A:HIS436 2.7 11.9 1.0 HB3 A:CYS413 2.8 9.6 1.0 CB A:CYS413 3.1 7.9 1.0 HB3 A:CYS416 3.1 13.5 1.0 H A:CYS416 3.1 11.6 1.0 CE1 A:HIS436 3.1 9.5 1.0 CG A:HIS436 3.1 9.1 1.0 HB2 A:CYS439 3.2 12.8 1.0 CB A:CYS439 3.3 10.6 1.0 HE1 A:HIS436 3.3 11.5 1.0 CB A:CYS416 3.3 11.2 1.0 HB2 A:CYS413 3.4 9.6 1.0 CB A:HIS436 3.4 9.8 1.0 HB3 A:CYS439 3.5 12.8 1.0 H A:HIS436 3.7 9.8 1.0 N A:CYS416 3.8 9.6 1.0 HB A:VAL415 3.9 11.2 1.0 HB3 A:HIS436 4.0 11.9 1.0 HB2 A:CYS416 4.1 13.5 1.0 CA A:CYS416 4.1 10.1 1.0 NE2 A:HIS436 4.2 10.1 1.0 CD2 A:HIS436 4.2 10.7 1.0 N A:HIS436 4.4 8.1 1.0 CA A:CYS413 4.5 9.3 1.0 H A:CYS439 4.5 16.0 1.0 CA A:HIS436 4.5 9.9 1.0 HB2 A:CYS418 4.5 10.9 1.0 O A:CYS413 4.6 9.3 1.0 H A:CYS418 4.6 12.0 1.0 CA A:CYS439 4.7 12.5 1.0 H A:VAL415 4.7 11.4 1.0 C A:CYS413 4.7 9.2 1.0 HG12 A:VAL415 4.8 14.9 1.0 CB A:VAL415 4.8 9.2 1.0 C A:VAL415 4.8 10.2 1.0 HA A:CYS416 4.9 12.2 1.0 O A:HOH686 4.9 32.7 1.0 HA A:CYS413 4.9 11.3 1.0 C A:CYS416 4.9 8.5 1.0 H A:MET417 4.9 11.8 1.0 HE2 A:HIS436 5.0 12.2 1.0 N A:CYS439 5.0 13.2 1.0

Zinc binding site 2 out of 2 in the High-Resolution Structure of RNF38 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Structure of RNF38 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:9.7 occ:1.00 ND1 A:HIS433 2.1 9.9 1.0 SG A:CYS453 2.3 10.8 1.0 SG A:CYS431 2.3 9.8 1.0 SG A:CYS450 2.3 8.6 1.0 HB2 A:HIS433 2.9 10.7 1.0 CE1 A:HIS433 3.0 10.1 1.0 H A:CYS453 3.1 13.0 1.0 HB2 A:CYS431 3.1 13.4 1.0 HB2 A:CYS450 3.1 9.9 1.0 CB A:CYS450 3.1 8.2 1.0 HB3 A:CYS450 3.1 9.9 1.0 CG A:HIS433 3.1 9.0 1.0 HE1 A:HIS433 3.2 12.2 1.0 CB A:CYS431 3.3 11.1 1.0 HB3 A:CYS453 3.3 12.6 1.0 CB A:CYS453 3.4 10.4 1.0 CB A:HIS433 3.5 8.8 1.0 HB3 A:CYS431 3.7 13.4 1.0 HB A:ILE452 3.7 11.3 1.0 N A:CYS453 3.8 10.8 1.0 H A:HIS433 3.8 11.1 1.0 HB3 A:HIS433 4.0 10.7 1.0 HB3 A:ALA455 4.1 13.4 1.0 CA A:CYS453 4.1 11.0 1.0 NE2 A:HIS433 4.2 12.2 1.0 HB2 A:CYS453 4.2 12.6 1.0 CD2 A:HIS433 4.2 11.3 1.0 H A:ALA455 4.2 11.3 1.0 H A:ILE452 4.3 10.9 1.0 N A:HIS433 4.5 9.1 1.0 O A:HOH690 4.5 25.5 1.0 HG22 A:ILE452 4.5 14.2 1.0 H A:ARG454 4.6 12.2 1.0 CA A:CYS450 4.6 8.2 1.0 CA A:CYS431 4.6 10.3 1.0 HD22 A:LEU429 4.6 13.3 1.0 CA A:HIS433 4.6 8.8 1.0 CB A:ILE452 4.6 9.3 1.0 O A:CYS431 4.7 14.1 1.0 C A:CYS431 4.7 11.4 1.0 HZ A:PHE435 4.7 10.9 1.0 HB2 A:LEU429 4.7 11.5 1.0 O A:HOH655 4.8 11.0 1.0 C A:CYS453 4.8 11.6 1.0 H A:CYS431 4.8 12.6 1.0 C A:ILE452 4.8 11.3 1.0 HB2 A:ALA455 4.8 13.4 1.0 CB A:ALA455 4.9 11.1 1.0 N A:ARG454 4.9 10.1 1.0 HA A:CYS450 4.9 10.0 1.0 HE2 A:HIS433 4.9 14.7 1.0 HA A:CYS453 5.0 13.3 1.0 N A:ILE452 5.0 9.0 1.0

M.A.Nakasone, L.Buetow, M.Gabrielsen, S.F.Ahmed, K.Majorek, G.J.Sibbet, B.O.Smith, D.T.Huang. Tuning Ubiquitin Transfer By Ring E3 Ubiquitin Ligases Through the Linchpin Residue To Be Published.