Zinc in PDB 9q8y: Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub

All present enzymatic activity of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub, PDB code: 9q8y 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)	43.92 / 2.63
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	116.079, 116.079, 90.315, 90, 90, 120
R / Rfree (%)	23.2 / 27.5

The binding sites of Zinc atom in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub (pdb code 9q8y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub, PDB code: 9q8y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:103.6 occ:1.00 HB2 C:CYS416 1.9 113.5 1.0 ND1 C:HIS436 2.1 100.4 1.0 SG C:CYS439 2.2 94.1 1.0 SG C:CYS416 2.3 134.6 1.0 SG C:CYS413 2.4 130.3 1.0 CB C:CYS416 2.5 94.5 1.0 HB2 C:HIS436 2.5 119.0 1.0 HB3 C:CYS413 2.7 118.4 1.0 H C:CYS416 2.8 110.7 1.0 CG C:HIS436 3.0 96.0 1.0 CB C:CYS413 3.0 98.6 1.0 CB C:HIS436 3.2 99.1 1.0 CE1 C:HIS436 3.2 96.6 1.0 HB3 C:CYS416 3.2 113.5 1.0 HB2 C:CYS413 3.4 118.4 1.0 CB C:CYS439 3.4 102.7 1.0 N C:CYS416 3.4 92.2 1.0 HB2 C:CYS439 3.4 123.3 1.0 HE1 C:HIS436 3.4 116.0 1.0 CA C:CYS416 3.5 100.2 1.0 HB3 C:CYS439 3.5 123.3 1.0 HB3 C:HIS436 3.6 119.0 1.0 H C:HIS436 3.9 118.2 1.0 HB2 C:CYS418 4.0 120.6 1.0 HA C:CYS416 4.1 120.4 1.0 CD2 C:HIS436 4.2 108.3 1.0 NE2 C:HIS436 4.2 101.5 1.0 HB C:VAL415 4.3 112.4 1.0 O C:CYS413 4.4 95.3 1.0 H C:CYS418 4.4 113.5 1.0 CA C:CYS413 4.4 105.6 1.0 CA C:HIS436 4.4 102.8 1.0 C C:CYS416 4.5 97.0 1.0 N C:HIS436 4.5 98.5 1.0 C C:VAL415 4.6 87.8 1.0 H C:MET417 4.6 114.8 1.0 C C:CYS413 4.6 94.1 1.0 H C:VAL415 4.7 112.7 1.0 N C:MET417 4.8 95.6 1.0 CA C:CYS439 4.8 105.7 1.0 H C:CYS413 4.9 125.8 1.0 HA C:CYS413 5.0 126.8 1.0 HG12 C:VAL415 5.0 106.8 1.0 HA C:CYS439 5.0 127.0 1.0 HD2 C:HIS436 5.0 130.0 1.0 CB C:CYS418 5.0 100.4 1.0

Zinc binding site 2 out of 4 in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:78.2 occ:1.00 ND1 C:HIS433 2.1 82.7 1.0 SG C:CYS450 2.2 79.3 1.0 SG C:CYS431 2.3 96.2 1.0 SG C:CYS453 2.4 92.4 1.0 HB2 C:HIS433 2.6 103.2 1.0 HB2 C:CYS431 2.7 107.8 1.0 HB2 C:CYS450 2.9 104.7 1.0 CB C:CYS450 2.9 87.1 1.0 HB3 C:CYS450 3.0 104.7 1.0 CG C:HIS433 3.0 91.7 1.0 CB C:CYS431 3.1 89.7 1.0 CE1 C:HIS433 3.1 88.5 1.0 CB C:HIS433 3.2 85.9 1.0 HE1 C:HIS433 3.3 106.3 1.0 H C:CYS453 3.3 107.3 1.0 HB3 C:CYS453 3.4 111.0 1.0 HB3 C:CYS431 3.5 107.8 1.0 CB C:CYS453 3.5 92.4 1.0 HB3 C:HIS433 3.7 103.2 1.0 HB3 C:ALA455 3.8 126.0 1.0 HB C:ILE452 3.9 109.5 1.0 N C:CYS453 4.0 89.3 1.0 CD2 C:HIS433 4.1 86.5 1.0 NE2 C:HIS433 4.2 96.3 1.0 H C:HIS433 4.2 104.3 1.0 HB2 C:CYS453 4.3 111.0 1.0 CA C:CYS453 4.3 93.1 1.0 O C:CYS431 4.3 79.5 1.0 CA C:CYS431 4.4 79.2 1.0 CA C:CYS450 4.4 90.6 1.0 H C:ALA455 4.4 126.1 1.0 H C:ILE452 4.5 104.5 1.0 CA C:HIS433 4.5 87.5 1.0 C C:CYS431 4.5 80.7 1.0 N C:HIS433 4.5 86.8 1.0 H C:CYS431 4.6 95.9 1.0 HD22 C:LEU429 4.7 112.9 1.0 HA C:CYS450 4.7 108.8 1.0 CB C:ALA455 4.7 104.9 1.0 HB2 C:ALA455 4.7 126.0 1.0 HB2 C:LEU429 4.7 104.3 1.0 CB C:ILE452 4.9 91.2 1.0 C C:CYS453 4.9 99.6 1.0 HD23 C:LEU429 4.9 112.9 1.0 H C:TYR454 4.9 120.3 1.0 HE2 C:HIS433 4.9 115.6 1.0 HD2 C:HIS433 5.0 103.9 1.0

Zinc binding site 3 out of 4 in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:127.5 occ:1.00 ND1 D:HIS436 2.0 143.5 1.0 SG D:CYS416 2.2 157.1 1.0 SG D:CYS439 2.3 116.2 1.0 SG D:CYS413 2.3 145.8 1.0 HB2 D:CYS416 2.7 178.1 1.0 HB3 D:CYS413 2.7 182.8 1.0 CE1 D:HIS436 2.8 145.0 1.0 H D:CYS416 2.8 159.0 1.0 HE1 D:HIS436 2.9 174.1 1.0 CB D:CYS416 3.0 148.3 1.0 CB D:CYS413 3.0 152.2 1.0 HB2 D:HIS436 3.1 186.5 1.0 CG D:HIS436 3.2 137.5 1.0 HB2 D:CYS413 3.3 182.8 1.0 N D:CYS416 3.5 132.4 1.0 CB D:HIS436 3.7 155.3 1.0 HB3 D:CYS416 3.7 178.1 1.0 CA D:CYS416 3.8 133.6 1.0 HB D:VAL415 3.8 142.1 1.0 CB D:CYS439 3.8 133.0 1.0 H D:HIS436 3.9 223.5 1.0 NE2 D:HIS436 3.9 145.8 1.0 HB2 D:CYS439 4.0 159.7 1.0 HB3 D:CYS439 4.0 159.7 1.0 CD2 D:HIS436 4.1 152.5 1.0 HB3 D:HIS436 4.3 186.5 1.0 HB2 D:CYS418 4.3 174.5 1.0 CA D:CYS413 4.3 158.4 1.0 O D:CYS413 4.3 147.1 1.0 HA D:CYS416 4.4 160.4 1.0 H D:VAL415 4.5 160.4 1.0 C D:CYS413 4.5 148.6 1.0 C D:VAL415 4.5 132.8 1.0 H D:CYS418 4.6 180.6 1.0 N D:HIS436 4.6 186.1 1.0 HE2 D:HIS436 4.7 175.1 1.0 CB D:VAL415 4.7 118.3 1.0 H D:MET417 4.7 174.1 1.0 C D:CYS416 4.8 143.0 1.0 CA D:HIS436 4.8 179.3 1.0 HA D:CYS413 4.8 190.2 1.0 N D:VAL415 4.9 133.6 1.0 CA D:VAL415 5.0 130.1 1.0 N D:MET417 5.0 145.0 1.0

Zinc binding site 4 out of 4 in the Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of RNF38 Ring with Linchpin Mutant R454Y in Complex with UBCH5B-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:130.8 occ:1.00 ND1 D:HIS433 1.9 146.1 1.0 SG D:CYS431 2.3 151.4 1.0 SG D:CYS453 2.3 157.7 1.0 SG D:CYS450 2.3 144.3 1.0 HE1 D:HIS433 2.4 179.5 1.0 CE1 D:HIS433 2.4 149.5 1.0 H D:CYS453 3.0 179.7 1.0 CG D:HIS433 3.1 154.2 1.0 CB D:CYS450 3.3 128.7 1.0 HB2 D:CYS431 3.3 191.3 1.0 HB2 D:CYS450 3.3 154.5 1.0 HB3 D:CYS450 3.4 154.5 1.0 HB2 D:HIS433 3.4 193.6 1.0 HB3 D:CYS453 3.5 195.2 1.0 CB D:CYS431 3.5 159.3 1.0 CB D:CYS453 3.5 162.6 1.0 NE2 D:HIS433 3.6 145.6 1.0 H D:ALA455 3.7 189.5 1.0 N D:CYS453 3.8 149.6 1.0 CB D:HIS433 3.8 161.3 1.0 HB3 D:ALA455 3.8 193.1 1.0 HB D:ILE452 3.9 174.4 1.0 HB3 D:CYS431 3.9 191.3 1.0 CD2 D:HIS433 3.9 153.7 1.0 CA D:CYS453 4.1 154.8 1.0 HB3 D:HIS433 4.2 193.6 1.0 HE2 D:HIS433 4.2 174.8 1.0 HB2 D:CYS453 4.3 195.2 1.0 O D:ALA455 4.3 153.6 1.0 H D:ILE452 4.3 164.8 1.0 O D:CYS431 4.5 167.3 1.0 N D:ALA455 4.5 157.9 1.0 CB D:ALA455 4.7 160.9 1.0 C D:CYS453 4.7 149.9 1.0 CA D:CYS431 4.7 168.0 1.0 CB D:ILE452 4.7 145.2 1.0 H D:CYS431 4.8 196.3 1.0 CA D:CYS450 4.8 127.3 1.0 HD2 D:HIS433 4.8 184.6 1.0 HG22 D:ILE452 4.8 174.0 1.0 C D:ILE452 4.8 144.7 1.0 H D:TYR454 4.8 180.7 1.0 C D:CYS431 4.9 171.6 1.0 HB2 D:ALA455 4.9 193.1 1.0 N D:TYR454 4.9 150.5 1.0 H D:HIS433 4.9 217.3 1.0 CA D:ALA455 5.0 168.2 1.0

M.A.Nakasone, L.Buetow, M.Gabrielsen, S.F.Ahmed, K.A.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.