Zinc in PDB 6ze9: Non-Native Fold of the Putative VPS39 Zinc Finger Domain

The structure of Non-Native Fold of the Putative VPS39 Zinc Finger Domain, PDB code: 6ze9 was solved by B.G.Butt, S.C.Graham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 2.90
Space group	P 42 2 2
Cell size a, b, c (Å), α, β, γ (°)	104.178, 104.178, 39.423, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 26.9

The binding sites of Zinc atom in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain (pdb code 6ze9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain, PDB code: 6ze9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.2 occ:1.00 NE2 A:HIS-3 2.0 0.0 1.0 O B:THR875 2.1 0.3 1.0 NE2 A:HIS-1 2.1 0.2 1.0 SG C:CYS844 2.3 0.2 1.0 CE1 A:HIS-3 2.9 0.6 1.0 C B:THR875 2.9 0.9 1.0 CD2 A:HIS-1 3.0 0.9 1.0 CD2 A:HIS-3 3.1 0.1 1.0 OXT B:THR875 3.1 0.1 1.0 CE1 A:HIS-1 3.2 0.3 1.0 CB C:CYS844 3.5 0.2 1.0 ND1 A:HIS-3 4.1 0.4 1.0 CG A:HIS-1 4.1 0.7 1.0 CG A:HIS-3 4.2 0.5 1.0 NZ C:LYS846 4.2 0.4 1.0 ND1 A:HIS-1 4.2 0.8 1.0 CA B:THR875 4.2 0.7 1.0 CA C:CYS844 4.3 0.9 1.0 N B:THR875 4.5 0.6 1.0 CG A:PRO872 4.7 0.3 1.0 OG1 B:THR875 4.7 0.7 1.0 O A:HIS-2 4.8 0.4 1.0 CE C:LYS846 4.8 0.7 1.0 O B:PRO872 4.8 0.2 1.0 C C:CYS844 4.9 0.0 1.0

Zinc binding site 2 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:0.3 occ:1.00 O A:THR875 1.9 1.0 1.0 NE2 B:HIS-1 2.0 1.0 1.0 NE2 B:HIS-3 2.1 0.4 1.0 C A:THR875 2.8 0.8 1.0 CE1 B:HIS-1 2.8 0.3 1.0 CE1 B:HIS-3 3.0 0.9 1.0 CD2 B:HIS-1 3.1 0.0 1.0 OXT A:THR875 3.1 0.7 1.0 CD2 B:HIS-3 3.1 0.9 1.0 ND1 B:HIS-1 4.0 0.0 1.0 CG B:HIS-1 4.1 0.2 1.0 CA A:THR875 4.2 0.5 1.0 ND1 B:HIS-3 4.2 0.4 1.0 CG B:HIS-3 4.2 0.8 1.0 N A:THR875 4.5 0.9 1.0 CG B:PRO872 4.5 0.2 1.0 OG1 A:THR875 4.6 0.2 1.0 O A:PRO872 4.8 0.3 1.0 O B:HIS-2 4.8 0.9 1.0 CB A:THR875 5.0 0.2 1.0

Zinc binding site 3 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:0.2 occ:1.00 NE2 C:HIS-1 2.0 0.1 1.0 NE2 C:HIS-3 2.1 0.3 1.0 SG A:CYS844 2.3 0.0 1.0 O C:HOH1101 2.3 0.0 1.0 CE1 C:HIS-3 2.7 0.3 1.0 CD2 C:HIS-1 2.9 0.1 1.0 CE1 C:HIS-1 3.1 0.2 1.0 CD2 C:HIS-3 3.3 0.1 1.0 CB A:CYS844 3.6 0.1 1.0 ND1 C:HIS-3 4.0 0.6 1.0 CG C:HIS-1 4.0 0.1 1.0 ND1 C:HIS-1 4.2 0.8 1.0 CG C:HIS-3 4.2 0.5 1.0 CA A:CYS844 4.5 0.9 1.0 O C:HIS-2 4.8 0.7 1.0 CD A:LYS846 5.0 0.6 1.0

B.G.Butt, E.J.Scourfield, S.C.Graham. Non-Native Fold of the Putative VPS39 Zinc Finger Domain To Be Published.