Zinc in PDB 7spy: GET3 Bound to Atp From G. Intestinalis in the Closed Form

The structure of GET3 Bound to Atp From G. Intestinalis in the Closed Form, PDB code: 7spy was solved by M.Y.Fry, A.O.Maggiolo, W.M.Clemons Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.39 / 2.23
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.646, 79.646, 130.07, 90, 90, 120
R / Rfree (%)	17.8 / 20.9

The structure of GET3 Bound to Atp From G. Intestinalis in the Closed Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the GET3 Bound to Atp From G. Intestinalis in the Closed Form (pdb code 7spy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the GET3 Bound to Atp From G. Intestinalis in the Closed Form, PDB code: 7spy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the GET3 Bound to Atp From G. Intestinalis in the Closed Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of GET3 Bound to Atp From G. Intestinalis in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:23.7 occ:0.45 SG A:CYS290 2.2 26.2 1.0 SG A:CYS287 2.3 29.9 1.0 CB A:CYS287 3.2 30.8 1.0 CB A:CYS290 3.4 24.8 1.0 N A:CYS290 4.0 26.4 1.0 CA A:CYS290 4.3 25.9 1.0 CA A:CYS287 4.6 32.1 1.0 O A:HOH673 4.8 31.2 1.0 CB A:MET289 4.8 27.7 1.0

Zinc binding site 2 out of 2 in the GET3 Bound to Atp From G. Intestinalis in the Closed Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of GET3 Bound to Atp From G. Intestinalis in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:24.8 occ:0.50 NE2 A:HIS6 2.0 25.8 1.0 OD2 A:ASP10 2.1 33.7 1.0 OD1 A:ASP10 2.6 32.8 1.0 CG A:ASP10 2.6 30.7 1.0 CD2 A:HIS6 2.9 25.9 1.0 CE1 A:HIS6 3.0 26.6 1.0 CG A:HIS6 4.0 26.6 1.0 ND1 A:HIS6 4.1 26.2 1.0 CB A:ASP10 4.1 31.1 1.0 O A:HOH541 4.3 44.6 1.0 O A:HIS6 4.9 25.0 1.0

M.Y.Fry, V.Najdrova, A.O.Maggiolo, S.M.Saladi, P.Dolezal, W.M.Clemons Jr.. Structurally Derived Universal Mechanism For the Catalytic Cycle of the Tail-Anchored Targeting Factor GET3. Nat.Struct.Mol.Biol. V. 29 820 2022.
ISSN: ESSN 1545-9985
PubMed: 35851188
DOI: 10.1038/S41594-022-00798-4