Zinc in PDB 7jtz: Yeast GLO3 Gap Domain

The structure of Yeast GLO3 Gap Domain, PDB code: 7jtz was solved by B.Xie, L.P.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.369, 74.031, 77.902, 90, 105.34, 90
R / Rfree (%)	18.1 / 23.8

The binding sites of Zinc atom in the Yeast GLO3 Gap Domain (pdb code 7jtz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast GLO3 Gap Domain, PDB code: 7jtz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast GLO3 Gap Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast GLO3 Gap Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:40.5 occ:1.00 SG B:CYS54 2.3 45.0 1.0 SG B:CYS51 2.3 38.7 1.0 SG B:CYS34 2.4 38.3 1.0 SG B:CYS31 2.5 34.2 1.0 CB B:CYS31 3.2 33.6 1.0 CB B:CYS54 3.3 36.9 1.0 CB B:CYS34 3.3 41.4 1.0 CB B:CYS51 3.6 35.3 1.0 N B:CYS34 3.7 43.3 1.0 CA B:CYS34 4.0 48.1 1.0 N B:CYS51 4.0 34.2 1.0 OE1 B:GLN53 4.1 60.1 1.0 N B:CYS54 4.1 38.9 1.0 CA B:CYS54 4.3 42.0 1.0 CA B:CYS51 4.4 32.8 1.0 CB B:ASP33 4.5 33.1 1.0 C B:ASP33 4.6 44.8 1.0 C B:CYS34 4.6 44.6 1.0 CB B:ASN36 4.7 59.1 1.0 CA B:CYS31 4.7 33.1 1.0 N B:GLY35 4.8 44.6 1.0 N B:ASP33 4.9 39.6 1.0 CA B:ASP33 4.9 39.0 1.0 C B:CYS51 5.0 44.9 1.0 O B:CYS51 5.0 34.9 1.0

Zinc binding site 2 out of 4 in the Yeast GLO3 Gap Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast GLO3 Gap Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:44.8 occ:1.00 SG A:CYS51 2.2 40.2 1.0 SG A:CYS34 2.4 41.6 1.0 SG A:CYS31 2.4 34.9 1.0 SG A:CYS54 2.5 48.7 1.0 CB A:CYS34 3.2 45.3 1.0 CB A:CYS31 3.2 30.1 1.0 CB A:CYS54 3.2 38.0 1.0 CB A:CYS51 3.5 35.5 1.0 N A:CYS34 3.7 33.7 1.0 O A:HOH339 3.8 57.5 1.0 N A:CYS51 3.9 30.5 1.0 CA A:CYS34 4.0 43.0 1.0 N A:CYS54 4.1 35.4 1.0 CA A:CYS51 4.2 27.1 1.0 CA A:CYS54 4.3 41.2 1.0 C A:CYS34 4.5 39.3 1.0 ND2 A:ASN36 4.5 59.7 1.0 CB A:ASN36 4.6 55.6 1.0 CA A:CYS31 4.6 24.7 1.0 N A:GLY35 4.7 37.2 1.0 CB A:ASP33 4.7 41.6 1.0 C A:ASP33 4.8 45.9 1.0 N A:ASN36 4.8 42.4 1.0 C A:CYS51 4.8 39.9 1.0 CG A:ASN36 4.9 65.4 1.0 O A:CYS51 5.0 32.1 1.0

Zinc binding site 3 out of 4 in the Yeast GLO3 Gap Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast GLO3 Gap Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:42.0 occ:1.00 SG C:CYS54 2.2 43.3 1.0 SG C:CYS34 2.3 43.4 1.0 SG C:CYS31 2.4 32.5 1.0 SG C:CYS51 2.5 46.3 1.0 CB C:CYS54 3.1 43.2 1.0 CB C:CYS31 3.2 35.3 1.0 CB C:CYS34 3.5 39.1 1.0 CB C:CYS51 3.6 42.7 1.0 N C:CYS34 3.8 44.4 1.0 N C:CYS54 4.0 42.7 1.0 N C:CYS51 4.0 32.8 1.0 CA C:CYS34 4.2 44.1 1.0 CA C:CYS54 4.2 46.5 1.0 ND2 C:ASN36 4.3 44.2 1.0 CA C:CYS51 4.3 34.9 1.0 CB C:ASN36 4.4 47.8 1.0 C C:ASP33 4.5 46.3 1.0 CB C:ASP33 4.6 39.1 1.0 N C:ASN36 4.7 58.4 1.0 CA C:CYS31 4.7 39.3 1.0 C C:CYS34 4.7 50.6 1.0 CG C:ASN36 4.8 50.6 1.0 N C:ASP33 4.8 34.4 1.0 C C:CYS51 4.9 37.2 1.0 CA C:ASP33 4.9 35.7 1.0 O C:CYS51 4.9 35.9 1.0 N C:GLY35 5.0 35.7 1.0

Zinc binding site 4 out of 4 in the Yeast GLO3 Gap Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast GLO3 Gap Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:58.6 occ:1.00 SG D:CYS54 2.1 59.2 1.0 SG D:CYS31 2.4 45.5 1.0 SG D:CYS34 2.5 65.7 1.0 SG D:CYS51 2.5 58.4 1.0 CB D:CYS54 3.2 47.1 1.0 CB D:CYS31 3.3 48.0 1.0 CB D:CYS34 3.4 67.5 1.0 CB D:CYS51 3.6 50.4 1.0 N D:CYS34 3.7 55.3 1.0 N D:CYS51 4.0 44.8 1.0 CA D:CYS34 4.1 64.2 1.0 N D:CYS54 4.1 48.2 1.0 CA D:CYS54 4.3 47.9 1.0 CA D:CYS51 4.4 44.7 1.0 ND2 D:ASN36 4.4 71.0 1.0 CB D:ASP33 4.4 47.2 1.0 C D:ASP33 4.6 46.0 1.0 C D:CYS34 4.7 61.4 1.0 CA D:CYS31 4.7 40.9 1.0 N D:GLY35 4.8 59.7 1.0 CB D:ASN36 4.8 66.4 1.0 C D:CYS51 4.8 48.5 1.0 CA D:ASP33 4.9 42.0 1.0 N D:ASP33 4.9 44.5 1.0 CG D:ASN36 4.9 71.2 1.0 N D:ASN36 4.9 58.4 1.0 O D:CYS51 5.0 49.2 1.0

B.Xie, C.Jung, M.Chandra, A.Engel, A.K.Kendall, L.P.Jackson. The GLO3 Gap Crystal Structure Supports the Molecular Niche Model For Arfgaps in Copi Coats Advances in Biological V. 79 2021REGULATION.
DOI: HTTPS://DOI.ORG/10.1016/J.JBIOR.2020.100781