Zinc in PDB 2j9u: 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II

The structure of 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II, PDB code: 2j9u was solved by D.J.Gill, H.L.Teo, J.Sun, O.Perisic, D.B.Veprintsev, S.D.Emr, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.03 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.645, 99.961, 115.619, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26

The binding sites of Zinc atom in the 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II (pdb code 2j9u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II, PDB code: 2j9u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1162 b:19.1 occ:1.00 SG B:CYS123 2.3 17.0 1.0 SG B:CYS146 2.3 23.9 1.0 SG B:CYS143 2.4 22.7 1.0 SG B:CYS120 2.4 23.9 1.0 CB B:CYS120 3.1 24.6 1.0 CB B:CYS143 3.2 25.9 1.0 CB B:CYS146 3.4 24.0 1.0 CB B:CYS123 3.4 21.7 1.0 N B:CYS146 3.8 24.1 1.0 N B:CYS123 3.9 21.7 1.0 CA B:CYS146 4.1 23.9 1.0 CA B:CYS123 4.2 21.9 1.0 CB B:ILE122 4.5 21.2 1.0 CA B:CYS120 4.6 25.0 1.0 CA B:CYS143 4.7 26.2 1.0 CB B:ASN145 4.7 25.2 1.0 C B:ASN145 4.8 24.9 1.0 ND2 B:ASN145 4.8 23.2 1.0 O B:HOH2004 4.8 17.2 1.0 C B:CYS146 4.9 23.7 1.0 C B:CYS123 4.9 23.6 1.0 C B:ILE122 4.9 21.4 1.0 N B:GLY147 4.9 24.0 1.0 N B:MET124 4.9 25.0 1.0

Zinc binding site 2 out of 2 in the 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2 Angstrom X-Ray Structure of the Yeast Escrt-I VPS28 C-Terminus in Complex with the Nzf-N Domain From Escrt-II within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1162 b:19.5 occ:1.00 SG D:CYS123 2.3 21.6 1.0 SG D:CYS120 2.3 23.1 1.0 SG D:CYS146 2.4 21.6 1.0 SG D:CYS143 2.4 24.4 1.0 CB D:CYS120 3.2 24.7 1.0 CB D:CYS143 3.2 26.1 1.0 CB D:CYS146 3.5 22.9 1.0 CB D:CYS123 3.5 22.8 1.0 N D:CYS146 3.8 23.9 1.0 N D:CYS123 3.8 22.1 1.0 CA D:CYS146 4.2 23.2 1.0 CA D:CYS123 4.2 22.5 1.0 CB D:ILE122 4.5 21.8 1.0 CA D:CYS120 4.6 25.1 1.0 CB D:ASN145 4.7 24.8 1.0 CA D:CYS143 4.7 26.9 1.0 C D:ILE122 4.8 22.3 1.0 O D:HOH2003 4.9 15.6 1.0 C D:ASN145 4.9 24.8 1.0 C D:CYS123 4.9 23.8 1.0 ND2 D:ASN145 4.9 23.1 1.0 N D:MET124 5.0 24.8 1.0 CB D:VAL125 5.0 29.2 1.0 C D:CYS146 5.0 23.3 1.0 N D:GLY147 5.0 22.9 1.0

D.J.Gill, H.L.Teo, J.Sun, O.Perisic, D.B.Veprintsev, S.D.Emr, R.L.Williams. Structural Insight Into the Escrt-I/-II Link and Its Role in Mvb Trafficking. Embo J. V. 26 600 2007.
ISSN: ISSN 0261-4189
PubMed: 17215868
DOI: 10.1038/SJ.EMBOJ.7601501