Zinc in PDB 3r3q: Crystal Structure of the Yeast VPS23 Uev Domain

The structure of Crystal Structure of the Yeast VPS23 Uev Domain, PDB code: 3r3q was solved by X.Ren, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.62 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.059, 47.139, 92.946, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.4

The structure of Crystal Structure of the Yeast VPS23 Uev Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Yeast VPS23 Uev Domain (pdb code 3r3q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the Yeast VPS23 Uev Domain, PDB code: 3r3q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn161 b:15.6 occ:0.92 OD2 A:ASP158 1.9 15.3 1.0 O A:HOH275 2.2 25.5 1.0 N1 A:IMD179 2.3 20.1 1.0 CG A:ASP158 2.8 17.9 1.0 C2 A:IMD179 2.9 18.5 0.6 OD1 A:ASP158 3.0 17.3 1.0 C5 A:IMD179 3.5 20.4 0.4 N3 A:IMD179 4.2 17.5 0.5 CB A:ASP158 4.2 16.3 1.0 CB A:ALA160 4.2 18.0 0.4 C4 A:IMD179 4.5 18.9 0.7 CB A:ALA160 4.5 18.4 0.6

Zinc binding site 2 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn162 b:8.1 occ:1.00 OE2 A:GLU11 2.0 7.4 1.0 N1 A:IMD174 2.0 8.1 1.0 O A:HOH243 2.1 11.2 1.0 CD A:GLU11 2.7 6.9 1.0 OE1 A:GLU11 2.9 11.6 1.0 C2 A:IMD174 3.0 8.9 1.0 C5 A:IMD174 3.0 8.8 1.0 OD1 A:ASN15 4.0 8.5 1.0 N3 A:IMD174 4.2 11.5 0.9 C4 A:IMD174 4.2 7.6 1.0 CG A:GLU11 4.2 7.1 1.0 ND2 A:ASN15 4.4 7.9 1.0 CG A:ASN15 4.6 9.3 1.0 CG1 A:VAL14 5.0 10.8 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn163 b:8.4 occ:1.00 OXT A:ACT178 2.0 12.6 1.0 N1 A:IMD171 2.0 10.2 1.0 NE2 A:HIS33 2.0 8.4 1.0 O A:ACT178 2.7 13.7 0.9 C A:ACT178 2.7 11.2 0.8 CD2 A:HIS33 3.0 7.6 1.0 C5 A:IMD171 3.0 10.4 1.0 CE1 A:HIS33 3.0 7.0 1.0 C2 A:IMD171 3.0 14.9 1.0 ND1 A:HIS33 4.1 6.4 1.0 CG A:HIS33 4.1 8.2 1.0 N3 A:IMD171 4.2 12.5 1.0 C4 A:IMD171 4.2 11.9 0.9 CH3 A:ACT178 4.2 16.4 1.0 CB A:ALA37 4.8 8.4 1.0 O A:HOH281 4.8 31.1 0.9

Zinc binding site 4 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn164 b:13.3 occ:0.99 OD1 A:ASP74 2.0 9.9 1.0 N1 A:IMD172 2.0 11.5 1.0 O A:HOH237 2.0 15.0 1.0 CG A:ASP74 2.8 14.0 1.0 C2 A:IMD172 2.9 15.5 0.9 C5 A:IMD172 3.0 13.7 1.0 OD2 A:ASP74 3.1 16.8 1.0 O A:HOH292 3.7 15.8 1.0 O A:HOH299 4.0 40.4 1.0 N3 A:IMD172 4.1 13.9 0.7 C4 A:IMD172 4.1 13.1 0.9 CB A:ASP74 4.2 11.0 1.0 C A:ASP74 4.4 8.8 1.0 N A:ASP74 4.5 9.3 1.0 CA A:ASP74 4.6 8.8 1.0 O A:ASP74 4.6 10.2 1.0 N A:GLY75 4.7 9.8 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn165 b:11.5 occ:1.00 OE2 A:GLU118 2.0 13.9 1.0 OE2 A:GLU154 2.0 10.5 1.0 O A:HOH276 2.3 15.3 1.0 CD A:GLU154 2.8 10.3 1.0 OE1 A:GLU154 3.0 10.7 1.0 CD A:GLU118 3.0 12.8 1.0 CG A:GLU118 3.5 17.2 1.0 O A:HOH264 3.7 17.9 0.7 OE1 A:GLU118 4.0 15.0 1.0 CB A:PRO115 4.1 20.2 1.0 CG A:GLU154 4.3 10.8 1.0 O A:HOH302 4.6 39.8 1.0 CA A:PRO115 4.6 18.7 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn166 b:10.9 occ:1.00 OE1 A:GLU73 2.0 14.5 1.0 N3 A:IMD173 2.0 11.8 1.0 CL A:CL170 2.2 14.6 0.9 CD A:GLU73 2.7 11.7 1.0 OE2 A:GLU73 2.8 15.9 1.0 C4 A:IMD173 3.0 12.3 1.0 C2 A:IMD173 3.1 13.8 1.0 O A:HOH218 4.1 15.7 0.8 C5 A:IMD173 4.1 11.0 1.0 N1 A:IMD173 4.2 14.7 0.8 CG A:GLU73 4.2 12.0 1.0 CD1 A:LEU114 4.2 25.9 1.0 CD A:PRO78 4.3 13.3 1.0 CB A:SER111 4.5 18.7 1.0 CG A:PRO78 4.7 14.7 1.0 N A:SER111 4.8 14.7 1.0 CB A:GLU73 5.0 10.6 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn167 b:11.6 occ:1.00 N1 A:IMD175 2.0 10.7 1.0 ND1 A:HIS153 2.1 12.1 1.0 OXT A:ACT176 2.2 12.2 0.9 O A:ACT176 2.4 12.9 0.9 C A:ACT176 2.7 13.5 0.9 C2 A:IMD175 2.8 11.9 0.6 CE1 A:HIS153 3.0 15.0 1.0 CG A:HIS153 3.1 12.6 1.0 C5 A:IMD175 3.2 14.2 0.8 CB A:HIS153 3.5 10.7 1.0 N3 A:IMD175 4.0 12.8 1.0 CA A:HIS153 4.0 11.0 1.0 NE2 A:HIS153 4.1 17.2 1.0 C4 A:IMD175 4.2 13.6 0.7 O A:HOH218 4.2 15.7 0.8 C5 A:IMD173 4.2 11.0 1.0 CD2 A:HIS153 4.2 17.1 1.0 CH3 A:ACT176 4.2 15.2 1.0 O A:LEU152 4.2 16.5 1.0 C4 A:IMD173 4.3 12.3 1.0 N A:HIS153 4.9 13.8 1.0 C A:LEU152 4.9 18.0 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn168 b:14.5 occ:0.88 O A:ACT177 1.9 16.0 0.9 OD2 A:ASP27 2.0 13.4 1.0 OG1 A:THR30 2.1 9.6 1.0 N1 A:IMD180 2.2 17.1 1.0 C5 A:IMD180 2.7 18.4 0.5 CG A:ASP27 2.7 11.8 1.0 OD1 A:ASP27 2.9 13.1 1.0 C A:ACT177 2.9 17.4 0.8 OXT A:ACT177 3.0 19.8 0.5 CB A:THR30 3.2 8.5 1.0 C2 A:IMD180 3.4 20.9 0.5 C4 A:IMD180 4.0 19.5 0.8 CG2 A:THR30 4.1 9.5 1.0 CB A:ASP27 4.2 12.6 1.0 CH3 A:ACT177 4.2 12.0 1.0 O A:HOH240 4.3 18.3 0.8 N3 A:IMD180 4.3 20.5 0.2 N A:THR30 4.3 10.0 1.0 CA A:THR30 4.3 7.8 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of the Yeast VPS23 Uev Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Yeast VPS23 Uev Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn169 b:16.8 occ:0.39 OD2 A:ASP40 2.1 29.4 1.0 N3 A:IMD171 2.1 12.5 1.0 O A:HOH250 2.3 21.3 0.5 O A:HOH274 2.4 35.8 1.0 C2 A:IMD171 2.9 14.9 1.0 CG A:ASP40 3.0 25.0 1.0 CB A:ASP40 3.2 13.6 1.0 C4 A:IMD171 3.2 11.9 0.9 N1 A:IMD171 4.1 10.2 1.0 OD1 A:ASP40 4.1 28.8 1.0 C5 A:IMD171 4.3 10.4 1.0 O A:HOH281 4.6 31.1 0.9 CA A:ASP40 4.7 12.1 1.0 O A:HOH245 4.8 22.9 0.7

X.Ren, J.H.Hurley. Structural Basis For Endosomal Recruitment of Escrt-I By Escrt-0 in Yeast. Embo J. V. 30 2130 2011.
ISSN: ISSN 0261-4189
PubMed: 21505419
DOI: 10.1038/EMBOJ.2011.122