Zinc in PDB 5ub8: Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II)

The structure of Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II), PDB code: 5ub8 was solved by P.J.Stogios, T.Skarina, R.Di Leo, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.303, 43.392, 41.662, 90.00, 89.05, 90.00
R / Rfree (%)	18.5 / 22.6

The binding sites of Zinc atom in the Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II) (pdb code 5ub8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II), PDB code: 5ub8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II)


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 YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:34.4 occ:1.00 O3B A:GDP301 2.1 23.8 1.0 OG A:SER29 2.2 39.3 1.0 O A:HOH412 2.2 24.6 1.0 O A:HOH407 2.2 25.5 1.0 O A:HOH417 2.3 18.5 1.0 O A:HOH411 2.4 28.3 1.0 PB A:GDP301 3.2 26.4 1.0 O2B A:GDP301 3.3 27.2 1.0 CB A:SER29 3.4 33.2 1.0 O A:HOH485 3.7 40.3 1.0 N A:SER29 3.9 23.8 1.0 OG1 A:THR71 3.9 23.2 1.0 O2A A:GDP301 4.0 24.2 1.0 NZ A:LYS28 4.1 24.4 1.0 OD1 A:ASP70 4.1 25.4 1.0 OD2 A:ASP70 4.1 28.1 1.0 O1B A:GDP301 4.2 29.0 1.0 O A:THR71 4.2 34.1 1.0 CA A:SER29 4.2 30.8 1.0 O A:HOH509 4.3 40.5 1.0 OE2 A:GLU75 4.4 20.9 1.0 O3A A:GDP301 4.4 27.8 1.0 PA A:GDP301 4.6 25.6 1.0 CG A:ASP70 4.6 26.6 1.0 N A:GLY73 4.6 25.5 1.0 O1A A:GDP301 4.7 25.3 1.0 CB A:LYS28 4.7 23.1 1.0 CA A:GLY73 4.7 26.0 1.0 O A:HOH440 4.8 23.4 1.0 C A:THR71 4.9 28.6 1.0 C A:LYS28 5.0 26.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II)


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 YPT31, A Rab Family Gtpase From Candida Albicans, in Complex with Gdp and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:31.3 occ:1.00 NE2 A:HIS116 2.2 37.8 1.0 OE1 A:GLU112 2.2 33.1 1.0 O A:HOH502 2.2 1.1 1.0 CE1 A:HIS116 3.0 35.9 1.0 CD A:GLU112 3.2 33.9 1.0 CD2 A:HIS116 3.3 35.1 1.0 OE2 A:GLU112 3.5 36.6 1.0 ND1 A:HIS116 4.2 37.0 1.0 O A:HOH408 4.2 15.0 1.0 O A:HOH447 4.2 29.2 1.0 CG A:GLU115 4.3 30.4 1.0 CG A:HIS116 4.4 33.7 1.0 CG A:GLU112 4.5 25.1 1.0 CB A:GLU115 4.5 25.2 1.0 CA A:GLU112 4.5 23.1 1.0 NZ A:LYS111 4.6 45.1 1.0 CB A:GLU112 4.8 21.3 1.0 O A:HOH453 4.8 42.0 1.0 CB A:ALA79 4.9 20.6 1.0

P.J.Stogios, P.J.Stogios, T.Skarina, R.Di Leo, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid). N/A N/A.