Zinc in PDB 1vfy: Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae

The structure of Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae, PDB code: 1vfy was solved by J.H.Hurley, S.Misra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	24.090, 26.570, 31.610, 111.79, 92.70, 105.70
R / Rfree (%)	17.4 / 18.1

The binding sites of Zinc atom in the Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae (pdb code 1vfy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae, PDB code: 1vfy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:5.8 occ:1.00 SG A:CYS222 2.3 6.5 1.0 SG A:CYS225 2.3 6.5 1.0 SG A:CYS195 2.4 6.2 1.0 SG A:CYS192 2.4 4.8 1.0 CB A:CYS195 3.2 6.8 1.0 CB A:CYS192 3.2 5.0 1.0 CB A:CYS225 3.3 5.1 1.0 CB A:CYS222 3.5 7.5 1.0 N A:CYS195 3.6 4.9 1.0 N A:CYS222 3.9 6.0 1.0 CA A:CYS195 4.0 6.2 1.0 N A:CYS225 4.2 6.6 1.0 CA A:CYS222 4.2 5.0 1.0 O A:HOH38 4.3 23.3 1.0 CA A:CYS225 4.4 4.4 1.0 CE1 A:PHE199 4.4 5.1 1.0 CB A:SER194 4.5 6.8 1.0 CZ A:PHE199 4.6 5.4 1.0 CA A:CYS192 4.7 4.8 1.0 C A:SER194 4.7 6.1 1.0 C A:CYS222 4.8 6.5 1.0 O A:CYS222 4.8 6.1 1.0 OG A:SER194 4.8 10.3 1.0 C A:CYS195 4.9 5.2 1.0 O A:HOH24 5.0 21.3 1.0 C A:VAL221 5.0 4.6 1.0

Zinc binding site 2 out of 2 in the Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphatidylinositol-3-Phosphate Binding Fyve Domain of VPS27P Protein From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.8 occ:1.00 ND1 A:HIS203 2.1 9.7 1.0 SG A:CYS179 2.3 10.3 1.0 SG A:CYS200 2.3 8.0 1.0 SG A:CYS176 2.3 8.2 1.0 CE1 A:HIS203 3.0 11.0 1.0 CB A:CYS176 3.2 7.6 1.0 CG A:HIS203 3.2 9.7 1.0 CB A:CYS179 3.5 12.7 1.0 CB A:CYS200 3.5 8.4 1.0 CB A:HIS203 3.6 8.7 1.0 N A:CYS179 3.7 11.7 1.0 N A:CYS200 4.0 6.9 1.0 CA A:CYS179 4.2 11.1 1.0 NE2 A:HIS203 4.2 12.7 1.0 CD2 A:HIS203 4.3 11.6 1.0 CA A:CYS200 4.3 7.1 1.0 O A:HOH41 4.3 23.0 1.0 CB A:ILE178 4.5 15.0 1.0 N A:HIS203 4.5 7.3 1.0 CA A:CYS176 4.6 7.2 1.0 CA A:HIS203 4.8 8.2 1.0 C A:ILE178 4.8 14.4 1.0 O A:HOH54 4.8 26.8 1.0 C A:CYS200 4.9 6.0 1.0 CG2 A:ILE178 4.9 17.4 1.0 N A:ILE178 4.9 12.9 1.0 O A:CYS200 5.0 7.2 1.0 C A:CYS179 5.0 13.1 1.0 CA A:ILE178 5.0 12.6 1.0

S.Misra, J.H.Hurley. Crystal Structure of A Phosphatidylinositol 3-Phosphate-Specific Membrane-Targeting Motif, the Fyve Domain of VPS27P. Cell(Cambridge,Mass.) V. 97 657 1999.
ISSN: ISSN 0092-8674
PubMed: 10367894
DOI: 10.1016/S0092-8674(00)80776-X