Zinc in PDB 2yw8: Crystal Structure of Human Run and Fyve Domain-Containing Protein

The structure of Crystal Structure of Human Run and Fyve Domain-Containing Protein, PDB code: 2yw8 was solved by H.Wang, S.Kishishita, K.Murayama, C.Takemoto, T.Terada, M.Shirouzu, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 3.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	115.150, 115.150, 115.150, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Human Run and Fyve Domain-Containing Protein (pdb code 2yw8). 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 Human Run and Fyve Domain-Containing Protein, PDB code: 2yw8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Run and Fyve Domain-Containing Protein


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 Human Run and Fyve Domain-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:48.1 occ:1.00 SG A:CYS69 2.3 37.8 1.0 SG A:CYS41 2.3 37.3 1.0 SG A:CYS66 2.4 36.8 1.0 SG A:CYS38 2.5 33.5 1.0 CB A:CYS41 3.1 33.5 1.0 CB A:CYS38 3.2 35.6 1.0 CB A:CYS69 3.3 31.1 1.0 N A:CYS41 3.7 33.1 1.0 CB A:CYS66 3.8 40.1 1.0 CA A:CYS41 4.0 28.2 1.0 N A:CYS66 4.1 40.6 1.0 CE2 A:PHE45 4.2 46.7 1.0 CZ A:PHE45 4.3 47.1 1.0 O A:HOH313 4.3 39.3 1.0 O A:HOH312 4.5 39.3 1.0 N A:CYS69 4.5 40.4 1.0 CA A:CYS69 4.5 35.7 1.0 CA A:CYS66 4.5 44.4 1.0 CB A:ASN40 4.6 49.9 1.0 C A:ASN40 4.6 31.6 1.0 CA A:CYS38 4.7 37.2 1.0 ND2 A:ASN40 4.7 47.0 1.0 C A:CYS41 4.8 34.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Run and Fyve Domain-Containing Protein


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 Human Run and Fyve Domain-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:51.5 occ:1.00 SG A:CYS22 2.4 46.0 1.0 SG A:CYS49 2.4 34.6 1.0 SG A:CYS46 2.4 37.2 1.0 SG A:CYS25 2.4 50.2 1.0 CB A:CYS22 3.1 39.8 1.0 CB A:CYS49 3.3 32.8 1.0 CB A:CYS46 3.3 20.7 1.0 CB A:CYS25 3.4 38.9 1.0 N A:CYS25 3.6 49.5 1.0 N A:CYS46 3.8 35.7 1.0 CA A:CYS25 4.1 46.2 1.0 CA A:CYS46 4.1 32.8 1.0 N A:CYS49 4.3 38.7 1.0 CA A:CYS49 4.4 33.4 1.0 CB A:GLN24 4.5 32.1 1.0 CA A:CYS22 4.5 46.3 1.0 O A:CYS46 4.7 33.5 1.0 C A:CYS46 4.7 37.8 1.0 N A:GLU26 4.7 43.9 1.0 C A:GLN24 4.7 45.9 1.0 C A:CYS25 4.7 46.3 1.0 N A:GLN24 5.0 45.0 1.0 CA A:GLN24 5.0 39.1 1.0

H.Wang, S.Kishishita, T.Murayama, C.Takemoto, T.Terada, L.Chen, Z.Q.Fu, J.Chrzas, B.C.Wang, M.Shirouzu, S.Yokoyama. Crystal Structure of Human Run and Fyve Domain-Containing Protein To Be Published.