Zinc in PDB 5f0p: Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled)

The structure of Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled), PDB code: 5f0p was solved by M.Lucas, D.Gershlick, A.Vidaurrazaga, A.L.Rojas, J.S.Bonifacino, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.76 / 2.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	371.290, 75.320, 57.270, 90.00, 97.66, 90.00
R / Rfree (%)	21.9 / 26.1

The binding sites of Zinc atom in the Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled) (pdb code 5f0p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled), PDB code: 5f0p:

Zinc binding site 1 out of 1 in the Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Retromer VPS26-VPS35 Subunits Bound to SNX3 and DMT1(L557M) (Semet Labeled) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn415 b:64.6 occ:1.00 OE2 B:GLU167 2.0 55.6 1.0 ND1 B:HIS175 2.0 62.9 1.0 NE2 D:HIS565 2.1 73.4 1.0 NE2 D:HIS563 2.1 80.0 1.0 CE1 B:HIS175 3.0 64.4 1.0 CG B:HIS175 3.0 60.5 1.0 CE1 D:HIS563 3.1 83.4 1.0 CE1 D:HIS565 3.1 71.9 1.0 CD2 D:HIS565 3.1 76.6 1.0 CD2 D:HIS563 3.1 83.5 1.0 CD B:GLU167 3.2 56.1 1.0 CB B:HIS175 3.3 55.5 1.0 OE1 B:GLU167 3.9 59.9 1.0 NE2 B:HIS175 4.1 64.8 1.0 CG B:GLU167 4.1 53.7 1.0 CD2 B:HIS175 4.1 62.9 1.0 ND1 D:HIS565 4.2 75.2 1.0 ND1 D:HIS563 4.2 86.1 1.0 CG D:HIS565 4.2 80.6 1.0 CG D:HIS563 4.2 89.2 1.0 CD1 B:LEU198 4.4 34.8 1.0 SE D:MSE560 4.6 79.6 1.0 CA B:HIS175 4.7 51.4 1.0 CB B:LEU198 4.7 35.7 1.0 CG D:MSE560 4.8 78.4 1.0

M.Lucas, D.C.Gershlick, A.Vidaurrazaga, A.L.Rojas, J.S.Bonifacino, A.Hierro. Structural Mechanism For Cargo Recognition By the Retromer Complex. Cell V. 167 1623 2016.
ISSN: ISSN 1097-4172
PubMed: 27889239
DOI: 10.1016/J.CELL.2016.10.056