Sodium in PDB 5osi: Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176)

The structure of Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176), PDB code: 5osi was solved by M.Romano-Moreno, A.L.Rojas, M.Lucas, M.N.Isupov, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	126.49 / 2.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.554, 138.993, 126.637, 90.00, 92.78, 90.00
R / Rfree (%)	20.5 / 26.7

The binding sites of Sodium atom in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176) (pdb code 5osi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176), PDB code: 5osi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na801 b:68.9 occ:1.00 CG E:GLU775 3.8 73.5 1.0 CB E:GLU775 3.9 69.0 1.0 OE2 E:GLU775 4.0 78.5 1.0 CA E:GLU775 4.0 62.7 1.0 CD E:GLU775 4.1 78.0 1.0 NH2 E:ARG778 4.1 86.8 1.0 CE1 E:HIS771 4.4 58.5 1.0 O E:HOH918 4.4 50.3 1.0 CD E:ARG778 4.5 83.0 1.0 NE2 E:HIS771 4.8 60.5 1.0 OE1 E:GLU775 4.8 76.4 1.0 O E:GLU775 4.9 61.3 1.0 N E:GLU775 5.0 59.5 1.0 C E:GLU775 5.0 61.0 1.0

Sodium binding site 2 out of 4 in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na802 b:58.4 occ:1.00 ND1 H:HIS565 3.1 42.4 1.0 CE1 H:HIS565 3.9 44.1 1.0 CG H:HIS565 4.0 41.1 1.0 CG H:GLU605 4.1 52.9 1.0 CE1 H:PHE606 4.2 45.0 1.0 CB H:HIS565 4.2 40.9 1.0 CD1 H:PHE606 4.7 44.7 1.0 CB H:GLU605 4.7 49.8 1.0 CA H:SER562 4.8 43.3 1.0 O H:PHE561 4.8 44.8 1.0 NE2 H:HIS565 5.0 42.5 1.0

Sodium binding site 3 out of 4 in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176) within 5.0Å range: probe atom residue distance (Å) B Occ K:Na804 b:47.3 occ:1.00 CA K:SER562 4.2 24.1 1.0 N K:SER562 4.4 24.0 1.0 O K:PHE561 4.4 24.0 1.0 CD2 K:HIS565 4.4 28.0 1.0 CB K:HIS565 4.5 27.4 1.0 C K:PHE561 4.6 24.2 1.0 CG2 K:VAL602 4.6 22.2 1.0 CG1 K:VAL602 4.6 21.4 1.0 CG K:HIS565 4.6 26.8 1.0 CE1 K:PHE606 4.7 19.5 1.0 CB K:SER562 4.7 24.4 1.0 CG K:GLU605 5.0 28.0 1.0

Sodium binding site 4 out of 4 in the Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Retromer VPS29-VPS35C Subunits Complexed with Ridl Harpin Loop (163-176) within 5.0Å range: probe atom residue distance (Å) B Occ K:Na805 b:56.6 occ:1.00 O K:PHE527 3.6 41.8 1.0 CD1 K:LEU490 4.0 49.5 1.0 CD K:ARG493 4.1 52.6 1.0 CG K:ARG493 4.3 52.8 1.0 C K:PHE527 4.3 41.1 1.0 CA K:THR528 4.3 40.1 1.0 O K:HOH940 4.5 46.5 1.0 CG K:LEU490 4.6 48.5 1.0 CG J:PRO12 4.6 31.9 1.0 OG1 K:THR528 4.6 48.0 1.0 N K:THR528 4.7 39.7 1.0 CB J:PRO12 4.7 31.9 1.0 CG K:PRO531 4.7 32.8 1.0 NH1 K:ARG493 4.7 52.7 1.0 CB K:THR528 4.9 42.5 1.0 CB K:PHE527 5.0 42.2 1.0

M.Romano-Moreno, A.L.Rojas, C.D.Williamson, D.C.Gershlick, M.Lucas, M.N.Isupov, J.S.Bonifacino, M.P.Machner, A.Hierro. Molecular Mechanism For the Subversion of the Retromer Coat By the Legionella Effector Ridl. Proc. Natl. Acad. Sci. V. 114 11151 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29229824
DOI: 10.1073/PNAS.1715361115