Sodium in PDB 6i3v: X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1

The structure of X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1, PDB code: 6i3v was solved by J.L.Berry, X.Miliara, R.M.L.Morgan, S.J.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.64 / 1.98
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	127.312, 127.312, 177.390, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.5

The structure of X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1 also contains other interesting chemical elements:

Chlorine

(Cl)

13 atoms

The binding sites of Sodium atom in the X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1 (pdb code 6i3v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1, PDB code: 6i3v:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:94.4 occ:1.00 NE2 B:GLN101 3.1 96.2 1.0 CL B:CL209 3.1 0.4 1.0 OE1 B:GLN101 3.5 97.8 1.0 CD B:GLN101 3.6 93.5 1.0 O B:HOH382 3.6 65.2 1.0 O B:GLN101 4.7 56.6 1.0 CA B:GLN101 4.8 60.3 1.0 CG B:GLN101 4.9 83.5 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:99.5 occ:1.00 CL B:CL205 2.8 0.2 1.0 CE B:LYS44 3.7 70.5 1.0 CD B:LYS44 4.0 67.6 1.0 NZ B:LYS44 5.0 69.5 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Human Mitochondrial PRELID1 in Complex with TRIAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:68.8 occ:1.00 O B:HOH395 2.2 57.5 1.0 O B:HOH407 2.3 76.4 1.0 O B:ALA84 4.1 50.9 1.0 O B:HOH322 4.1 66.5 1.0 CB B:ALA84 4.3 49.6 1.0 CL B:CL207 4.6 64.3 1.0 C B:ALA84 4.6 49.3 1.0 CE1 B:HIS88 4.9 60.8 1.0

X.Miliara, T.Tatsuta, J.L.Berry, S.L.Rouse, K.Solak, D.S.Chorev, D.Wu, C.V.Robinson, S.Matthews, T.Langer. Structural Determinants of Lipid Specificity Within Ups/Preli Lipid Transfer Proteins. Nat Commun V. 10 1130 2019.
ISSN: ESSN 2041-1723
PubMed: 30850607
DOI: 10.1038/S41467-019-09089-X