Sodium in PDB 6y3e: Scaffold-Ligand Complex with Ligand Unmodelled

All present enzymatic activity of Scaffold-Ligand Complex with Ligand Unmodelled:
5.2.1.8;

The structure of Scaffold-Ligand Complex with Ligand Unmodelled, PDB code: 6y3e was solved by T.Zacharchenko, L.Y.Lian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.39 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.450, 57.450, 114.910, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.4

The binding sites of Sodium atom in the Scaffold-Ligand Complex with Ligand Unmodelled (pdb code 6y3e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Scaffold-Ligand Complex with Ligand Unmodelled, PDB code: 6y3e:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Scaffold-Ligand Complex with Ligand Unmodelled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Scaffold-Ligand Complex with Ligand Unmodelled within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:61.0 occ:1.00 O A:HOH426 2.9 50.8 1.0 ND2 A:ASN106 4.2 17.7 1.0

Sodium binding site 2 out of 3 in the Scaffold-Ligand Complex with Ligand Unmodelled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Scaffold-Ligand Complex with Ligand Unmodelled within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:50.8 occ:1.00 CG A:PHE60 3.9 17.6 1.0 CD2 A:PHE60 4.0 18.0 1.0 O A:HOH451 4.1 36.3 1.0 CB A:PHE60 4.1 18.0 1.0 CZ2 A:TRP121 4.3 31.4 1.0 CD1 A:PHE60 4.4 18.6 1.0 CE2 A:PHE60 4.6 16.9 1.0 O A:SER59 4.6 22.9 1.0 CH2 A:TRP121 4.8 33.9 1.0 CE1 A:PHE60 4.9 19.1 1.0

Sodium binding site 3 out of 3 in the Scaffold-Ligand Complex with Ligand Unmodelled


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Scaffold-Ligand Complex with Ligand Unmodelled within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:33.2 occ:1.00 O A:HOH320 2.9 33.6 1.0 O A:HOH464 3.6 37.4 1.0 OE2 A:GLU23 5.0 26.9 1.0

T.Zacharchenko, L.Y.Lian. Human Cyclophilin D Complexed with Inhibitor To Be Published.