Sodium in PDB 5if6: Structure of A Computationally Designed 17-Ohp Binder

The structure of Structure of A Computationally Designed 17-Ohp Binder, PDB code: 5if6 was solved by B.L.Stoddard, L.A.Doyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.68 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.020, 100.787, 118.154, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.4

The binding sites of Sodium atom in the Structure of A Computationally Designed 17-Ohp Binder (pdb code 5if6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of A Computationally Designed 17-Ohp Binder, PDB code: 5if6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of A Computationally Designed 17-Ohp Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Computationally Designed 17-Ohp Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:30.0 occ:1.00 HA A:GLN10 3.2 61.8 1.0 O A:SER9 3.6 55.2 1.0 HA3 A:GLY13 3.6 72.1 1.0 HB2 A:CYS73 3.7 64.5 1.0 HD21 A:LEU89 3.8 58.4 1.0 O A:HOH301 3.8 30.0 1.0 HD22 A:LEU89 3.9 58.4 1.0 CA A:GLN10 4.1 51.5 1.0 HG2 A:GLN10 4.2 69.2 1.0 H A:GLY13 4.2 67.9 1.0 C A:SER9 4.2 55.7 1.0 CD2 A:LEU89 4.3 48.7 1.0 HG12 A:VAL71 4.4 73.2 1.0 CA A:GLY13 4.5 60.0 1.0 N A:GLN10 4.5 52.0 1.0 HB2 A:SER9 4.5 57.8 1.0 HG11 A:VAL71 4.6 73.2 1.0 CB A:CYS73 4.6 53.7 1.0 HB A:VAL71 4.6 73.0 1.0 HH A:TYR109 4.7 58.9 1.0 N A:GLY13 4.7 56.6 1.0 OH A:TYR109 4.7 49.0 1.0 HA2 A:GLY13 4.7 72.1 1.0 HD11 A:LEU89 4.8 62.4 1.0 O A:GLN10 4.8 56.1 1.0 HD13 A:LEU89 4.9 62.4 1.0 HD23 A:LEU89 4.9 58.4 1.0 CG A:GLN10 4.9 57.7 1.0 C A:GLN10 4.9 50.4 1.0 CG1 A:VAL71 4.9 61.0 1.0 HB3 A:CYS73 5.0 64.5 1.0 H A:CYS73 5.0 64.4 1.0

Sodium binding site 2 out of 3 in the Structure of A Computationally Designed 17-Ohp Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Computationally Designed 17-Ohp Binder within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:30.0 occ:1.00 HB2 B:CYS73 3.5 57.0 1.0 HA B:GLN10 3.6 70.6 1.0 HD22 B:LEU89 3.6 59.0 1.0 HA3 B:GLY13 3.6 61.0 1.0 O B:SER9 3.7 58.6 1.0 O B:HOH301 3.9 52.6 1.0 C B:SER9 4.3 56.5 1.0 HD21 B:LEU89 4.4 59.0 1.0 H B:GLY13 4.4 67.0 1.0 CD2 B:LEU89 4.4 49.2 1.0 HB2 B:SER9 4.4 63.8 1.0 HG12 B:VAL71 4.4 76.2 1.0 CA B:GLN10 4.4 58.8 1.0 CB B:CYS73 4.5 47.5 1.0 CA B:GLY13 4.5 50.9 1.0 HG2 B:GLN10 4.6 72.6 1.0 HB B:VAL71 4.6 68.9 1.0 N B:GLN10 4.7 55.4 1.0 HD13 B:LEU89 4.7 62.2 1.0 HG11 B:VAL71 4.7 76.2 1.0 H B:CYS73 4.7 60.9 1.0 HB3 B:CYS73 4.8 57.0 1.0 HA2 B:GLY13 4.8 61.0 1.0 HD23 B:LEU89 4.8 59.0 1.0 N B:GLY13 4.9 55.9 1.0 N B:CYS73 5.0 50.7 1.0 CG1 B:VAL71 5.0 63.5 1.0

Sodium binding site 3 out of 3 in the Structure of A Computationally Designed 17-Ohp Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Computationally Designed 17-Ohp Binder within 5.0Å range: probe atom residue distance (Å) B Occ D:Na202 b:30.0 occ:1.00 HB2 D:CYS73 3.2 76.8 1.0 HA D:GLN10 3.4 75.1 1.0 HD21 D:LEU89 3.8 71.1 1.0 O D:SER9 4.0 63.9 1.0 HD22 D:LEU89 4.0 71.1 1.0 HA3 D:GLY13 4.0 73.5 1.0 HG2 D:GLN10 4.1 75.8 1.0 CB D:CYS73 4.2 64.0 1.0 HG23 D:VAL71 4.3 78.9 1.0 CA D:GLN10 4.3 62.6 1.0 CD2 D:LEU89 4.3 59.2 1.0 HB3 D:CYS73 4.4 76.8 1.0 C D:SER9 4.5 64.9 1.0 H D:CYS73 4.6 75.6 1.0 HB2 D:SER9 4.6 71.1 1.0 N D:GLN10 4.7 64.9 1.0 H D:GLY13 4.7 73.8 1.0 HG21 D:VAL71 4.7 78.9 1.0 HD23 D:LEU89 4.8 71.1 1.0 N D:CYS73 4.9 63.0 1.0 CA D:GLY13 4.9 61.2 1.0 CG D:GLN10 4.9 63.2 1.0 CG2 D:VAL71 5.0 65.8 1.0

J.Dou, L.Doyle, P.Jr Greisen, A.Schena, H.Park, K.Johnsson, B.L.Stoddard, D.Baker. Sampling and Energy Evaluation Challenges in Ligand Binding Protein Design. Protein Sci. V. 26 2426 2017.
ISSN: ESSN 1469-896X
PubMed: 28980354
DOI: 10.1002/PRO.3317