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

The structure of Structure of A Computationally Designed 17-Ohp Binder, PDB code: 5ier 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)	36.25 / 2.01
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.832, 78.832, 184.478, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21

The binding sites of Sodium atom in the Structure of A Computationally Designed 17-Ohp Binder (pdb code 5ier). 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 A Computationally Designed 17-Ohp Binder, PDB code: 5ier:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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:Na204 b:47.6 occ:1.00 O4 A:SO4203 2.7 55.5 1.0 S A:SO4203 3.6 74.3 1.0 O3 A:SO4203 3.8 70.0 1.0 O2 A:SO4203 3.8 71.4 1.0 O A:HOH355 4.4 29.7 1.0 O1 A:SO4203 4.9 60.8 1.0 NA A:NA205 5.0 47.5 1.0

Sodium binding site 2 out of 4 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 A:Na205 b:47.5 occ:1.00 H A:LYS113 2.2 27.3 1.0 HB2 A:ASN112 2.3 31.4 1.0 O A:HOH362 2.7 43.0 1.0 HG2 A:LYS113 2.8 33.2 1.0 N A:LYS113 3.0 22.8 1.0 O4 A:SO4203 3.1 55.5 1.0 O2 A:SO4203 3.2 71.4 1.0 CB A:ASN112 3.2 26.1 1.0 HB2 A:LYS113 3.3 31.1 1.0 O1 A:SO4203 3.3 60.8 1.0 S A:SO4203 3.4 74.3 1.0 HA A:ASN112 3.4 27.1 1.0 HB3 A:ASN112 3.6 31.4 1.0 CG A:LYS113 3.6 27.6 1.0 CA A:ASN112 3.7 22.6 1.0 CB A:LYS113 3.7 25.9 1.0 C A:ASN112 3.8 23.1 1.0 HG3 A:LYS113 3.9 33.2 1.0 CA A:LYS113 4.0 27.0 1.0 H A:ALA114 4.2 25.3 1.0 CG A:ASN112 4.3 19.6 1.0 HA A:LYS113 4.6 32.4 1.0 HH22 A:ARG110 4.6 59.1 1.0 HB3 A:LYS113 4.7 31.1 1.0 O A:HOH340 4.7 34.5 1.0 HD22 A:ASN112 4.8 26.1 1.0 O3 A:SO4203 4.8 70.0 1.0 CD A:LYS113 4.8 29.6 1.0 HE2 A:LYS113 4.9 45.2 1.0 N A:ALA114 4.9 21.1 1.0 HD3 A:LYS113 4.9 35.6 1.0 ND2 A:ASN112 4.9 21.8 1.0 NA A:NA204 5.0 47.6 1.0 HH12 A:ARG110 5.0 47.0 1.0 OD1 A:ASN112 5.0 22.4 1.0 C A:LYS113 5.0 21.2 1.0

Sodium binding site 3 out of 4 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:Na203 b:68.6 occ:1.00 H D:LYS113 2.3 53.6 1.0 O3 D:SO4202 2.6 83.9 1.0 HB2 D:ASN112 2.7 55.5 1.0 O1 D:SO4202 3.0 79.6 1.0 N D:LYS113 3.2 44.7 1.0 S D:SO4202 3.4 89.9 1.0 CB D:LYS113 3.5 47.1 1.0 CB D:ASN112 3.6 46.2 1.0 HA D:ASN112 3.8 50.3 1.0 CA D:LYS113 4.0 50.2 1.0 HB3 D:ASN112 4.0 55.5 1.0 CA D:ASN112 4.1 41.9 1.0 C D:ASN112 4.1 44.6 1.0 O2 D:SO4202 4.3 68.5 1.0 HH22 D:ARG110 4.4 50.8 1.0 O4 D:SO4202 4.4 65.2 1.0 HA D:LYS113 4.5 60.2 1.0 H D:ALA114 4.6 57.5 1.0 CG D:ASN112 4.7 44.9 1.0 O D:HOH320 4.8 43.1 1.0

Sodium binding site 4 out of 4 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 4 of Structure of A Computationally Designed 17-Ohp Binder within 5.0Å range: probe atom residue distance (Å) B Occ D:Na204 b:59.9 occ:1.00 HD22 D:ASN112 2.5 55.0 1.0 O2 D:SO4202 2.5 68.5 1.0 OD1 D:ASP31 3.0 55.4 1.0 HG22 D:THR118 3.3 54.0 1.0 OD2 D:ASP31 3.3 61.8 1.0 HB3 D:ASN112 3.4 55.5 1.0 ND2 D:ASN112 3.4 45.9 1.0 O3 D:SO4202 3.5 83.9 1.0 CG D:ASP31 3.5 61.9 1.0 HB1 D:ALA29 3.5 58.0 1.0 HG21 D:THR118 3.5 54.0 1.0 S D:SO4202 3.6 89.9 1.0 HD21 D:ASN112 3.9 55.0 1.0 CG2 D:THR118 3.9 45.0 1.0 HB2 D:ASN112 4.0 55.5 1.0 CB D:ASN112 4.0 46.2 1.0 CG D:ASN112 4.2 44.9 1.0 CB D:ALA29 4.2 48.3 1.0 HB2 D:ALA29 4.3 58.0 1.0 HG23 D:THR118 4.4 54.0 1.0 HB3 D:ALA29 4.4 58.0 1.0 O4 D:SO4202 4.4 65.2 1.0 H D:ASP31 4.6 59.2 1.0 O1 D:SO4202 4.6 79.6 1.0 HB D:THR118 4.8 46.6 1.0 HH12 D:ARG110 4.9 51.5 1.0 CB D:ASP31 4.9 52.3 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