Sodium in PDB 4iil: Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin

The structure of Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin, PDB code: 4iil was solved by C.A.Brautigam, R.K.Deka, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.29 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.955, 107.790, 72.881, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 15.3

The structure of Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin (pdb code 4iil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin, PDB code: 4iil:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:11.3 occ:1.00 OD2 A:ASP208 2.4 11.0 1.0 O A:ASP146 2.4 13.3 1.0 O A:ASN144 2.5 13.0 1.0 O A:SER136 2.5 11.6 1.0 OG A:SER136 2.5 9.3 1.0 O A:HOH503 2.6 12.2 1.0 HG A:SER136 3.0 11.1 1.0 OD1 A:ASN144 3.0 13.5 1.0 H A:ASN144 3.1 13.6 1.0 CG A:ASP208 3.2 9.9 1.0 C A:SER136 3.3 10.7 1.0 C A:ASN144 3.4 12.9 1.0 C A:ASP146 3.4 12.7 1.0 OD1 A:ASP208 3.4 9.9 1.0 HA A:SER136 3.4 11.2 1.0 CB A:SER136 3.6 8.8 1.0 CA A:SER136 3.7 9.4 1.0 N A:ASN144 3.7 11.3 1.0 H A:ASP146 3.8 17.1 1.0 O A:HOH532 3.8 20.3 1.0 HA A:LYS147 3.9 16.6 1.0 N A:ASP146 3.9 14.2 1.0 H A:LYS148 3.9 12.5 1.0 CG A:ASN144 3.9 11.7 1.0 NA A:NA403 4.1 15.9 1.0 CA A:ASN144 4.1 10.9 1.0 HB2 A:ASP146 4.1 21.2 1.0 HB3 A:SER136 4.1 10.6 1.0 CA A:ASP146 4.2 13.9 1.0 HB1 A:ALA143 4.2 15.2 1.0 HB2 A:SER136 4.3 10.6 1.0 N A:ALA145 4.3 14.8 1.0 HA A:ALA137 4.4 15.2 1.0 N A:LYS147 4.4 12.6 1.0 C A:ALA145 4.4 16.1 1.0 N A:ALA137 4.4 10.4 1.0 CB A:ASP208 4.5 9.5 1.0 CA A:LYS147 4.6 13.8 1.0 HB3 A:ASP208 4.6 11.4 1.0 HA A:ALA143 4.6 14.1 1.0 HD3 A:LYS147 4.6 29.4 1.0 HA A:ALA145 4.6 19.3 1.0 CB A:ASN144 4.6 12.1 1.0 HE1 A:PHE179 4.6 13.9 1.0 CB A:ASP146 4.7 17.7 1.0 CA A:ALA145 4.7 16.1 1.0 N A:LYS148 4.7 10.4 1.0 ND2 A:ASN144 4.8 13.6 1.0 HD22 A:ASN144 4.8 16.2 1.0 C A:ALA143 4.8 11.7 1.0 HZ A:PHE179 4.9 14.0 1.0 CA A:ALA137 4.9 12.6 1.0 HA A:ASN144 4.9 13.1 1.0 HB3 A:ASP146 5.0 21.2 1.0 O A:LYS148 5.0 10.1 1.0 HB2 A:ASP208 5.0 11.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rfua (TP0298) of T. Pallidum Bound to Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:15.9 occ:1.00 O A:ASN144 2.6 13.0 1.0 O A:SER138 2.7 16.7 1.0 O A:SER136 2.8 11.6 1.0 O A:HOH532 3.0 20.3 1.0 O A:HOH781 3.1 37.1 1.0 HA A:ALA137 3.2 15.2 1.0 HA A:ALA145 3.3 19.3 1.0 C A:ALA137 3.3 13.2 1.0 O A:ALA137 3.3 15.8 1.0 HB1 A:ALA143 3.4 15.2 1.0 C A:ASN144 3.5 12.9 1.0 CA A:ALA137 3.7 12.6 1.0 N A:SER138 3.7 11.9 1.0 C A:SER138 3.8 13.7 1.0 C A:SER136 3.8 10.7 1.0 H A:SER138 4.0 14.3 1.0 NA A:NA402 4.1 11.3 1.0 CA A:ALA145 4.1 16.1 1.0 N A:ALA145 4.2 14.8 1.0 N A:ALA137 4.2 10.4 1.0 HB3 A:ALA143 4.2 15.2 1.0 CB A:ALA143 4.2 12.7 1.0 CA A:SER138 4.3 12.1 1.0 N A:ASN144 4.3 11.3 1.0 O A:HOH645 4.4 31.4 1.0 CA A:ASN144 4.4 10.9 1.0 H A:ASN144 4.4 13.6 1.0 HZ3 A:LYS147 4.5 32.3 1.0 HA A:ALA139 4.5 20.6 1.0 HA A:ASN144 4.6 13.1 1.0 C A:ALA143 4.6 11.7 1.0 HA A:SER138 4.8 14.5 1.0 C A:ALA145 4.8 16.1 1.0 O A:ASP146 4.8 13.3 1.0 HB2 A:ALA143 4.9 15.2 1.0 N A:ALA139 4.9 15.4 1.0 H A:ALA145 5.0 17.7 1.0 HG A:SER138 5.0 13.6 1.0

R.K.Deka, C.A.Brautigam, B.A.Biddy, W.Z.Liu, M.V.Norgard. Evidence For An Abc-Type Riboflavin Transporter System in Pathogenic Spirochetes. Mbio V. 4 00615 2013.
ISSN: ESSN 2150-7511
PubMed: 23404400
DOI: 10.1128/MBIO.00615-12