Sodium in PDB 6lz2: Crystal Structure of A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44)

The structure of Crystal Structure of A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44), PDB code: 6lz2 was solved by H.Cai, H.Yao, T.Li, C.Hutter, Y.Tang, Y.Li, M.Seeger, D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.04 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.610, 83.486, 184.562, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.5

The binding sites of Sodium atom in the Crystal Structure of A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44) (pdb code 6lz2). 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 A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44), PDB code: 6lz2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44)


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 A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:37.9 occ:1.00 O A:LEU138 2.7 32.3 1.0 OD1 A:ASP56 2.8 29.4 1.0 O A:HOH457 2.8 36.7 1.0 O A:HOH491 2.8 28.6 1.0 OD2 A:ASP56 3.4 33.5 1.0 CG A:ASP56 3.5 36.4 1.0 C A:LEU138 3.7 31.4 1.0 CD1 A:ILE198 3.7 23.8 1.0 CA A:LYS139 3.9 35.7 1.0 CB A:ILE198 4.0 26.4 1.0 CG1 A:ILE198 4.0 25.0 1.0 NA A:NA302 4.1 39.6 1.0 N A:LYS139 4.2 29.2 1.0 CB A:LYS139 4.3 28.7 1.0 O A:HOH459 4.4 26.0 1.0 O C:HOH516 4.4 34.7 1.0 O C:HOH674 4.7 36.1 1.0 N A:ILE198 4.7 24.1 1.0 CA A:LEU138 4.8 32.2 1.0 CG2 A:ILE198 4.8 27.5 1.0 O A:HOH514 4.9 52.9 1.0 CB A:ASP56 5.0 25.6 1.0 CA A:ILE198 5.0 24.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44)


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 A Thermostable Green Fluorescent Protein (Tgp) with A Synthetic Nanobody (SB44) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:39.6 occ:1.00 OD1 A:ASP56 2.7 29.4 1.0 O A:HOH459 2.9 26.0 1.0 OG1 A:THR59 2.9 27.6 1.0 CG2 A:THR59 3.4 22.5 1.0 CB A:THR59 3.6 22.6 1.0 CD1 A:TRP140 3.7 26.9 1.0 CG A:ASP56 3.7 36.4 1.0 CG1 A:ILE198 3.7 25.0 1.0 O A:HOH491 4.0 28.6 1.0 CD1 A:ILE198 4.0 23.8 1.0 NA A:NA301 4.1 37.9 1.0 CA A:ASP56 4.1 27.5 1.0 CB A:ASP56 4.1 25.6 1.0 NE1 A:TRP140 4.3 27.9 1.0 CD1 A:LEU210 4.3 25.3 1.0 N A:ILE198 4.4 24.1 1.0 O A:ASP56 4.6 23.2 1.0 CG2 A:ILE196 4.7 26.5 1.0 OD2 A:ASP56 4.7 33.5 1.0 CB A:ILE198 4.7 26.4 1.0 N A:TRP140 4.7 29.4 1.0 CG A:TRP140 4.8 28.1 1.0 CG1 A:ILE196 4.8 23.6 1.0 O A:ILE196 4.9 27.5 1.0 C A:ASP56 4.9 30.5 1.0 C A:GLU197 4.9 25.0 1.0

H.Cai, H.Yao, T.Li, C.A.J.Hutter, Y.Li, Y.Tang, M.A.Seeger, D.Li. An Improved Fluorescent Tag and Its Nanobodies For Membrane Protein Expression, Stability Assay, and Purification. Commun Biol V. 3 753 2020.
ISSN: ESSN 2399-3642
PubMed: 33303987
DOI: 10.1038/S42003-020-01478-Z