Sodium in PDB 5jzl: The Structure of Monomeric Ultra Stable Green Fluorescent Protein

The structure of The Structure of Monomeric Ultra Stable Green Fluorescent Protein, PDB code: 5jzl was solved by N.J.Gunn, K.J.Yong, D.J.Scott, M.D.W.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.82 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.352, 95.706, 59.649, 90.00, 104.21, 90.00
R / Rfree (%)	17.5 / 21.8

The structure of The Structure of Monomeric Ultra Stable Green Fluorescent Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Structure of Monomeric Ultra Stable Green Fluorescent Protein (pdb code 5jzl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Monomeric Ultra Stable Green Fluorescent Protein, PDB code: 5jzl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of Monomeric Ultra Stable Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Monomeric Ultra Stable Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:27.1 occ:1.00 O B:HOH566 2.1 32.7 1.0 O B:PHE145 2.3 23.0 1.0 O B:SER205 2.5 22.0 1.0 O B:HOH608 2.6 39.4 1.0 O B:HOH621 2.6 32.3 1.0 O B:HOH401 2.7 18.2 1.0 C B:PHE145 3.4 22.2 1.0 C B:SER205 3.7 19.3 1.0 CA B:ASN146 3.8 28.1 1.0 C B:ASN146 3.9 30.2 1.0 N B:SER205 3.9 19.1 1.0 N B:ASN146 4.1 24.2 1.0 N B:SER147 4.2 33.0 1.0 O B:ASN146 4.2 30.2 1.0 CA B:SER205 4.3 18.4 1.0 OG B:SER147 4.3 35.1 1.0 O B:HOH618 4.4 35.4 1.0 O B:HOH613 4.5 9.8 1.0 CA B:PHE145 4.6 19.5 1.0 O B:HOH433 4.7 41.5 1.0 CB B:SER205 4.7 17.7 1.0 N B:VAL206 4.7 18.3 1.0 CB B:PHE145 4.8 17.8 1.0 N B:PHE145 4.8 19.1 1.0 CA B:VAL206 4.9 19.1 1.0 CG2 B:VAL206 4.9 22.1 1.0 CA B:SER147 4.9 31.6 1.0 C B:GLN204 5.0 20.4 1.0

Sodium binding site 2 out of 2 in the The Structure of Monomeric Ultra Stable Green Fluorescent Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Monomeric Ultra Stable Green Fluorescent Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:27.3 occ:1.00 O A:HOH576 2.4 20.3 1.0 O B:HOH447 2.5 8.9 1.0 O B:HOH623 2.5 20.1 1.0 O B:HOH533 2.7 19.8 1.0 O A:HOH450 2.9 22.5 1.0 O B:HOH609 3.0 26.0 1.0 O B:HOH570 4.0 18.2 1.0 O A:HOH701 4.0 36.4 1.0 OD1 B:ASN198 4.0 11.2 1.0 O A:HOH689 4.2 17.0 1.0 CB B:ALA154 4.3 11.5 1.0 OG1 B:THR153 4.3 13.3 1.0 NZ A:LYS45 4.5 17.1 1.0 O B:HOH677 4.6 23.1 1.0 O B:PRO196 4.6 13.0 1.0 N B:ALA154 4.6 10.3 1.0 O B:HOH486 4.7 21.1 1.0 O A:HOH704 4.7 22.9 1.0 O A:HOH551 4.7 17.7 1.0 CD A:LYS45 4.8 15.1 1.0 OD2 A:ASP210 4.9 15.1 1.0 O B:ALA154 5.0 11.6 1.0 CA B:ALA154 5.0 10.9 1.0

D.J.Scott, N.J.Gunn, K.J.Yong, V.C.Wimmer, N.A.Veldhuis, L.M.Challis, M.Haidar, S.Petrou, R.A.D.Bathgate, M.D.W.Griffin. A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using Clarity. Sci Rep V. 8 667 2018.
ISSN: ESSN 2045-2322
PubMed: 29330459
DOI: 10.1038/S41598-017-18045-Y