Sodium in PDB 7oin: Crystal Structure of Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift

The structure of Crystal Structure of Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift, PDB code: 7oin was solved by K.M.Boyko, A.Y.Nikolaeva, P.V.Dorovatovskii, O.M.Subach, A.V.Vlaskina, Y.K.Agapova, O.I.Ivashkina, V.O.Popov, F.V.Subach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.519, 45.357, 59.042, 90, 102.34, 90
R / Rfree (%)	16.4 / 19

The binding sites of Sodium atom in the Crystal Structure of Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift (pdb code 7oin). 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 Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift, PDB code: 7oin:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift


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 Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:11.9 occ:1.00 O B:HOH614 2.7 15.9 1.0 O B:HOH498 3.0 7.2 1.0 N B:ILE203 3.2 7.7 1.0 O B:HOH441 3.6 29.4 1.0 NH2 B:ARG168 3.7 8.9 0.5 CA B:ASP202 3.8 7.0 1.0 O B:HOH416 3.8 13.6 1.0 CA B:GLY144 3.8 7.3 1.0 CB B:ILE203 4.0 8.2 1.0 C B:ASP202 4.0 7.4 1.0 CA B:ILE203 4.1 7.8 1.0 NH1 B:ARG168 4.1 8.1 0.5 CG1 B:ILE203 4.1 9.5 1.0 O B:ILE203 4.2 10.4 1.0 O B:HOH420 4.3 32.5 1.0 O B:MET143 4.3 9.6 1.0 CB B:ASP202 4.4 8.5 1.0 O B:LEU201 4.4 6.8 1.0 C B:ILE203 4.6 8.6 1.0 OD1 B:ASP202 4.6 10.5 1.0 N B:GLY144 4.7 7.6 1.0 N B:LEU145 4.8 7.3 1.0 O B:HOH516 4.8 15.1 1.0 C B:GLY144 4.8 7.4 1.0 C B:MET143 4.8 9.6 1.0 O B:HOH616 4.8 25.9 1.0 N B:ASP202 4.9 7.0 1.0 CZ B:ARG168 5.0 8.7 0.5 CG B:ASP202 5.0 9.7 1.0 O B:HOH470 5.0 8.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift


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 Lssmscarlet - A Genetically Encoded Red Fluorescent Protein with A Large Stokes Shift within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:8.2 occ:1.00 OE2 B:GLU217 3.0 15.1 1.0 N B:SER71 3.3 6.8 1.0 C2 B:NRQ67 3.4 5.4 1.0 CA2 B:NRQ67 3.5 6.0 1.0 O B:SER71 3.5 6.3 1.0 N2 B:NRQ67 3.5 6.0 1.0 N3 B:NRQ67 3.5 5.9 1.0 C1 B:NRQ67 3.6 5.9 1.0 C B:SER71 3.6 6.3 1.0 NH2 B:ARG199 3.8 19.6 1.0 CA B:SER71 3.9 6.5 1.0 NE2 B:GLN43 3.9 8.2 1.0 CD B:GLU217 4.0 12.4 1.0 O2 B:NRQ67 4.0 5.9 1.0 NE B:ARG199 4.0 17.7 1.0 CD B:ARG72 4.0 8.5 1.0 OE1 B:GLU217 4.1 17.8 1.0 CB2 B:NRQ67 4.2 6.5 1.0 N B:ARG72 4.2 6.5 1.0 C3 B:NRQ67 4.2 7.8 1.0 CZ B:ARG199 4.3 17.2 1.0 CB B:SER71 4.3 6.6 1.0 CA B:ARG72 4.4 7.2 1.0 CA3 B:NRQ67 4.4 6.4 1.0 CA1 B:NRQ67 4.4 6.5 1.0 NH1 B:ARG72 4.5 10.0 1.0 NE B:ARG72 4.5 9.3 1.0 OG B:SER219 4.6 11.2 1.0 CG1 B:NRQ67 4.6 7.6 1.0 CZ B:ARG72 4.8 9.6 1.0 CD1 B:ILE75 4.8 17.7 1.0 CD B:ARG199 4.9 14.8 1.0 CG1 B:ILE75 4.9 12.7 1.0 O B:HOH510 5.0 10.9 1.0 CG B:ARG72 5.0 8.2 1.0 CB1 B:NRQ67 5.0 7.0 1.0

O.M.Subach, A.V.Vlaskina, Y.K.Agapova, P.V.Dorovatovskii, A.Y.Nikolaeva, O.I.Ivashkina, V.O.Popov, K.D.Piatkevich, M.G.Khrenova, T.A.Smirnova, K.M.Boyko, F.V.Subach. Lssmscarlet, DCYRFP2S, DCYOFP2S and CRISPRED2S, Genetically Encoded Red Fluorescent Proteins with A Large Stokes Shift. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34884694
DOI: 10.3390/IJMS222312887