Sodium in PDB 9c74: Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66

The structure of Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66, PDB code: 9c74 was solved by C.M.Phillips-Piro, D.P.Broughton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.15 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.809, 37.967, 68.464, 90, 112.73, 90
R / Rfree (%)	17 / 22

The binding sites of Sodium atom in the Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66 (pdb code 9c74). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66, PDB code: 9c74:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.2 occ:1.00 O A:HOH590 2.8 20.7 1.0 O A:ARG80 3.1 23.2 1.0 HD22 A:LEU194 3.1 24.4 1.0 HB3 A:ARG80 3.2 32.1 1.0 HG2 A:ARG80 3.8 43.7 1.0 HE A:ARG80 3.8 40.1 1.0 HD23 A:LEU194 3.9 24.4 1.0 CD2 A:LEU194 3.9 20.4 1.0 H A:LEU195 3.9 24.8 1.0 HB3 A:LEU194 4.0 19.4 1.0 O A:HOH542 4.0 35.6 1.0 O A:LEU195 4.0 25.1 1.0 HH21 A:ARG80 4.0 47.3 1.0 CB A:ARG80 4.0 26.8 1.0 C A:ARG80 4.1 21.8 1.0 NE A:ARG80 4.2 33.4 1.0 HA A:LEU194 4.3 20.9 1.0 HA A:ARG80 4.3 28.1 1.0 NH2 A:ARG80 4.3 39.4 1.0 CG A:ARG80 4.4 36.4 1.0 HD21 A:LEU194 4.4 24.4 1.0 CA A:ARG80 4.4 23.4 1.0 CZ A:ARG80 4.5 39.1 1.0 O A:HOH424 4.5 37.7 1.0 N A:LEU195 4.6 20.7 1.0 CB A:LEU194 4.7 16.2 1.0 HA A:PRO196 4.8 23.6 1.0 HB2 A:ARG80 4.8 32.1 1.0 C A:LEU195 4.8 22.5 1.0 HH22 A:ARG80 4.9 47.3 1.0 CA A:LEU194 4.9 17.4 1.0 CD A:ARG80 4.9 36.8 1.0 CG A:LEU194 4.9 18.7 1.0 HA A:HIS81 5.0 22.4 1.0

Sodium binding site 2 out of 3 in the Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:63.4 occ:1.00 O A:HOH646 2.5 46.9 1.0 HD22 A:ASN164 2.6 45.3 1.0 O A:HOH652 3.1 45.3 1.0 ND2 A:ASN164 3.1 37.8 1.0 HD21 A:ASN164 3.3 45.3 1.0 HD1 A:TYR182 3.5 45.5 1.0 HB2 A:TYR182 3.6 30.2 1.0 CD1 A:TYR182 4.1 37.9 1.0 CG A:ASN164 4.2 38.9 1.0 CB A:TYR182 4.4 25.2 1.0 CG A:TYR182 4.6 35.2 1.0 OD1 A:ASN164 4.6 41.8 1.0 O A:HOH731 4.7 38.5 1.0 O A:HOH653 4.9 47.4 1.0 CE1 A:TYR182 4.9 32.1 1.0 HE1 A:TYR182 4.9 38.5 1.0 O A:HOH403 4.9 48.7 1.0 HA A:TYR182 5.0 27.0 1.0 HB3 A:TYR182 5.0 30.2 1.0

Sodium binding site 3 out of 3 in the Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Superfolder Green Fluorescent Protein with Meta-Nitro-Tyrosine Incorporated at Position 66 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:59.6 occ:1.00 OD1 A:ASN212 3.3 39.6 1.0 O A:HOH414 3.3 52.8 1.0 O A:HOH451 3.4 47.8 1.0 HB2 A:PRO211 3.5 44.4 1.0 HG2 A:PRO211 3.8 48.8 1.0 HD21 A:ASN212 4.0 50.7 1.0 CG A:ASN212 4.2 43.9 1.0 CB A:PRO211 4.4 37.0 1.0 ND2 A:ASN212 4.5 42.3 1.0 CG A:PRO211 4.6 40.7 1.0 HB3 A:PRO211 4.9 44.4 1.0

D.P.Broughton, C.G.Holod, A.Camilo-Contreras, D.R.Harris, S.H.Brewer, C.M.Phillips-Piro. Modulating the pH Dependent Photophysical Properties of Green Fluorescent Protein Rsc Adv 2024.
ISSN: ESSN 2046-2069
DOI: 10.1039/D4RA05058D