Sodium in PDB 5dpg: Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine

The structure of Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine, PDB code: 5dpg was solved by A.B.Dippel, G.M.Olenginski, N.Maurici, M.T.Liskov, S.H.Brewer, C.M.Phillips-Piro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.33 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.774, 68.057, 53.268, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 19.2

The binding sites of Sodium atom in the Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine (pdb code 5dpg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine, PDB code: 5dpg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:27.8 occ:1.00 H A:ASN149 2.5 25.0 1.0 HA A:HIS148 2.8 19.5 1.0 HH21 A:ARG168 3.2 43.8 1.0 O A:HOH502 3.3 27.3 1.0 N A:ASN149 3.3 20.8 1.0 O A:HOH424 3.3 36.7 1.0 O A:HOH471 3.3 37.3 1.0 HD2 A:HIS148 3.5 31.8 1.0 HB3 A:HIS148 3.5 25.8 1.0 CA A:HIS148 3.6 16.2 1.0 HB2 A:ASN149 3.8 23.6 1.0 C A:HIS148 3.9 24.7 1.0 CB A:HIS148 4.0 21.5 1.0 NH2 A:ARG168 4.0 36.5 1.0 HE A:ARG168 4.2 51.5 1.0 CD2 A:HIS148 4.2 26.5 1.0 CA A:ASN149 4.3 17.7 1.0 HH A:TYR151 4.4 34.7 1.0 O A:ASN149 4.4 23.6 1.0 HH22 A:ARG168 4.4 43.8 1.0 CB A:ASN149 4.4 19.7 1.0 HD22 A:ASN149 4.4 37.9 1.0 O A:SER147 4.4 19.5 1.0 CG A:HIS148 4.4 24.4 1.0 O A:LYS166 4.6 26.1 1.0 HE2 A:TYR151 4.6 34.0 1.0 ND2 A:ASN149 4.6 31.6 1.0 CG A:ASN149 4.7 28.4 1.0 N A:HIS148 4.8 18.6 1.0 NE A:ARG168 4.8 42.9 1.0 C A:ASN149 4.9 20.2 1.0 HB2 A:HIS148 4.9 25.8 1.0 CZ A:ARG168 4.9 40.5 1.0 O A:HOH573 4.9 33.1 1.0

Sodium binding site 2 out of 2 in the Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sfgfp Mutant - 133 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:39.5 occ:1.00 HE A:ARG73 1.9 32.1 0.5 OG1 A:THR225 2.5 34.1 0.5 NE A:ARG73 2.7 26.7 0.5 HG1 A:THR225 2.8 40.9 0.5 O A:ASN39 2.9 21.0 1.0 HH11 A:ARG73 2.9 35.4 0.5 HB A:THR225 3.0 32.1 0.5 HB3 A:ARG73 3.1 28.9 0.5 HA3 A:GLY40 3.2 21.1 1.0 HB3 A:ARG73 3.2 28.9 0.5 HD3 A:ARG73 3.5 35.9 0.5 NH1 A:ARG73 3.5 29.5 0.5 HG1 A:THR225 3.5 48.5 0.5 CZ A:ARG73 3.6 28.1 0.5 C A:ASN39 3.6 23.2 1.0 CD A:ARG73 3.6 29.9 0.5 HB2 A:ARG73 3.8 28.9 0.5 CB A:ARG73 3.8 24.1 0.5 CB A:THR225 3.8 26.8 0.5 HB2 A:ARG73 3.9 28.9 0.5 CB A:THR225 3.9 26.8 0.5 OG1 A:THR225 3.9 40.4 0.5 HG2 A:ARG73 3.9 31.3 0.5 CB A:ARG73 3.9 24.1 0.5 HD1 A:PHE223 4.0 24.2 1.0 HG23 A:THR225 4.0 32.5 0.5 CA A:GLY40 4.0 17.6 1.0 O A:VAL224 4.0 18.7 1.0 N A:GLY40 4.1 22.7 1.0 HG21 A:THR225 4.1 32.5 0.5 CG A:ARG73 4.2 27.8 0.5 HB3 A:PHE223 4.2 26.8 1.0 CG2 A:THR225 4.2 27.0 0.5 HG2 A:ARG73 4.3 33.4 0.5 HA A:ASN39 4.3 22.7 1.0 HH12 A:ARG73 4.3 35.4 0.5 CG A:ARG73 4.4 26.1 0.5 HA A:THR225 4.4 25.1 0.5 HD2 A:ARG73 4.5 35.9 0.5 HB A:THR225 4.5 32.2 0.5 C A:VAL224 4.5 22.7 1.0 H A:VAL224 4.5 22.7 1.0 CA A:ASN39 4.6 18.9 1.0 CA A:THR225 4.6 20.9 0.5 CA A:THR225 4.6 20.9 0.5 C A:GLY40 4.6 19.2 1.0 H A:ARG73 4.7 30.2 0.5 O A:HOH422 4.7 27.5 1.0 CD1 A:PHE223 4.7 20.2 1.0 H A:ARG73 4.7 30.2 0.5 HG3 A:ARG73 4.7 31.3 0.5 HA2 A:GLY40 4.7 21.1 1.0 H A:GLY40 4.8 27.2 1.0 O A:GLY40 4.8 24.7 1.0 HG21 A:THR225 4.8 29.6 0.5 NH2 A:ARG73 4.8 41.2 0.5 N A:THR225 4.8 18.8 1.0 CG2 A:THR225 4.9 24.7 0.5 N A:VAL224 5.0 18.9 1.0

A.B.Dippel, G.M.Olenginski, N.Maurici, M.T.Liskov, S.H.Brewer, C.M.Phillips-Piro. Probing the Effectiveness of Spectroscopic Reporter Unnatural Amino Acids: A Structural Study. Acta Crystallogr D Struct V. 72 121 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894540
DOI: 10.1107/S2059798315022858