Sodium in PDB 7yzn: Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp

The structure of Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp, PDB code: 7yzn was solved by G.Bourgeois, E.Schmitt, Y.Mechulam, P.D.Coureux, R.Kazan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.26, 72.26, 205.82, 90, 90, 90
R / Rfree (%)	16.9 / 19.6

The structure of Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp (pdb code 7yzn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp, PDB code: 7yzn:

Sodium binding site 1 out of 1 in the Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of C-Terminally Truncated AIF5B From Pyrococcus Abyssi Complexed with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:31.7 occ:1.00 OD1 A:ASP17 2.7 26.7 1.0 O A:GLY39 2.8 24.2 1.0 HA A:ILE40 2.9 25.3 1.0 O3G A:GTP502 2.9 21.2 1.0 O1A A:GTP502 2.9 19.0 1.0 O3B A:GTP502 3.0 17.0 1.0 H5'' A:GTP502 3.2 22.4 1.0 HG22 A:ILE40 3.2 28.6 1.0 HA A:ASP17 3.4 24.4 1.0 PG A:GTP502 3.5 18.4 1.0 O A:HOH675 3.7 17.6 1.0 O A:HOH692 3.7 24.5 1.0 CA A:ILE40 3.8 21.1 1.0 C A:GLY39 3.8 22.5 1.0 O3A A:GTP502 3.8 18.2 1.0 O A:HOH823 3.8 44.2 1.0 H A:ASP17 3.9 22.7 1.0 CG A:ASP17 3.9 29.6 1.0 PA A:GTP502 3.9 18.7 1.0 O A:HOH875 4.0 36.5 1.0 CG2 A:ILE40 4.0 23.9 1.0 HG23 A:ILE40 4.1 28.6 1.0 C5' A:GTP502 4.1 18.6 1.0 PB A:GTP502 4.1 17.5 1.0 H5' A:GTP502 4.1 22.4 1.0 HG22 A:VAL16 4.2 27.1 1.0 CA A:ASP17 4.2 20.4 1.0 H A:THR41 4.2 22.7 1.0 N A:ILE40 4.2 22.2 1.0 O A:HOH626 4.3 26.9 1.0 N A:ASP17 4.3 18.9 1.0 O1G A:GTP502 4.4 17.7 1.0 CB A:ILE40 4.4 23.1 1.0 O5' A:GTP502 4.5 17.4 1.0 HG23 A:VAL16 4.6 27.1 1.0 CB A:ASP17 4.6 23.6 1.0 O2G A:GTP502 4.6 20.2 1.0 HB A:ILE40 4.7 27.7 1.0 O1B A:GTP502 4.7 15.9 1.0 N A:THR41 4.8 18.9 1.0 HG21 A:ILE40 4.8 28.6 1.0 C A:ILE40 4.8 23.2 1.0 CG2 A:VAL16 4.8 22.6 1.0 OD2 A:ASP17 4.9 33.4 1.0 OE1 A:GLU36 4.9 27.2 1.0 HB3 A:ASP17 4.9 28.3 1.0 MG A:MG501 5.0 19.1 1.0

R.Kazan, G.Bourgeois, C.Lazennec-Schurdevin, E.Larquet, Y.Mechulam, P.D.Coureux, E.Schmitt. Role of AIF5B in Archaeal Translation Initiation. Nucleic Acids Res. V. 50 6532 2022.
ISSN: ESSN 1362-4962
PubMed: 35694843
DOI: 10.1093/NAR/GKAC490