Sodium in PDB 8old: Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains

The structure of Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains, PDB code: 8old was solved by E.N.Manakova, M.Zaremba, S.Grazulis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.033, 57.843, 61.622, 73.94, 89.56, 89.75
R / Rfree (%)	17.9 / 21.8

The structure of Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains also contains other interesting chemical elements:

Arsenic	(As)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains (pdb code 8old). 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 Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains, PDB code: 8old:

Sodium binding site 1 out of 1 in the Crystal Structure of Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains


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 Archaeoglobus Fulgidus Afago-N Protein Representing N-L1-L2 Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:34.1 occ:1.00 OD1 B:ASN30 2.4 29.3 1.0 O B:TYR31 2.4 26.7 1.0 O B:HOH433 2.5 26.7 1.0 O B:HOH500 2.6 38.0 1.0 O B:HOH408 2.7 50.2 1.0 O C:HOH408 2.7 39.1 1.0 CG B:ASN30 3.3 24.6 1.0 C B:TYR31 3.3 24.2 1.0 ND2 B:ASN30 3.5 29.0 1.0 O B:HOH480 3.9 46.0 1.0 N B:TYR31 3.9 22.9 1.0 N B:PRO32 4.0 25.1 1.0 CA B:PRO32 4.1 26.5 1.0 CA B:TYR31 4.2 27.2 1.0 OE1 C:GLU231 4.3 44.8 1.0 N B:GLU33 4.3 28.1 1.0 O B:HOH495 4.5 43.8 1.0 C B:PRO32 4.6 28.2 1.0 CB B:ASN30 4.6 24.9 1.0 O B:GLU231 4.7 25.2 1.0 C B:ASN30 4.8 24.3 1.0 OE2 B:GLU33 4.8 71.0 1.0 OE2 C:GLU231 4.9 67.8 1.0 O B:HOH485 4.9 35.5 1.0 CA B:ASN30 4.9 24.4 1.0 CD C:GLU231 4.9 52.8 1.0 O C:HOH464 5.0 48.6 1.0

E.Manakova, E.Golovinas, R.Poceviciute, G.Sasnauskas, A.Silanskas, D.Rutkauskas, M.Jankunec, E.Zagorskaite, E.Jurgelaitis, A.Grybauskas, C.Venclovas, M.Zaremba. The Missing Part: the Archaeoglobus Fulgidus Argonaute Forms A Functional Heterodimer with An N-L1-L2 Domain Protein. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38197228
DOI: 10.1093/NAR/GKAD1241