Sodium in PDB 8fr5: Crystal Structure of the Human Smacovirus 1 Rep Domain

The structure of Crystal Structure of the Human Smacovirus 1 Rep Domain, PDB code: 8fr5 was solved by L.K.Limon, K.Shi, A.Dao, J.Rugloski, K.J.Tompkins, H.Aihara, W.R.Gordon, R.L.Evans Iiii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.16, 49.37, 31.38, 90, 110.3, 90
R / Rfree (%)	18.7 / 22.4

The structure of Crystal Structure of the Human Smacovirus 1 Rep Domain also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Human Smacovirus 1 Rep Domain (pdb code 8fr5). 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 the Human Smacovirus 1 Rep Domain, PDB code: 8fr5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Human Smacovirus 1 Rep Domain


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 the Human Smacovirus 1 Rep Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:31.7 occ:1.00 OD2 A:ASP97 2.6 28.6 1.0 O A:TRP92 2.7 25.0 1.0 NZ A:LYS94 2.8 25.9 1.0 CB A:CYS90 3.5 20.5 1.0 CG A:LYS94 3.5 21.7 1.0 CG A:ASP97 3.7 30.1 1.0 O A:CYS90 3.8 24.3 1.0 C A:TRP92 3.9 22.9 1.0 CE A:LYS94 3.9 24.9 1.0 N A:LYS94 3.9 21.4 1.0 OD1 A:ASP97 4.1 33.1 1.0 CD A:LYS94 4.2 23.3 1.0 CA A:CYS90 4.2 21.3 1.0 C A:CYS90 4.3 22.5 1.0 CB A:LYS94 4.3 21.0 1.0 N A:CYS90 4.3 21.6 1.0 CA A:ILE93 4.3 22.3 1.0 SG A:CYS90 4.3 22.8 1.0 C A:ILE93 4.5 21.8 1.0 N A:ILE93 4.5 22.5 1.0 O A:HOH222 4.6 37.2 1.0 CA A:LYS94 4.8 21.1 1.0 N A:TRP92 4.9 22.9 1.0 CD1 A:TRP92 5.0 22.8 1.0 CB A:ASP97 5.0 28.4 1.0 CA A:TRP92 5.0 22.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human Smacovirus 1 Rep Domain


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 the Human Smacovirus 1 Rep Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:32.2 occ:1.00 O A:VAL82 2.7 22.1 1.0 O A:HOH235 3.1 26.4 1.0 CE A:LYS94 3.5 24.9 1.0 C A:VAL82 3.8 20.8 1.0 CB A:VAL82 3.8 21.3 1.0 O A:HOH222 3.9 37.2 1.0 CG2 A:VAL82 4.0 21.0 1.0 NZ A:LYS94 4.2 25.9 1.0 CD2 A:PHE88 4.2 23.5 1.0 CD A:LYS94 4.2 23.3 1.0 CA A:VAL82 4.3 20.9 1.0 CB A:PHE88 4.5 22.1 1.0 CG A:PHE88 4.8 22.4 1.0 N A:LEU83 4.8 22.2 1.0 SG A:CYS90 4.9 22.8 1.0

L.K.Limon, K.Shi, A.Dao, J.Rugloski, K.J.Tompkins, H.Aihara, W.R.Gordon, R.L.Evans 3Rd. The Crystal Structure of the Human Smacovirus 1 Rep Domain. Acta Crystallogr.,Sect.F V. 79 295 2023.
ISSN: ESSN 2053-230X
PubMed: 38051309
DOI: 10.1107/S2053230X23009536