Sodium in PDB 7f4x: Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp

The structure of Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp, PDB code: 7f4x was solved by T.Yokoyama, A.Ostermann, T.E.Schrader, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.677, 64.618, 145.593, 90, 90, 90
R / Rfree (%)	18.4 / 22.2

The structure of Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp (pdb code 7f4x). 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 Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp, PDB code: 7f4x:

Sodium binding site 1 out of 1 in the Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Joint Neutron and X-Ray Crystal Structure of the Nucleotide-Binding Domain of HSP72 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:19.9 occ:1.00 O A:HOH547 2.3 19.9 1.0 O2B A:ADP401 2.4 18.1 1.0 O A:TYR15 2.4 17.8 1.0 OD2 A:ASP10 2.5 18.9 1.0 D2 A:HOH547 2.7 23.2 1.0 O A:HOH535 2.9 22.7 1.0 D2 A:HOH535 2.9 23.4 1.0 D2 A:HOH523 3.0 19.1 1.0 D1 A:HOH547 3.0 19.6 1.0 HA3 A:GLY12 3.1 16.6 1.0 CG A:ASP10 3.3 19.6 1.0 PB A:ADP401 3.3 16.8 1.0 O3A A:ADP401 3.4 16.9 1.0 C A:TYR15 3.5 18.7 1.0 MG A:MG402 3.5 18.1 1.0 OD1 A:ASP10 3.5 18.0 1.0 D1 A:HOH535 3.6 21.1 1.0 O A:HOH523 3.7 19.9 1.0 O1B A:ADP401 3.7 17.5 1.0 HB2 A:TYR15 3.8 19.1 1.0 HA A:SER16 3.8 18.1 1.0 D2 A:HOH538 3.8 19.8 1.0 PA A:ADP401 3.9 16.9 1.0 O1A A:ADP401 3.9 18.5 1.0 H A:TYR15 4.0 20.0 0.2 D A:TYR15 4.0 20.0 0.8 CA A:GLY12 4.0 17.2 1.0 O2A A:ADP401 4.0 19.3 1.0 HA2 A:GLY12 4.2 17.8 1.0 HB3 A:TYR15 4.3 17.6 1.0 D2 A:HOH517 4.3 22.9 1.0 CB A:TYR15 4.3 18.0 1.0 D1 A:HOH538 4.4 20.2 1.0 N A:SER16 4.4 16.2 1.0 CA A:TYR15 4.4 17.1 1.0 D A:GLY12 4.4 20.8 0.6 H A:GLY12 4.4 20.8 0.4 CA A:SER16 4.5 15.8 1.0 O A:HOH538 4.5 18.2 1.0 D1 A:HOH523 4.5 25.8 1.0 N A:GLY12 4.5 17.6 1.0 HB3 A:ASP10 4.5 17.6 1.0 O A:ASP366 4.5 18.9 1.0 O A:HOH517 4.6 20.1 1.0 D2 A:HOH578 4.6 29.8 1.0 N A:TYR15 4.6 16.4 1.0 CB A:ASP10 4.6 15.2 1.0 HB2 A:CYS17 4.6 17.9 1.0 O3B A:ADP401 4.6 20.5 1.0 D1 A:HOH550 4.9 21.7 1.0 C A:SER16 4.9 18.7 1.0 O A:ASP10 4.9 16.0 1.0 O A:HOH550 5.0 20.1 1.0 D2 A:HOH551 5.0 23.8 1.0 HB3 A:CYS17 5.0 17.5 1.0

T.Yokoyama, S.Fujii, A.Ostermann, T.E.Schrader, Y.Nabeshima, M.Mizuguchi. Neutron Crystallographic Analysis of the Nucleotide-Binding Domain of HSP72 in Complex with Adp. Iucrj V. 9 562 2022.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252522006297