Sodium in PDB 4uqo: Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp

The structure of Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp, PDB code: 4uqo was solved by M.E.Marsh, M.T.Ehebauer, D.Scott, C.Abell, T.L.Blundell, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.32 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.308, 87.130, 62.322, 90.00, 90.55, 90.00
R / Rfree (%)	17.124 / 23.14

The structure of Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp (pdb code 4uqo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp, PDB code: 4uqo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1352 b:38.8 occ:1.00 O A:HOH2260 3.1 29.1 1.0 N A:ARG112 3.3 17.1 1.0 CD2 A:LEU164 3.4 14.0 1.0 O A:HOH2006 3.6 35.9 1.0 CA A:GLY111 3.6 17.0 1.0 O A:ARG112 3.8 19.5 1.0 C A:GLY111 4.0 17.3 1.0 CA A:ARG112 4.2 16.9 1.0 C A:ARG112 4.4 17.3 1.0 CB A:ARG112 4.5 19.4 1.0 CG A:LEU164 4.7 13.7 1.0 O A:ILE110 4.7 22.2 1.0 O A:GLY163 4.8 11.0 1.0 N A:GLY111 4.9 18.3 1.0

Sodium binding site 2 out of 3 in the Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1352 b:22.8 occ:1.00 OD2 B:ASP267 2.7 14.4 1.0 CD2 B:HIS264 3.0 15.3 1.0 O B:MET212 3.2 14.2 1.0 CA B:MET212 3.4 16.1 1.0 CB B:MET212 3.6 17.3 1.0 CG B:ASP267 3.6 14.9 1.0 CB B:VAL215 3.6 17.9 1.0 CB B:ASP267 3.7 14.5 1.0 C B:MET212 3.7 16.9 1.0 CA B:HIS264 3.8 15.0 1.0 CG2 B:VAL215 3.8 16.9 1.0 CG B:MET212 3.9 19.5 1.0 CG B:HIS264 3.9 16.3 1.0 NE2 B:HIS264 4.0 17.4 1.0 CG1 B:VAL215 4.1 17.9 1.0 CE B:MET212 4.2 21.2 1.0 O B:HIS264 4.2 13.6 1.0 CB B:HIS264 4.2 15.1 1.0 OE1 B:GLN216 4.2 54.1 1.0 C B:HIS264 4.5 13.9 1.0 NZ B:LYS263 4.5 32.9 1.0 N B:MET212 4.7 13.9 1.0 N B:HIS264 4.7 13.9 1.0 OD1 B:ASP267 4.8 14.3 1.0 O B:GLN211 4.8 12.4 1.0 CA B:VAL215 4.9 18.1 1.0 CD B:GLN216 4.9 42.6 1.0 O B:LYS263 5.0 12.6 1.0 SD B:MET212 5.0 22.5 1.0

Sodium binding site 3 out of 3 in the Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Bound to Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1353 b:44.4 occ:1.00 N B:LYS319 3.4 26.0 1.0 NH1 B:ARG316 3.6 30.3 1.0 CA B:GLY318 3.7 24.0 1.0 CG B:LYS319 3.9 41.0 1.0 C B:GLY318 4.0 24.2 1.0 NH2 B:ARG316 4.1 29.5 1.0 CD1 B:ILE324 4.2 24.9 1.0 CB B:LYS319 4.2 33.4 1.0 CZ B:ARG316 4.4 27.6 1.0 CA B:LYS319 4.4 26.4 1.0 CD B:LYS319 4.6 47.0 1.0

M.E.Marsh, M.T.Ehebauer, D.Scott, C.Abell, T.L.Blundell, M.Hyvonen. Pyrococcus Furiosus Rada Atp-Half Site Binds Nucleotides To Be Published.