Sodium in PDB 8vyd: A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome

The structure of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome, PDB code: 8vyd was solved by P.S.Ho, T.J.Santangelo, K.Fluke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.54 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.67, 97.28, 89.02, 90, 99.64, 90
R / Rfree (%)	23.8 / 28.7

The binding sites of Sodium atom in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome (pdb code 8vyd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome, PDB code: 8vyd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:32.0 occ:1.00 OD1 A:ASP133 2.3 32.8 1.0 O A:HOH453 2.3 24.1 1.0 O A:HOH412 2.5 41.7 1.0 O A:CYS135 2.8 27.4 0.4 O A:CYS135 2.8 27.1 0.6 CG A:ASP133 3.2 28.0 1.0 OD2 A:ASP133 3.4 29.1 1.0 CB A:ASP205 3.6 33.2 1.0 O A:HOH439 3.6 24.8 1.0 C A:CYS135 3.8 27.8 0.4 C A:CYS135 3.8 24.7 0.6 CB A:THR141 3.9 24.6 1.0 N A:CYS135 4.2 24.8 0.4 N A:CYS135 4.2 23.9 0.6 OG1 A:THR141 4.2 31.2 1.0 CG2 A:THR141 4.2 18.6 1.0 NA A:NA303 4.2 43.4 1.0 O A:ILE203 4.4 21.1 1.0 CA A:CYS135 4.4 28.0 0.4 OD2 A:ASP205 4.4 26.6 1.0 CA A:CYS135 4.5 28.4 0.6 CB A:ASP133 4.5 24.5 1.0 CG2 A:ILE203 4.5 17.6 1.0 CG A:ASP205 4.6 33.8 1.0 CB A:CYS135 4.6 28.5 0.4 N A:ASP205 4.6 24.4 1.0 CA A:ASP205 4.7 22.5 1.0 O A:MET136 4.7 26.5 1.0 N A:MET136 4.8 24.5 1.0 CB A:CYS135 4.8 28.5 0.6 N A:THR134 4.9 19.8 1.0 C A:ASP133 4.9 19.8 1.0 CA A:ASP133 4.9 19.4 1.0 O A:ASP205 4.9 30.6 1.0 CA A:MET136 5.0 31.4 1.0

Sodium binding site 2 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:35.3 occ:1.00 O A:HOH404 2.7 33.5 1.0 O A:HOH445 2.8 32.4 1.0 O A:TYR140 3.0 23.4 1.0 CA A:TYR140 3.6 21.6 1.0 C A:TYR140 3.7 28.7 1.0 CG2 A:ILE143 3.8 30.3 1.0 CB A:ILE143 3.8 26.0 1.0 N A:GLU144 3.8 27.5 1.0 CB A:TYR140 3.9 30.6 1.0 CB A:GLU144 4.2 30.8 1.0 NZ A:LYS147 4.3 44.5 1.0 CD1 A:TYR140 4.3 27.6 1.0 CA A:GLU144 4.4 24.8 1.0 CG A:TYR140 4.4 28.2 1.0 C A:ILE143 4.5 25.2 1.0 OE1 A:GLU144 4.5 40.5 1.0 CA A:ILE143 4.7 25.9 1.0 OG1 A:THR116 4.8 37.8 1.0 CD1 A:ILE143 4.9 24.9 1.0 CG1 A:ILE143 4.9 26.8 1.0 N A:TYR140 4.9 23.1 1.0

Sodium binding site 3 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:43.4 occ:1.00 O A:HOH474 2.4 31.6 1.0 O A:HOH439 2.8 24.8 1.0 O A:MET136 3.0 26.5 1.0 N A:THR141 3.2 22.8 1.0 N A:TYR140 3.4 23.1 1.0 OG1 A:THR141 3.4 31.2 1.0 O A:HOH412 3.5 41.7 1.0 O A:HOH455 3.7 38.7 1.0 CB A:THR141 3.8 24.6 1.0 N A:GLY139 4.1 28.9 1.0 CA A:TYR140 4.1 21.6 1.0 C A:GLY139 4.1 20.4 1.0 CA A:THR141 4.1 29.2 1.0 C A:TYR140 4.1 28.7 1.0 C A:MET136 4.1 30.6 1.0 CB A:TYR140 4.1 30.6 1.0 NA A:NA301 4.2 32.0 1.0 CA A:GLY139 4.3 25.1 1.0 O A:CYS135 4.5 27.4 0.4 O A:CYS135 4.6 27.1 0.6 N A:LEU138 4.7 30.6 1.0 N A:ALA142 4.9 23.5 1.0 O A:GLY139 4.9 27.4 1.0 N A:GLY137 4.9 24.0 1.0 CA A:GLY137 4.9 26.8 1.0 CG A:TYR140 5.0 28.2 1.0

Sodium binding site 4 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:46.6 occ:1.00 OD1 A:ASP186 2.3 49.5 1.0 NE2 A:HIS214 2.9 37.6 1.0 CG A:ASP186 3.2 49.5 1.0 N A:ALA187 3.6 33.0 1.0 N A:PHE188 3.6 32.2 1.0 CD2 A:HIS214 3.6 39.0 1.0 OD2 A:ASP186 3.7 53.5 1.0 CB A:PHE188 3.9 37.4 1.0 CD2 A:LEU215 4.0 32.1 1.0 CE1 A:HIS214 4.0 41.0 1.0 O A:HOH421 4.1 37.8 1.0 C A:ASP186 4.1 33.6 1.0 CD1 A:LEU215 4.2 39.4 1.0 O A:HOH418 4.2 43.1 1.0 CA A:ASP186 4.2 37.4 1.0 CB A:ASP186 4.3 40.0 1.0 NZ A:LYS157 4.3 42.7 1.0 CG A:LEU215 4.3 33.2 1.0 CA A:ALA187 4.3 31.0 1.0 CB A:ALA187 4.3 32.3 1.0 CA A:PHE188 4.4 32.4 1.0 C A:ALA187 4.4 33.1 1.0 CD A:LYS157 4.7 53.1 1.0 CG A:HIS214 4.9 33.3 1.0 O A:ASP186 4.9 32.5 1.0 CE A:LYS157 4.9 44.2 1.0 ND1 A:HIS214 5.0 39.2 1.0

Sodium binding site 5 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:60.6 occ:1.00 O A:HOH462 2.3 50.9 1.0 CB A:LYS77 3.7 49.3 1.0 N A:LYS77 4.4 49.7 1.0 CD A:LYS77 4.6 47.0 1.0 CG A:LYS77 4.7 50.0 1.0 CE A:LYS77 4.7 56.8 1.0 CA A:LYS77 4.7 46.3 1.0

Sodium binding site 6 out of 6 in the A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:49.4 occ:1.00 O A:HOH438 2.3 40.9 1.0 OE2 A:GLU129 2.8 33.2 1.0 NH2 A:ARG233 3.7 34.3 1.0 CG A:ARG126 3.7 48.1 1.0 CD A:GLU129 3.8 31.5 1.0 NH1 A:ARG233 3.8 35.2 1.0 CD A:ARG126 3.8 56.3 1.0 CZ A:ARG233 3.9 34.1 1.0 CB A:ARG126 3.9 42.4 1.0 OE1 A:GLU129 4.0 37.7 1.0 O A:MET124 4.3 30.0 1.0 NE A:ARG233 4.8 36.5 1.0 NH1 A:ARG126 4.9 55.8 1.0 N A:ARG126 4.9 39.1 1.0

K.Fluke, N.Dai, R.T.Fuchs, P.S.Ho, H.P.Febvre, V.Talbott, E.J.Wolf, Y.-L.Tsai, L.Elkins, J.Schiltz, R.Czarny, B.Robb, I.R.Correa Jr, T.J.Santangelo. A Novel Synthase Generates M4(2)C to Stabilize the Archaeal Ribosome To Be Published.