Potassium in PDB 5dar: Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii, PDB code: 5dar was solved by A.G.Gabdulkhakov, I.V.Mitroshin, M.B.Garber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.396, 88.451, 95.231, 90.00, 102.19, 90.00
R / Rfree (%)	26.4 / 29.7

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Potassium atom in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii (pdb code 5dar). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii, PDB code: 5dar:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:K1307 b:18.1 occ:1.00 OP2 A:G1173 2.7 10.8 1.0 O3' A:U1171 3.0 11.4 1.0 OP1 A:A1180 3.0 14.4 1.0 OP1 A:G1172 3.3 11.8 1.0 P A:G1172 3.5 11.5 1.0 O5' A:G1172 3.6 11.1 1.0 P A:G1173 4.1 11.0 1.0 O5' A:A1180 4.1 13.1 1.0 O2' A:U1171 4.2 11.6 1.0 P A:A1180 4.2 13.6 1.0 C3' A:U1171 4.3 11.6 1.0 O A:HOH1401 4.3 30.0 1.0 C5' A:G1172 4.4 10.6 1.0 C5' A:A1180 4.5 12.5 1.0 C2' A:U1171 4.5 11.8 1.0 C1' A:U1171 4.6 12.1 1.0 C4' A:A1180 4.6 12.2 1.0 C3' A:G1172 4.6 10.1 1.0 O3' A:G1172 4.7 10.3 1.0 O4' A:A1180 4.8 12.4 1.0 OP1 A:G1173 4.9 10.9 1.0 N7 A:G1173 4.9 11.9 1.0 O2 A:U1171 5.0 13.4 1.0 OP2 A:G1172 5.0 11.5 1.0

Potassium binding site 2 out of 5 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:K1308 b:30.0 occ:1.00 OD1 B:ASN61 2.2 14.7 1.0 CE B:MET58 2.3 19.2 1.0 N B:ALA91 2.9 16.4 1.0 O B:ALA91 3.1 17.9 1.0 O3' A:C1216 3.2 11.2 1.0 CG B:ASN61 3.3 14.7 1.0 O B:SER59 3.3 14.2 1.0 O2' A:C1216 3.6 9.6 1.0 O B:ARG89 3.6 16.9 1.0 CA B:GLY90 3.8 16.9 1.0 C B:GLY90 3.8 16.7 1.0 CA B:ALA91 3.8 16.3 1.0 ND2 B:ASN61 3.8 14.9 1.0 C B:ALA91 3.8 16.7 1.0 OP1 A:G1217 3.9 12.1 1.0 CB B:ALA91 4.0 16.0 1.0 SD B:MET58 4.1 20.2 1.0 C3' A:C1216 4.1 10.2 1.0 N B:ASN61 4.1 14.2 1.0 C B:SER59 4.2 13.6 1.0 P A:G1217 4.2 11.9 1.0 C4' A:C1216 4.2 9.8 1.0 C5' A:G1217 4.3 14.5 1.0 C2' A:C1216 4.4 9.8 1.0 CA B:ARG60 4.5 14.4 1.0 CB B:ASN61 4.5 15.1 1.0 CG B:MET58 4.5 18.8 1.0 C B:ARG60 4.5 14.2 1.0 C B:ARG89 4.6 17.3 1.0 CA B:ASN61 4.7 14.8 1.0 N B:GLY90 4.7 17.4 1.0 N B:ARG60 4.7 13.8 1.0 O5' A:G1217 4.7 13.3 1.0 N B:SER59 4.8 14.0 1.0 O B:GLY90 4.9 16.8 1.0

Potassium binding site 3 out of 5 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:K201 b:23.2 occ:1.00 O C:LYS110 2.7 19.4 1.0 O C:MET113 2.8 17.3 1.0 O C:SER115 3.3 17.3 1.0 C C:LYS110 3.8 21.1 1.0 C C:SER115 3.9 18.3 1.0 C C:MET113 3.9 17.0 1.0 CA C:TYR116 4.2 22.4 1.0 N C:TYR116 4.3 21.0 1.0 C C:LEU114 4.3 15.3 1.0 OD2 B:ASP48 4.3 25.6 1.0 N C:SER115 4.4 16.4 1.0 CA C:LEU114 4.4 15.1 1.0 CA C:ASP111 4.4 23.8 1.0 O C:ASP111 4.6 22.0 1.0 N C:LEU114 4.6 15.4 1.0 N C:ASP111 4.6 22.0 1.0 CG C:LYS110 4.6 20.8 1.0 O C:LEU114 4.7 14.8 1.0 C C:ASP111 4.7 22.5 1.0 CD C:LYS110 4.8 21.1 1.0 CA C:SER115 4.8 17.2 1.0 CA C:LYS110 4.8 21.2 1.0 CA C:MET113 4.8 18.6 1.0 CB C:MET113 4.9 18.8 1.0 CB C:TYR116 5.0 24.1 1.0 CB C:LYS110 5.0 20.9 1.0

Potassium binding site 4 out of 5 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:K1304 b:11.8 occ:1.00 OP2 D:A1180 2.8 14.6 1.0 O2' D:A1179 2.9 16.4 1.0 O3' D:A1179 3.1 15.7 1.0 OP1 D:C1182 3.3 11.8 1.0 OP2 D:A1183 3.4 13.4 1.0 P D:A1180 3.5 15.5 1.0 OP1 D:A1183 3.6 14.3 1.0 OP2 D:C1182 3.6 11.5 1.0 P D:C1182 3.6 11.5 1.0 O5' D:C1182 3.7 11.9 1.0 C2' D:A1179 3.7 15.9 1.0 C1' D:A1179 3.9 15.4 1.0 P D:A1183 4.0 13.6 1.0 C3' D:A1179 4.0 15.6 1.0 C5' D:A1180 4.1 14.5 1.0 N7 D:A1183 4.1 12.1 1.0 C5' D:C1182 4.3 12.6 1.0 O5' D:A1180 4.4 14.7 1.0 MG D:MG1302 4.4 17.3 1.0 N3 D:A1179 4.4 13.1 1.0 OP1 D:C1207 4.5 17.4 1.0 C8 D:A1183 4.6 12.0 1.0 O6 D:G1184 4.6 11.5 1.0 N9 D:A1179 4.7 14.6 1.0 O4' D:A1179 4.9 15.6 1.0 C4 D:A1179 4.9 13.9 1.0 OP1 D:A1180 4.9 15.2 1.0 O5' D:A1183 4.9 13.3 1.0 C4' D:A1179 4.9 15.2 1.0 N7 D:G1184 5.0 11.7 1.0

Potassium binding site 5 out of 5 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ F:K202 b:49.8 occ:1.00 O F:SER115 2.8 34.3 1.0 O F:MET113 3.1 30.2 1.0 O F:LEU114 3.4 27.2 1.0 OD2 E:ASP48 3.7 36.1 1.0 C F:LEU114 3.8 27.2 1.0 O F:LYS110 3.8 32.5 1.0 C F:SER115 3.8 34.7 1.0 C F:MET113 4.0 30.0 1.0 CA F:LEU114 4.2 26.2 1.0 N F:SER115 4.3 29.5 1.0 N F:LEU114 4.5 27.9 1.0 CA F:TYR116 4.6 43.6 1.0 N F:TYR116 4.6 40.6 1.0 O F:ASP111 4.7 37.1 1.0 CA F:SER115 4.7 31.1 1.0 CG E:ASP48 4.8 33.4 1.0 C F:LYS110 4.9 35.0 1.0 CA F:ASP111 4.9 37.6 1.0 C F:ASP111 4.9 38.4 1.0 CA F:MET113 5.0 32.3 1.0

A.G.Gabdulkhakov, I.V.Mitroshin, M.B.Garber. Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii To Be Published.