Sodium in PDB 5d8h: Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton

The structure of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton, PDB code: 5d8h 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)	45.55 / 2.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	125.070, 127.160, 132.930, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.5

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

Magnesium

(Mg)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton (pdb code 5d8h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton, PDB code: 5d8h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


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 Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1311 b:87.1 occ:1.00 O A:HOH1447 2.9 69.1 1.0 O2' A:U1176 3.2 80.4 1.0 O3' A:U1176 3.2 82.6 1.0 N7 A:A1177 3.4 69.8 1.0 C8 A:A1177 3.7 70.9 1.0 OP1 A:A1177 3.9 85.2 1.0 C3' A:U1176 4.1 79.7 1.0 P A:A1177 4.2 95.6 1.0 C2' A:U1176 4.2 79.3 1.0 O6 A:G1178 4.3 70.3 1.0 C4' A:U1176 4.5 80.7 1.0 O5' A:A1177 4.5 84.7 1.0 N7 A:G1178 4.6 65.3 1.0 C5 A:A1177 4.7 64.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


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 Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1312 b:0.5 occ:1.00 OP2 A:U1171 2.8 82.1 1.0 OP2 A:G1169 3.0 76.2 1.0 O3' A:U1170 3.7 83.7 1.0 P A:U1171 3.7 86.3 1.0 OP1 A:G1168 3.8 77.1 1.0 OP2 A:G1168 3.9 77.1 1.0 P A:G1168 4.1 79.8 1.0 P A:G1169 4.2 81.8 1.0 O5' A:G1168 4.2 71.5 1.0 OP1 A:U1171 4.3 80.1 1.0 C3' A:U1170 4.4 83.5 1.0 O2' A:U1170 4.4 81.4 1.0 OP1 A:G1169 4.6 91.5 1.0 O3' A:G1168 4.7 83.6 1.0 C5' A:G1168 4.9 70.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1313 b:84.1 occ:1.00 O A:HOH1401 2.1 71.7 1.0 O3' A:A1179 2.6 87.1 1.0 O5' A:A1180 3.0 80.1 1.0 OP2 A:A1180 3.1 78.3 1.0 P A:A1180 3.1 78.5 1.0 OP1 A:C1182 3.2 70.2 1.0 OP2 A:C1182 3.2 78.7 1.0 C5' A:A1180 3.4 79.3 1.0 MG A:MG1303 3.5 68.2 1.0 OP1 A:A1183 3.5 64.0 1.0 P A:C1182 3.6 80.2 1.0 C3' A:A1179 3.8 83.9 1.0 O2' A:A1179 3.9 76.9 1.0 C1' A:A1179 4.0 81.3 1.0 OP1 A:C1207 4.1 80.8 1.0 C2' A:A1179 4.1 81.0 1.0 O5' A:C1182 4.2 60.6 1.0 O A:HOH1432 4.4 65.1 1.0 C4' A:A1179 4.4 82.9 1.0 O4' A:A1179 4.5 80.4 1.0 OP1 A:A1180 4.6 81.5 1.0 O6 A:G1184 4.7 75.6 1.0 C5' A:C1182 4.7 61.8 1.0 C4' A:A1180 4.8 82.4 1.0 O A:HOH1428 4.8 69.5 1.0 N7 A:A1183 4.9 71.3 1.0 N3 A:A1179 4.9 74.5 1.0 P A:A1183 5.0 77.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Base of the Ribosomal P Stalk From Methanococcus Jannaschii with Antibiotic Thiostrepton within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:86.0 occ:1.00 OD2 B:ASP34 3.3 89.0 1.0 SE B:MSE36 3.5 0.7 1.0 CB B:MSE36 3.7 80.0 1.0 CG B:ARG89 3.8 91.3 1.0 CD B:ARG89 4.0 97.8 1.0 OD2 B:ASP37 4.2 78.3 1.0 CG B:MSE36 4.2 78.2 1.0 CG B:ASP34 4.3 82.1 1.0 CB B:ARG89 4.3 84.4 1.0 NE B:ARG89 4.4 0.8 1.0 OD1 B:ASP34 4.5 76.0 1.0 CA B:MSE36 5.0 80.8 1.0 CG B:ASP37 5.0 78.4 1.0 O B:MSE36 5.0 76.5 1.0

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