Sodium in PDB 8om0: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B, PDB code: 8om0 was solved by I.Silvestri, M.Marcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.35 / 3.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.813, 94.282, 223.875, 90, 90, 90
R / Rfree (%)	23.8 / 29.6

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B also contains other interesting chemical elements:

Magnesium

(Mg)

10 atoms

The binding sites of Sodium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B (pdb code 8om0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B, PDB code: 8om0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:172.8 occ:1.00 OP2 A:G320 2.2 174.9 1.0 OP2 A:A319 2.7 200.2 1.0 OP1 A:A319 3.3 211.1 1.0 P A:A319 3.4 203.7 1.0 P A:G320 3.6 185.0 1.0 O5' A:A319 3.8 202.1 1.0 N7 A:G320 4.0 193.2 1.0 O6 A:G320 4.0 180.8 1.0 C3' A:A319 4.1 184.6 1.0 OP1 A:G320 4.2 196.4 1.0 C5 A:G320 4.4 186.6 1.0 C6 A:G320 4.4 182.4 1.0 O3' A:A319 4.5 170.6 1.0 C5' A:A319 4.6 205.5 1.0 O5' A:G320 4.6 195.8 1.0 C8 A:G320 4.8 196.6 1.0 C8 A:A319 4.9 211.8 1.0 O3' A:A318 4.9 188.3 1.0 C4' A:A319 5.0 186.8 1.0

Sodium binding site 2 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:164.2 occ:1.00 O6 A:G14 3.7 192.8 1.0 O6 A:G15 3.8 178.3 1.0 OP2 A:U13 4.0 211.8 1.0 N7 A:G14 4.0 195.2 1.0 O4 A:U256 4.3 223.2 1.0 C6 A:G14 4.3 192.8 1.0 C5 A:G14 4.5 193.3 1.0 O4 A:U255 4.5 228.4 1.0 N7 A:G15 4.6 215.4 1.0 C2' A:A12 4.6 165.4 1.0 C6 A:G15 4.7 193.3 1.0 O2' A:A12 4.8 150.1 1.0 C3' A:A12 4.9 169.6 1.0

Sodium binding site 3 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:163.0 occ:1.00 O6 A:G194 2.7 190.0 1.0 N7 A:G194 3.5 200.2 1.0 C6 A:G194 3.6 189.7 1.0 C5 A:G194 3.9 189.7 1.0 O4 A:U195 4.0 193.0 1.0 N7 A:A193 4.3 192.6 1.0 N6 A:A193 4.4 180.3 1.0 C4 A:U195 4.7 169.2 1.0 C5 A:U195 4.7 172.1 1.0 C8 A:G194 4.7 204.5 1.0 N1 A:G194 4.9 187.2 1.0 C5 A:A193 4.9 178.7 1.0 C6 A:A193 4.9 174.0 1.0

Sodium binding site 4 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:159.3 occ:1.00 OP2 A:G269 2.0 195.0 1.0 O6 A:G270 2.8 206.2 1.0 P A:G269 3.3 237.9 1.0 OP2 A:A268 3.7 202.9 1.0 O5' A:A268 3.8 224.2 1.0 O5' A:G269 3.9 226.7 1.0 C6 A:G270 3.9 213.7 1.0 OP1 A:G269 3.9 241.9 1.0 O4 A:U271 4.1 218.3 1.0 P A:A268 4.2 208.6 1.0 N7 A:G270 4.3 217.0 1.0 OP1 A:A268 4.4 211.9 1.0 C5 A:G270 4.5 219.8 1.0 O3' A:A268 4.5 242.7 1.0 N7 A:G269 4.5 210.1 1.0 C8 A:G269 4.7 220.9 1.0 C3' A:A268 4.8 227.8 1.0 C5' A:A268 4.9 227.9 1.0 C4 A:U271 4.9 213.9 1.0 N2 A:G284 4.9 170.1 1.0

Sodium binding site 5 out of 5 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:264.9 occ:1.00 O4 A:U332 3.4 264.9 1.0 O2' A:A348 3.7 216.6 1.0 N7 A:G331 4.0 231.4 1.0 O6 A:G331 4.0 262.7 1.0 C2' A:A348 4.0 226.8 1.0 C8 A:A348 4.1 229.4 1.0 C4 A:U332 4.4 254.2 1.0 N7 A:A348 4.6 226.1 1.0 C5 A:G331 4.6 230.3 1.0 C6 A:G331 4.6 247.6 1.0 N9 A:A348 4.7 240.6 1.0 C5 A:U332 4.8 244.8 1.0 OP2 A:A348 4.9 232.1 1.0 C1' A:A348 5.0 237.1 1.0 C8 A:G331 5.0 223.6 1.0

I.Silvestri, J.Manigrasso, A.Andreani, N.Brindani, C.Mas, J.B.Reiser, P.Vidossich, G.Martino, A.Mccarthy, M.De Vivo, M.Marcia. Targeting the Conserved Active Site of Splicing Machines with Specific and Selective Small Molecule Modulators Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48697-0