Sodium in PDB 8ruk: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850, PDB code: 8ruk 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)	48.55 / 4.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.845, 95.144, 225.535, 90, 90, 90
R / Rfree (%)	19.1 / 24.3

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850 also contains other interesting chemical elements:

Magnesium	(Mg)	10 atoms
Bromine	(Br)	2 atoms

The binding sites of Sodium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850 (pdb code 8ruk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850, PDB code: 8ruk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 ARN25850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:61.8 occ:1.00 OP2 A:G320 2.4 143.3 1.0 N7 A:G320 2.5 126.0 1.0 C8 A:G320 3.4 125.6 1.0 O6 A:G321 3.5 169.0 1.0 C5 A:G320 3.6 118.1 1.0 N7 A:G321 3.6 157.6 1.0 O6 A:G320 3.8 123.8 1.0 P A:G320 3.8 145.1 1.0 C6 A:G320 4.1 116.2 1.0 C6 A:G321 4.1 169.6 1.0 C5 A:G321 4.1 163.2 1.0 O5' A:G320 4.3 130.5 1.0 N9 A:G320 4.6 118.3 1.0 N1 A:A297 4.6 197.8 1.0 C8 A:G321 4.6 157.5 1.0 OP1 A:G320 4.7 151.4 1.0 C4 A:G320 4.7 112.7 1.0 OP1 A:A319 4.7 140.1 1.0 OP2 A:A319 4.8 139.5 1.0 O3' A:A319 5.0 140.8 1.0 C3' A:A319 5.0 143.2 1.0

Sodium binding site 2 out of 4 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 ARN25850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:64.8 occ:1.00 OP2 A:U13 4.4 140.3 1.0 O2' A:A12 4.4 158.3 1.0 O6 A:G15 4.7 159.4 1.0 C2' A:A12 4.9 164.2 1.0

Sodium binding site 3 out of 4 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 ARN25850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:37.9 occ:1.00 OP2 A:G269 2.4 115.8 1.0 P A:G269 3.9 128.2 1.0 O6 A:G270 3.9 139.2 1.0 O5' A:A268 4.0 115.8 1.0 N7 A:G270 4.2 127.3 1.0 C5' A:A268 4.4 118.0 1.0 O5' A:G269 4.5 131.3 1.0 N7 A:G269 4.6 118.9 1.0 OP2 A:A268 4.6 117.4 1.0 O4 A:U271 4.6 125.9 1.0 OP1 A:G269 4.6 126.3 1.0 P A:A268 4.7 114.8 1.0 C6 A:G270 4.7 132.0 1.0 OP1 A:A268 4.8 117.9 1.0 C5 A:G270 4.8 128.4 1.0 C8 A:G269 4.9 119.2 1.0 O3' A:A268 4.9 124.8 1.0

Sodium binding site 4 out of 4 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 ARN25850 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na415 b:53.7 occ:1.00 O A:HOH508 3.7 42.4 1.0 O4 A:U332 3.9 211.9 1.0 O2' A:A348 4.0 176.1 1.0 N7 A:G331 4.2 164.8 1.0 O6 A:G331 4.2 156.1 1.0 C2' A:A348 4.4 176.6 1.0 N7 A:A330 4.5 172.1 1.0 OP2 A:A330 4.7 195.2 1.0 C4 A:U332 4.8 215.7 1.0 C6 A:G331 4.9 156.2 1.0 C5 A:G331 4.9 160.3 1.0 C8 A:A330 5.0 169.2 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