Sodium in PDB 6t3s: Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon

The structure of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3s was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 3.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.890, 95.240, 227.896, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23

The structure of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon also contains other interesting chemical elements:

Magnesium

(Mg)

20 atoms

The binding sites of Sodium atom in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon (pdb code 6t3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na421 b:77.1 occ:1.00 OP2 A:U358 2.4 0.5 1.0 OP1 A:C377 2.8 0.6 1.0 O4 A:U289 3.2 0.9 1.0 O5' A:C377 3.7 0.5 1.0 P A:C377 3.7 0.3 1.0 O6 A:G288 3.8 0.1 1.0 P A:U358 3.8 0.3 1.0 N7 A:G288 3.9 0.4 1.0 O3' A:A376 4.0 95.9 1.0 O4' A:C377 4.1 0.0 1.0 C4 A:U289 4.3 0.1 1.0 OP1 A:U358 4.5 0.7 1.0 O5' A:U358 4.5 0.4 1.0 C6 A:G288 4.5 0.1 1.0 C5' A:C377 4.6 0.8 1.0 C5 A:G288 4.6 0.6 1.0 OP2 A:G359 4.7 0.6 1.0 C6 A:C377 4.7 0.9 1.0 N3 A:U289 4.8 0.9 1.0 O3' A:C357 4.9 0.6 1.0 C4' A:C377 4.9 0.0 1.0

Sodium binding site 2 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na422 b:96.0 occ:1.00 OP2 A:G320 2.7 0.7 1.0 N7 A:G320 2.9 0.0 1.0 O6 A:G320 3.6 1.0 1.0 C5 A:G320 3.8 0.8 1.0 C8 A:G320 3.9 0.6 1.0 O6 A:G321 4.0 0.1 1.0 C6 A:G320 4.1 0.9 1.0 P A:G320 4.2 0.8 1.0 N1 A:A297 4.2 0.9 1.0 N7 A:G321 4.4 0.6 1.0 OP2 A:A319 4.7 0.3 1.0 OP1 A:A319 4.7 0.0 1.0 C6 A:G321 4.7 0.6 1.0 O5' A:A319 4.7 0.4 1.0 O5' A:G320 4.7 0.3 1.0 C3' A:A319 4.8 0.7 1.0 C5 A:G321 4.9 0.9 1.0 P A:A319 4.9 0.2 1.0 C2 A:A297 4.9 0.2 1.0 N6 A:A297 5.0 0.9 1.0

Sodium binding site 3 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na423 b:0.8 occ:1.00 O A:HOH524 2.3 83.7 1.0 O6 A:G15 3.6 0.4 1.0 N7 A:G15 3.6 0.8 1.0 N7 A:G14 3.9 95.6 1.0 O6 A:G14 4.1 0.9 1.0 C6 A:G15 4.3 0.0 1.0 C5 A:G15 4.3 0.1 1.0 O2' A:A12 4.3 0.7 1.0 C5 A:G14 4.4 94.6 1.0 C6 A:G14 4.4 98.1 1.0 C8 A:G15 4.7 0.6 1.0 C8 A:G14 4.8 94.2 1.0 C2' A:A12 4.8 0.9 1.0

Sodium binding site 4 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na424 b:83.7 occ:1.00 O6 A:G28 2.8 0.3 1.0 N7 A:G28 3.0 0.4 1.0 OP2 A:A27 3.4 1.0 1.0 C6 A:G28 3.5 0.0 1.0 C5 A:G28 3.6 0.4 1.0 O5' A:A25 4.0 90.9 1.0 C5' A:A25 4.2 88.5 1.0 C8 A:G28 4.2 0.8 1.0 OP1 A:U26 4.3 85.7 1.0 N2 A:G41 4.4 82.9 1.0 C3' A:A25 4.6 82.5 1.0 OP1 A:A25 4.7 91.3 1.0 P A:A27 4.8 0.5 1.0 N1 A:G28 4.8 90.4 1.0 P A:A25 4.9 93.1 1.0 C4 A:G28 4.9 91.6 1.0

Sodium binding site 5 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na425 b:82.9 occ:1.00 O6 A:G264 3.5 0.5 1.0 O6 A:G265 3.9 0.9 1.0 N7 A:G264 4.3 0.8 1.0 C6 A:G264 4.4 0.0 1.0 N7 A:G265 4.7 0.6 1.0 N4 A:C263 4.7 0.8 1.0 C5 A:G264 4.7 1.0 1.0 C6 A:G265 4.8 0.8 1.0 C5 A:C263 4.9 0.4 1.0

Sodium binding site 6 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na426 b:1.0 occ:1.00 O6 A:G194 2.9 0.4 1.0 O4 A:U195 3.7 90.5 1.0 C6 A:G194 3.9 95.5 1.0 N7 A:G194 4.4 0.2 1.0 C4 A:U195 4.5 84.2 1.0 C5 A:G194 4.5 91.3 1.0 C5 A:U195 4.6 85.2 1.0 N1 A:G194 4.9 91.7 1.0

Sodium binding site 7 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na427 b:85.5 occ:1.00 O A:HOH520 1.7 0.6 1.0 OP2 A:G269 2.1 0.3 1.0 P A:G269 3.4 0.0 1.0 O5' A:A268 3.7 0.6 1.0 O5' A:G269 3.8 0.4 1.0 N7 A:G270 4.1 0.1 1.0 N7 A:G269 4.3 0.8 1.0 C5' A:A268 4.4 0.5 1.0 OP1 A:G269 4.4 0.6 1.0 C8 A:G269 4.4 0.7 1.0 O6 A:G270 4.5 0.3 1.0 O3' A:A268 4.5 0.9 1.0 OP2 A:A268 4.6 0.5 1.0 C3' A:A268 4.6 0.3 1.0 P A:A268 4.7 0.6 1.0 OP2 A:G270 4.9 0.8 1.0

Sodium binding site 8 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Na429 b:0.2 occ:1.00 O6 A:G266 3.1 0.6 1.0 N7 A:G266 3.1 0.9 1.0 C5 A:G266 3.6 0.4 1.0 C6 A:G266 3.6 0.0 1.0 N7 A:G267 4.0 0.8 1.0 C8 A:G266 4.2 0.8 1.0 C8 A:G267 4.8 0.1 1.0 C4 A:G266 4.8 0.1 1.0 N1 A:G266 4.9 0.4 1.0

J.Manigrasso, I.Chillon, V.Genna, S.Somarowthu, A.M.Pyle, M.De Vivo, M.Marcia. Visualizing Group II Intron Dynamics Between the First and Second Steps of Splicing To Be Published.