Sodium in PDB 4fax: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+, PDB code: 4fax 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)	48.41 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.370, 95.370, 224.750, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.8

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

21 atoms

The binding sites of Sodium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+ (pdb code 4fax). 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 in A Ligand-Free State in the Presence of Na+ and MG2+, PDB code: 4fax:
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 in A Ligand-Free State in the Presence of Na+ and MG2+


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 A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na422 b:91.5 occ:1.00 OP2 A:G320 3.0 0.0 1.0 N7 A:G320 3.1 0.9 1.0 O6 A:G320 3.5 0.1 1.0 C5 A:G320 3.8 0.1 1.0 O6 A:G321 4.0 0.2 1.0 N1 A:A297 4.0 0.6 1.0 C6 A:G320 4.0 0.3 1.0 C8 A:G320 4.1 97.5 1.0 N7 A:G321 4.3 0.6 1.0 P A:G320 4.4 97.1 1.0 OP2 A:A319 4.5 0.3 1.0 O5' A:A319 4.6 0.1 1.0 N6 A:A297 4.7 0.0 1.0 C6 A:G321 4.7 0.7 1.0 C2 A:A297 4.7 0.9 1.0 C6 A:A297 4.8 0.6 1.0 C5 A:G321 4.9 0.3 1.0 C3' A:A319 5.0 90.8 1.0 P A:A319 5.0 0.9 1.0

Sodium binding site 2 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na423 b:84.9 occ:1.00 O A:HOH520 2.7 59.6 1.0 N7 A:G15 3.3 97.5 1.0 O6 A:G15 3.3 0.9 1.0 N7 A:G14 3.8 91.2 1.0 C6 A:G15 4.0 0.8 1.0 C5 A:G15 4.0 99.4 1.0 O2' A:A12 4.1 99.8 1.0 O6 A:G14 4.1 0.1 1.0 C5 A:G14 4.3 90.3 1.0 C6 A:G14 4.4 0.8 1.0 C8 A:G15 4.4 0.6 1.0 C8 A:G14 4.6 92.8 1.0 C2' A:A12 4.8 0.9 1.0

Sodium binding site 3 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na424 b:67.6 occ:1.00 N7 A:G28 2.8 85.7 1.0 O6 A:G28 2.9 90.1 1.0 C5 A:G28 3.5 80.2 1.0 C6 A:G28 3.5 83.0 1.0 OP2 A:A27 3.8 89.0 1.0 C8 A:G28 4.0 87.3 1.0 O5' A:A25 4.5 81.4 1.0 N2 A:G41 4.6 70.8 1.0 C5' A:A25 4.7 83.3 1.0 C4 A:G28 4.8 78.3 1.0 N1 A:G28 4.9 78.3 1.0 N7 A:G29 4.9 74.6 1.0 OP1 A:A25 4.9 77.6 1.0

Sodium binding site 4 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na425 b:76.8 occ:1.00 O6 A:G264 3.8 85.8 1.0 N4 A:C263 4.4 82.1 1.0 C5 A:C263 4.6 83.6 1.0 O6 A:G265 4.6 99.0 1.0 N7 A:G264 4.7 93.4 1.0 C4 A:C263 4.8 84.5 1.0 C6 A:G264 4.8 86.8 1.0

Sodium binding site 5 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na426 b:94.9 occ:1.00 O6 A:G194 3.1 0.8 1.0 O4 A:U195 3.6 83.1 1.0 C6 A:G194 4.1 92.0 1.0 C4 A:U195 4.4 83.4 1.0 C5 A:U195 4.5 86.0 1.0 C5 A:G194 4.7 92.4 1.0 N7 A:G194 4.7 0.0 1.0

Sodium binding site 6 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 in A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na427 b:66.5 occ:1.00 OP2 A:G269 2.0 97.7 1.0 O A:HOH524 2.3 0.3 1.0 P A:G269 3.5 99.3 1.0 N7 A:G270 3.8 93.7 1.0 O5' A:A268 3.8 84.0 1.0 O6 A:G270 4.0 88.1 1.0 O5' A:G269 4.0 94.4 1.0 N7 A:G269 4.2 95.7 1.0 C8 A:G269 4.3 97.5 1.0 OP1 A:G269 4.4 0.5 1.0 C5 A:G270 4.6 89.5 1.0 O3' A:A268 4.6 94.4 1.0 C5' A:A268 4.6 89.7 1.0 C6 A:G270 4.6 85.2 1.0 OP2 A:A268 4.7 93.1 1.0 C3' A:A268 4.7 93.1 1.0 P A:A268 4.7 86.2 1.0 C8 A:G270 4.8 96.8 1.0 OP2 A:G270 4.9 1.0 1.0

Sodium binding site 7 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 in A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na428 b:78.2 occ:1.00 O2' A:A348 3.1 0.6 1.0 O6 A:G331 4.1 0.7 1.0 N7 A:A330 4.4 0.1 1.0 O4 A:U332 4.4 0.4 1.0 C2' A:A348 4.4 0.3 1.0 N7 A:G331 4.8 0.5 1.0 N6 A:A330 4.9 0.2 1.0

Sodium binding site 8 out of 8 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Na+ and MG2+


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 in A Ligand-Free State in the Presence of Na+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na430 b:82.4 occ:1.00 O6 A:G266 3.2 92.3 1.0 N7 A:G266 3.3 0.4 1.0 C6 A:G266 3.7 93.7 1.0 C5 A:G266 3.8 98.2 1.0 N7 A:G267 4.2 0.3 1.0 C8 A:G266 4.4 0.7 1.0 C8 A:G267 4.9 0.8 1.0 OP2 A:G266 5.0 97.4 1.0 N1 A:G266 5.0 89.5 1.0

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033