Rubidium in PDB 4e8p: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p 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)	48.16 / 3.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.987, 95.024, 223.492, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.4

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

Magnesium

(Mg)

27 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Rubidium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ (pdb code 4e8p). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 18 binding sites of Rubidium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Rubidium binding site 1 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb428 b:54.0 occ:0.30 OP1 A:C358 2.6 96.1 1.0 O3' A:A376 3.0 87.7 1.0 OP1 A:C377 3.1 84.5 1.0 MG A:MG403 3.5 64.8 1.0 P A:C377 3.6 83.9 1.0 RB A:RB437 3.6 93.0 1.0 P A:C358 3.7 94.4 1.0 O5' A:C377 3.8 86.8 1.0 OP2 A:C358 3.8 98.4 1.0 N4 A:C289 4.1 0.2 1.0 C3' A:A376 4.2 95.1 1.0 C2 A:A287 4.3 0.6 1.0 O2' A:A376 4.4 93.4 1.0 C1' A:A376 4.5 0.9 1.0 O3' A:C357 4.6 95.2 1.0 C2' A:A376 4.7 96.3 1.0 O6 A:G288 4.7 0.7 1.0 C5' A:C377 4.7 86.2 1.0 N1 A:A287 4.8 0.8 1.0 C4' A:A376 4.8 92.5 1.0 O5' A:C358 4.9 97.0 1.0 O4' A:A376 5.0 99.7 1.0

Rubidium binding site 2 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb429 b:0.4 occ:0.69 O6 A:G275 3.1 0.1 1.0 O4 A:U273 3.1 82.7 1.0 O A:HOH901 3.2 67.4 1.0 O6 A:G274 3.3 89.0 1.0 C4 A:U273 3.7 76.1 1.0 C6 A:G275 3.9 98.4 1.0 C5 A:U273 4.0 78.3 1.0 C6 A:G274 4.3 89.2 1.0 N7 A:G274 4.4 95.0 1.0 N1 A:G275 4.5 94.8 1.0 N3 A:U273 4.6 73.9 1.0 C5 A:G274 4.8 91.7 1.0 C5 A:G275 4.8 97.1 1.0

Rubidium binding site 3 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb430 b:0.2 occ:0.98 N7 A:G266 2.5 87.6 1.0 O A:HOH903 2.7 94.9 1.0 O A:HOH902 3.1 60.9 1.0 C5 A:G266 3.4 84.1 1.0 C8 A:G266 3.4 90.0 1.0 O6 A:G266 3.6 80.0 1.0 C6 A:G266 3.8 80.2 1.0 OP2 A:G266 4.1 95.5 1.0 N7 A:G267 4.4 1.0 1.0 C4 A:G266 4.5 83.0 1.0 N9 A:G266 4.5 87.5 1.0 C8 A:G267 4.9 0.6 1.0 N7 A:G265 4.9 90.8 1.0

Rubidium binding site 4 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb431 b:88.7 occ:0.79 O4 A:U4 2.8 0.7 1.0 O6 A:G107 2.9 88.7 1.0 O2' A:U375 3.1 74.2 1.0 O3' A:U375 3.1 83.9 1.0 OP2 A:A376 3.3 82.3 1.0 C4 A:U4 3.7 0.8 1.0 P A:A376 3.8 80.6 1.0 N3 A:U4 3.9 0.4 1.0 O6 A:G3 4.0 0.7 1.0 C6 A:G107 4.1 85.0 1.0 C3' A:U375 4.1 80.0 1.0 C2' A:U375 4.1 77.6 1.0 N7 A:A106 4.3 91.6 1.0 RB A:RB434 4.4 0.9 0.7 OP1 A:A376 4.5 82.1 1.0 C4' A:U375 4.6 76.7 1.0 O2' A:G1 4.6 0.3 1.0 C8 A:A106 4.7 92.6 1.0 N7 A:G107 4.8 87.5 1.0 N1 A:G5 4.8 79.0 1.0 C5 A:G107 4.8 83.4 1.0 C5 A:U4 4.9 0.3 1.0 C6 A:G3 5.0 99.0 1.0 N7 A:G3 5.0 0.9 1.0

Rubidium binding site 5 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb432 b:0.0 occ:0.89 O6 A:G28 2.7 71.1 1.0 N7 A:G28 3.5 73.7 1.0 C6 A:G28 3.5 68.3 1.0 C5 A:G28 3.8 69.1 1.0 O6 A:G29 4.4 75.3 1.0 OP2 A:A27 4.5 97.1 1.0 O5' A:A25 4.6 95.6 1.0 C8 A:G28 4.7 76.9 1.0 C3' A:A25 4.8 75.4 1.0 C5' A:A25 4.8 0.3 1.0 N1 A:G28 4.8 65.9 1.0 N2 A:G41 4.8 71.5 1.0 N7 A:G29 4.8 75.6 1.0 OP1 A:U26 4.9 75.1 1.0 N4 A:C40 4.9 72.6 1.0

Rubidium binding site 6 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb433 b:73.5 occ:0.58 O6 A:G87 2.8 75.7 1.0 O4 A:U96 3.0 82.6 1.0 O6 A:G97 3.1 73.6 1.0 N4 A:C86 3.1 98.4 1.0 N6 A:A95 3.5 82.7 1.0 O4 A:U88 3.8 86.1 1.0 C6 A:G87 3.8 75.3 1.0 C6 A:G97 3.9 72.9 1.0 C4 A:U96 4.0 78.2 1.0 C4 A:C86 4.0 93.9 1.0 N7 A:G87 4.2 82.7 1.0 N3 A:U96 4.2 76.4 1.0 N1 A:G97 4.3 71.8 1.0 C5 A:G87 4.4 78.4 1.0 C6 A:A95 4.5 79.8 1.0 C4 A:U88 4.6 88.3 1.0 C5 A:C86 4.7 95.2 1.0 N3 A:C86 4.7 88.8 1.0 C5 A:G97 4.9 71.2 1.0 N3 A:U88 5.0 89.5 1.0

Rubidium binding site 7 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb434 b:0.9 occ:0.73 OP2 A:A376 2.8 82.3 1.0 O6 A:G5 3.1 85.6 1.0 O4 A:U4 3.1 0.7 1.0 OP2 A:G3 3.4 0.4 1.0 O4' A:A376 3.6 99.7 1.0 C5' A:A376 3.8 87.0 1.0 P A:A376 4.0 80.6 1.0 C6 A:G5 4.0 83.9 1.0 C4 A:U4 4.1 0.8 1.0 N1 A:G5 4.1 79.0 1.0 C4' A:A376 4.1 92.5 1.0 O5' A:A376 4.3 77.5 1.0 RB A:RB431 4.4 88.7 0.8 O3' A:U375 4.4 83.9 1.0 C5 A:U4 4.5 0.3 1.0 P A:G3 4.5 0.7 1.0 OP1 A:G3 4.7 0.8 1.0 N3 A:A376 4.8 90.6 1.0 C1' A:A376 4.9 0.9 1.0 C4 A:A376 4.9 95.3 1.0 N9 A:A376 5.0 100.0 1.0

Rubidium binding site 8 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb435 b:0.6 occ:0.94 O6 A:G80 3.6 84.3 1.0 O6 A:G79 3.7 0.9 1.0 N7 A:G79 3.9 84.9 1.0 RB A:RB439 4.2 0.3 0.8 C6 A:G79 4.3 96.6 1.0 C5 A:G79 4.4 84.9 1.0 O4 A:U103 4.4 0.3 1.0 N7 A:G80 4.6 85.5 1.0 C6 A:G80 4.6 87.0 1.0 C8 A:G79 4.9 89.6 1.0 N4 A:C102 4.9 97.0 1.0 C5 A:G80 5.0 91.6 1.0

Rubidium binding site 9 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb436 b:0.1 occ:0.57 O2' A:G32 2.8 89.8 1.0 O6 A:G34 2.9 87.4 1.0 N7 A:A33 3.6 79.7 1.0 C6 A:G34 3.8 85.5 1.0 N6 A:A33 3.9 82.6 1.0 O3' A:G32 4.1 0.8 1.0 C2' A:G32 4.1 96.7 1.0 C5 A:A33 4.4 80.3 1.0 C5 A:G34 4.5 82.4 1.0 N7 A:G34 4.5 82.8 1.0 C3' A:G32 4.5 0.4 1.0 C6 A:A33 4.6 81.8 1.0 C8 A:A33 4.6 78.6 1.0 C4' A:G32 4.6 0.0 1.0 N1 A:G34 4.8 87.0 1.0

Rubidium binding site 10 out of 18 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb437 b:93.0 occ:1.00 O6 A:G288 2.3 0.7 1.0 O5' A:C377 2.4 86.8 1.0 OP2 A:C358 2.9 98.4 1.0 O5' A:G359 2.9 99.5 1.0 O4' A:C377 3.0 81.7 1.0 C5' A:C377 3.3 86.2 1.0 OP1 A:C358 3.4 96.1 1.0 P A:C358 3.4 94.4 1.0 MG A:MG403 3.5 64.8 1.0 OP2 A:G359 3.5 94.9 1.0 C6 A:G288 3.5 0.8 1.0 C4' A:C377 3.5 88.0 1.0 P A:C377 3.5 83.9 1.0 OP1 A:C377 3.6 84.5 1.0 RB A:RB428 3.6 54.0 0.3 O5' A:C358 3.6 97.0 1.0 C5' A:G359 3.6 0.7 1.0 P A:G359 3.8 0.7 1.0 O3' A:A376 4.1 87.7 1.0 N4 A:C289 4.1 0.2 1.0 C1' A:C377 4.3 91.1 1.0 N1 A:G288 4.4 0.9 1.0 C5 A:G288 4.5 0.5 1.0 C6 A:C377 4.5 91.7 1.0 OP2 A:C377 4.7 78.0 1.0 OP1 A:G359 4.7 0.7 1.0 C3' A:C358 4.8 0.0 1.0 N7 A:G288 4.8 0.6 1.0 N1 A:C377 4.9 92.4 1.0 O3' A:C358 4.9 0.8 1.0 C4' A:G359 5.0 0.7 1.0 C3' A:C377 5.0 91.9 1.0 O3' A:C357 5.0 95.2 1.0 C5 A:C358 5.0 0.9 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