Barium in PDB 4e8v: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+, PDB code: 4e8v 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)	47.91 / 4.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.727, 96.548, 227.673, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 34.5

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Potassium	(K)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Barium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ (pdb code 4e8v). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 42 binding sites of Barium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+, PDB code: 4e8v:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba406 b:0.7 occ:0.73 OP1 A:C377 2.6 0.3 1.0 OP1 A:C358 3.1 0.5 1.0 OP2 A:G359 3.4 0.2 1.0 P A:C377 3.7 0.4 1.0 OP2 A:C377 3.8 0.5 1.0 P A:C358 4.4 0.2 1.0 O5' A:C377 4.5 0.6 1.0 P A:G359 4.6 0.3 1.0 O5' A:C358 4.6 0.8 1.0 BA A:BA436 4.6 0.2 0.7 C5' A:C358 4.7 0.1 1.0 OP1 A:G359 4.9 0.2 1.0 O3' A:C357 4.9 0.9 1.0 O3' A:A376 4.9 0.2 1.0

Barium binding site 2 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba407 b:0.3 occ:0.71 N7 A:G374 3.9 0.0 1.0 OP2 A:G374 4.0 0.6 1.0 OP1 A:C360 4.2 0.2 1.0 OP2 A:G378 4.2 0.6 1.0 C8 A:G374 4.4 0.3 1.0 OP2 A:C361 4.6 0.9 1.0 O A:HOH522 4.8 0.8 1.0

Barium binding site 3 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba408 b:0.3 occ:1.00 OP2 A:A260 3.0 0.2 1.0 O A:HOH520 3.6 0.0 1.0 O A:HOH521 4.0 0.5 1.0 O6 A:G10 4.0 0.0 1.0 O6 A:G9 4.1 0.2 1.0 P A:A260 4.2 0.0 1.0 OP1 A:A260 4.6 0.6 1.0 N7 A:G9 4.8 0.3 1.0 O5' A:A260 4.8 0.3 1.0 C6 A:G9 4.8 0.0 1.0

Barium binding site 4 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba409 b:0.2 occ:1.00 O6 A:G324 3.0 0.6 1.0 OP2 A:C323 4.2 0.3 1.0 C6 A:G324 4.2 0.3 1.0 BA A:BA438 4.8 1.0 0.8 N7 A:G324 4.9 0.5 1.0 C5 A:G324 4.9 0.7 1.0

Barium binding site 5 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba410 b:0.5 occ:0.76 O6 A:G46 3.4 0.5 1.0 O4 A:U45 3.6 0.6 1.0 OP2 A:U59 3.9 0.7 1.0 O A:HOH501 4.2 65.7 1.0 C4 A:U45 4.3 0.7 1.0 C5 A:U45 4.5 0.3 1.0 C6 A:G46 4.5 0.9 1.0 N7 A:G46 5.0 0.2 1.0

Barium binding site 6 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba411 b:0.9 occ:0.91 O2' A:A35 4.1 0.8 1.0 O6 A:G30 4.4 0.1 1.0 C2' A:A35 4.7 0.9 1.0 O4 A:U31 4.8 0.8 1.0

Barium binding site 7 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba412 b:0.7 occ:1.00 OP1 A:G173 3.3 0.6 1.0 OP1 A:A240 4.8 0.1 1.0 P A:G173 4.8 0.9 1.0 OP2 A:A240 4.9 0.4 1.0

Barium binding site 8 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba413 b:0.1 occ:1.00 N7 A:G270 2.9 0.5 1.0 O A:HOH526 3.0 0.5 1.0 O6 A:G270 3.0 0.2 1.0 OP2 A:G269 3.4 0.5 1.0 C5 A:G270 3.6 0.8 1.0 O4 A:U271 3.6 0.0 1.0 C6 A:G270 3.6 0.9 1.0 C8 A:G270 4.0 0.7 1.0 C4 A:U271 4.4 0.2 1.0 OP2 A:A268 4.5 0.6 1.0 C5 A:U271 4.8 0.0 1.0 N6 A:A282 4.8 0.5 1.0 O5' A:A268 4.8 0.6 1.0 C4 A:G270 4.9 0.8 1.0 P A:G269 4.9 0.2 1.0 N1 A:G270 5.0 0.8 1.0

Barium binding site 9 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba414 b:0.5 occ:1.00 N7 A:G275 2.7 0.1 1.0 O6 A:G275 3.4 0.3 1.0 C5 A:G275 3.5 0.7 1.0 C8 A:G275 3.8 0.8 1.0 C6 A:G275 3.8 0.8 1.0 N7 A:G274 4.2 0.9 1.0 K A:K449 4.5 0.7 1.0 C8 A:G274 4.7 0.3 1.0 OP2 A:G275 4.7 0.8 1.0 C4 A:G275 4.8 0.2 1.0 OP2 A:A277 4.8 0.8 1.0 OP2 A:G274 4.8 0.7 1.0 N9 A:G275 4.9 0.2 1.0 C5 A:G274 4.9 0.4 1.0

Barium binding site 10 out of 42 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of K+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ba415 b:0.8 occ:1.00 O6 A:G97 2.7 0.3 1.0 O4 A:U96 3.1 0.4 1.0 O6 A:G98 3.5 0.5 1.0 O3S A:EPE450 3.6 69.0 0.7 C6 A:G97 3.6 0.8 1.0 N7 A:G97 3.8 0.6 1.0 C4 A:U96 3.9 0.3 1.0 C5 A:G97 4.1 0.6 1.0 O2S A:EPE450 4.1 76.8 0.7 N7 A:G98 4.3 1.0 1.0 C6 A:G98 4.4 0.6 1.0 S A:EPE450 4.4 58.6 0.7 C5 A:U96 4.5 0.9 1.0 C5 A:G98 4.7 0.4 1.0 N3 A:U96 4.7 0.1 1.0 N1 A:G97 4.8 0.9 1.0 N4 A:C86 4.9 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