Potassium in PDB 6t3k: Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon

The structure of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon, PDB code: 6t3k 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)	48.46 / 3.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.659, 95.453, 224.978, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.7

The structure of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon also contains other interesting chemical elements:

Magnesium

(Mg)

28 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon (pdb code 6t3k). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon, PDB code: 6t3k:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K425 b:0.5 occ:1.00 N7 A:G266 2.8 0.9 1.0 O A:HOH509 3.1 72.7 1.0 O6 A:G266 3.3 95.7 1.0 C5 A:G266 3.5 0.1 1.0 C6 A:G266 3.7 0.6 1.0 C8 A:G266 3.8 0.7 1.0 N7 A:G267 4.4 97.4 1.0 N7 A:G265 4.7 0.1 1.0 C4 A:G266 4.7 0.2 1.0 OP2 A:G266 4.9 0.9 1.0 N9 A:G266 4.9 0.1 1.0 O6 A:G265 4.9 0.8 1.0 C8 A:G267 5.0 98.2 1.0

Potassium binding site 2 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K430 b:97.7 occ:1.00 O6 A:G107 3.0 77.0 1.0 O2' A:U375 3.0 78.3 1.0 O4 A:U4 3.1 83.5 1.0 OP2 A:A376 3.1 74.2 1.0 O3' A:U375 3.4 79.3 1.0 P A:A376 3.7 77.0 1.0 C4 A:U4 3.9 84.6 1.0 O6 A:G3 4.0 95.8 1.0 C6 A:G107 4.1 77.7 1.0 N3 A:U4 4.1 84.1 1.0 C2' A:U375 4.1 85.8 1.0 C3' A:U375 4.2 86.7 1.0 OP1 A:A376 4.4 85.9 1.0 N7 A:A106 4.4 89.7 1.0 C8 A:A106 4.5 92.8 1.0 N7 A:G107 4.5 97.7 1.0 C5 A:G107 4.7 87.9 1.0 C4' A:U375 4.7 88.1 1.0 N1 A:G5 4.9 87.7 1.0 N7 A:G3 4.9 93.8 1.0 K A:K435 4.9 97.2 1.0 C6 A:G3 5.0 87.6 1.0

Potassium binding site 3 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K431 b:0.2 occ:1.00 O6 A:G275 3.1 0.3 1.0 C6 A:G275 3.6 0.6 1.0 N7 A:G275 3.7 0.8 1.0 O A:HOH516 3.7 91.2 1.0 C5 A:G275 3.8 0.7 1.0 OP2 A:A277 4.0 0.6 1.0 OP1 A:A277 4.1 0.7 1.0 P A:A277 4.5 0.5 1.0 N1 A:G275 4.6 0.7 1.0 C8 A:G275 4.7 0.5 1.0 C4 A:G275 4.9 0.4 1.0

Potassium binding site 4 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K432 b:95.1 occ:1.00 O6 A:G28 2.5 0.2 1.0 N7 A:G28 3.1 0.9 1.0 C6 A:G28 3.3 0.8 1.0 C5 A:G28 3.5 0.4 1.0 OP2 A:A27 4.1 0.5 1.0 N2 A:G41 4.2 87.6 1.0 OP1 A:U26 4.2 86.3 1.0 C8 A:G28 4.3 0.7 1.0 O5' A:A25 4.4 93.8 1.0 N1 A:G28 4.7 0.8 1.0 C3' A:A25 4.7 85.2 1.0 N7 A:G29 4.8 0.4 1.0 C5' A:A25 4.8 0.8 1.0 C4 A:G28 4.9 0.2 1.0

Potassium binding site 5 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K433 b:0.5 occ:1.00 O6 A:G80 3.4 98.4 1.0 O6 A:G79 3.7 78.0 1.0 N7 A:G79 3.9 82.4 1.0 N7 A:G80 4.0 96.2 1.0 C6 A:G79 4.2 79.7 1.0 C6 A:G80 4.2 0.9 1.0 C5 A:G79 4.3 74.4 1.0 O4 A:U103 4.4 66.8 1.0 C5 A:G80 4.5 99.3 1.0 OP2 A:A78 4.8 99.7 1.0 N4 A:C102 4.8 0.3 1.0 C8 A:G79 4.9 82.8 1.0

Potassium binding site 6 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K434 b:0.1 occ:1.00 O6 A:G264 3.1 0.5 1.0 O6 A:G265 3.9 0.8 1.0 N7 A:G264 3.9 0.0 1.0 C6 A:G264 3.9 0.2 1.0 C5 A:G264 4.2 0.9 1.0 N7 A:G265 4.5 0.1 1.0 N4 A:C263 4.7 0.1 1.0 C6 A:G265 4.7 0.5 1.0 C5 A:G265 5.0 0.0 1.0 N4 A:C7 5.0 99.7 1.0

Potassium binding site 7 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K435 b:97.2 occ:1.00 O6 A:G5 3.3 83.0 1.0 OP3 A:G1 3.3 0.9 1.0 OP2 A:A376 3.3 74.2 1.0 O4 A:U4 3.5 83.5 1.0 OP1 A:G3 3.8 0.9 1.0 O4' A:A376 4.1 78.3 1.0 C6 A:G5 4.3 86.9 1.0 C4 A:U4 4.4 84.6 1.0 C5' A:A376 4.5 81.2 1.0 P A:A376 4.5 77.0 1.0 N1 A:G5 4.5 87.7 1.0 O5' A:A376 4.6 74.0 1.0 C4' A:A376 4.6 79.3 1.0 P A:G1 4.7 0.8 1.0 O3' A:U2 4.8 0.8 1.0 C5 A:U4 4.8 88.7 1.0 P A:G3 4.8 0.6 1.0 OP1 A:G1 4.9 0.3 1.0 K A:K430 4.9 97.7 1.0 O3' A:U375 4.9 79.3 1.0

Potassium binding site 8 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K436 b:0.9 occ:1.00 O2' A:G32 3.0 0.9 1.0 O6 A:G34 3.3 0.2 1.0 N7 A:A33 3.8 0.1 1.0 O3' A:G32 4.1 0.1 1.0 C2' A:G32 4.2 0.1 1.0 C6 A:G34 4.4 1.0 1.0 C4' A:G32 4.4 0.6 1.0 C3' A:G32 4.5 0.9 1.0 C8 A:A33 4.6 0.9 1.0 N6 A:A33 4.7 0.2 1.0 C5 A:A33 4.8 0.0 1.0 O4' A:G32 5.0 0.9 1.0 C1' A:G32 5.0 0.4 1.0

Potassium binding site 9 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K437 b:83.3 occ:1.00 O5' A:C377 2.4 86.1 1.0 OP1 A:C377 2.7 77.8 1.0 O6 A:G288 2.9 0.1 1.0 OP2 A:G358 2.9 0.6 1.0 O4' A:C377 3.0 0.4 1.0 P A:C377 3.1 79.4 1.0 O5' A:G359 3.1 91.5 1.0 OP2 A:G359 3.3 87.0 1.0 C5' A:C377 3.3 91.4 1.0 P A:G358 3.6 0.7 1.0 O3' A:A376 3.6 76.9 1.0 C4' A:C377 3.6 95.5 1.0 O5' A:G358 3.7 99.5 1.0 OP1 A:G358 3.8 98.8 1.0 P A:G359 3.8 87.4 1.0 O6 A:G289 3.8 0.8 1.0 C5' A:G359 4.0 96.8 1.0 C6 A:G288 4.0 0.2 1.0 C1' A:C377 4.3 0.9 1.0 MG A:MG401 4.4 68.3 1.0 N1 A:G289 4.4 0.7 1.0 C6 A:C377 4.4 99.1 1.0 OP2 A:C377 4.4 68.7 1.0 C6 A:G289 4.5 0.0 1.0 O2' A:A376 4.6 71.5 1.0 OP1 A:G359 4.7 83.4 1.0 N7 A:G288 4.8 0.9 1.0 C5 A:G288 4.8 0.9 1.0 N1 A:C377 4.8 1.0 1.0 C3' A:A376 4.9 77.6 1.0

Potassium binding site 10 out of 15 in the Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron G-Mutant (C289G/C358G/G385C) in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:K438 b:0.0 occ:1.00 N7 A:G331 3.2 0.9 1.0 O4 A:U332 3.4 0.7 1.0 C8 A:G331 4.1 0.1 1.0 C4 A:U332 4.2 0.1 1.0 O6 A:G331 4.2 0.4 1.0 O2' A:A348 4.2 0.9 1.0 C5 A:G331 4.3 0.9 1.0 C5 A:U332 4.3 0.6 1.0 C6 A:G331 4.6 0.7 1.0 C8 A:A348 4.8 0.6 1.0 C2' A:A348 4.8 0.3 1.0 N7 A:A330 4.8 0.3 1.0 C5 A:A330 4.9 0.6 1.0 N6 A:A330 4.9 0.8 1.0 C6 A:A330 5.0 1.0 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.