Potassium in PDB 3igi: Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron

The structure of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron, PDB code: 3igi was solved by N.Toor, K.S.Keating, O.Fedorova, K.Rajashankar, J.Wang, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.70 / 3.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.092, 94.969, 225.972, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

The structure of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron also contains other interesting chemical elements:

Magnesium

(Mg)

44 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Potassium atom in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron (pdb code 3igi). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 22 binding sites of Potassium where determined in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron, PDB code: 3igi:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K457 b:82.1 occ:1.00 O2' A:U375 3.0 61.8 1.0 O3' A:U375 3.1 61.0 1.0 O4 A:U4 3.1 86.8 1.0 O6 A:G107 3.2 65.5 1.0 OP2 A:A376 3.3 63.3 1.0 P A:A376 3.7 60.6 1.0 C4 A:U4 3.9 71.1 1.0 N3 A:U4 3.9 44.4 1.0 C3' A:U375 4.0 67.6 1.0 C2' A:U375 4.0 62.1 1.0 C6 A:G107 4.3 57.1 1.0 O6 A:G3 4.4 66.1 1.0 OP1 A:A376 4.4 62.5 1.0 C4' A:U375 4.4 57.1 1.0 N7 A:G107 4.5 61.6 1.0 K A:K467 4.6 93.0 1.0 N7 A:A106 4.6 51.7 1.0 N1 A:G5 4.6 52.2 1.0 C8 A:A106 4.7 54.4 1.0 C5 A:G107 4.8 59.5 1.0 N2 A:G5 4.9 60.2 1.0

Potassium binding site 2 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K458 b:0.2 occ:1.00 OP2 A:C116 3.0 92.5 1.0 N7 A:G117 3.1 62.8 1.0 O6 A:G117 3.5 74.7 1.0 O A:HOH524 3.6 80.9 1.0 OP1 A:C116 3.8 96.8 1.0 C5 A:G117 3.9 55.7 1.0 P A:C116 3.9 89.3 1.0 C6 A:G117 4.0 56.5 1.0 C8 A:G117 4.1 64.9 1.0

Potassium binding site 3 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K459 b:0.6 occ:1.00 MG A:MG433 3.7 1.0 1.0 O6 A:G275 3.7 0.0 1.0 N7 A:G275 3.7 62.6 1.0 C6 A:G275 4.4 67.0 1.0 C5 A:G275 4.4 46.3 1.0 C8 A:G275 4.8 61.6 1.0

Potassium binding site 4 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K460 b:0.7 occ:1.00 O6 A:G28 3.0 77.0 1.0 N7 A:G28 3.4 84.1 1.0 OP2 A:A27 3.7 93.9 1.0 C6 A:G28 3.8 63.5 1.0 C5 A:G28 4.0 65.8 1.0 OP1 A:U26 4.1 85.7 1.0 N2 A:G41 4.5 72.1 1.0 C8 A:G28 4.6 76.8 1.0 O5' A:A25 4.6 61.0 1.0 C3' A:A25 4.8 53.0 1.0 N4 A:C40 4.8 77.3 1.0 C5' A:A25 4.9 63.5 1.0 OP1 A:A25 4.9 74.6 1.0 N7 A:G29 4.9 67.1 1.0 O6 A:G29 5.0 56.4 1.0

Potassium binding site 5 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K461 b:0.2 occ:1.00 O4 A:U251 3.7 97.6 1.0 O6 A:G252 3.9 0.6 1.0 O6 A:G18 4.0 0.9 1.0 O4 A:U17 4.3 98.0 1.0 C4 A:U251 4.5 98.1 1.0 C5 A:U251 4.8 97.5 1.0 N4 A:C253 4.9 0.5 1.0 N4 A:C19 5.0 0.5 1.0

Potassium binding site 6 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K462 b:0.7 occ:1.00 O6 A:G264 3.7 83.4 1.0 O6 A:G265 3.7 82.5 1.0 N7 A:G264 4.3 86.2 1.0 N4 A:C263 4.5 62.1 1.0 C6 A:G264 4.5 76.2 1.0 C6 A:G265 4.7 65.9 1.0 C5 A:G264 4.8 78.4 1.0 C4 A:C263 4.8 63.0 1.0 N7 A:G265 4.8 71.0 1.0 C5 A:C263 4.9 71.4 1.0

Potassium binding site 7 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K463 b:0.3 occ:1.00 OP2 A:A283 3.1 76.1 1.0 O6 A:G284 3.7 78.3 1.0 N7 A:G284 3.7 71.1 1.0 N7 A:A283 4.1 72.9 1.0 P A:A283 4.3 70.2 1.0 C6 A:G284 4.4 65.5 1.0 C8 A:A283 4.4 70.2 1.0 C5 A:G284 4.4 59.9 1.0 O5' A:A283 4.5 56.1 1.0 C8 A:G284 4.8 70.1 1.0 OP1 A:A283 4.9 69.1 1.0

Potassium binding site 8 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K464 b:0.8 occ:1.00 O6 A:G194 3.1 86.6 1.0 N7 A:G194 3.1 60.4 1.0 C6 A:G194 3.7 76.2 1.0 C5 A:G194 3.8 62.9 1.0 N6 A:A193 3.8 74.1 1.0 O4 A:U195 4.1 74.4 1.0 N7 A:A193 4.2 81.5 1.0 C8 A:G194 4.3 75.0 1.0 C6 A:A193 4.6 67.5 1.0 OP2 A:A192 4.6 79.0 1.0 C5 A:A193 4.7 66.9 1.0 C4 A:U195 4.8 57.2 1.0 O4 A:U172 4.9 88.2 1.0

Potassium binding site 9 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K465 b:0.3 occ:1.00 N7 A:G142 3.9 0.1 1.0 OP1 A:A144 4.1 0.6 1.0 C8 A:G142 4.1 0.1 1.0 OP2 A:G142 4.3 0.2 1.0 OP2 A:A144 4.4 0.5 1.0 C5 A:G142 4.7 0.0 1.0 P A:A144 4.8 0.5 1.0 N9 A:G142 5.0 1.0 1.0

Potassium binding site 10 out of 22 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:K466 b:98.3 occ:1.00 O6 A:G97 3.1 82.0 1.0 O4 A:U96 3.2 65.1 1.0 O6 A:G87 3.2 55.1 1.0 N4 A:C86 3.3 63.1 1.0 N6 A:A95 3.4 64.7 1.0 O A:HOH491 3.5 58.8 1.0 C6 A:G97 3.9 61.6 1.0 C4 A:U96 4.1 45.8 1.0 O4 A:U88 4.1 64.5 1.0 N3 A:U96 4.1 36.5 1.0 C6 A:G87 4.2 50.6 1.0 N7 A:G87 4.2 61.0 1.0 C4 A:C86 4.2 64.7 1.0 N1 A:G97 4.4 44.0 1.0 C6 A:A95 4.5 59.7 1.0 C5 A:G87 4.6 52.1 1.0 N3 A:C86 4.8 59.2 1.0 C4 A:U88 4.8 57.4 1.0 C5 A:G97 4.9 55.9 1.0

N.Toor, K.S.Keating, O.Fedorova, K.Rajashankar, J.Wang, A.M.Pyle. Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron. Rna V. 16 57 2010.
ISSN: ISSN 1355-8382
PubMed: 19952115
DOI: 10.1261/RNA.1844010