Potassium in PDB 8xtp: Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State

The structure of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State also contains other interesting chemical elements:

Magnesium

(Mg)

38 atoms

The binding sites of Potassium atom in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State (pdb code 8xtp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State, PDB code: 8xtp:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:K901 b:30.0 occ:1.00 OP2 B:C223 2.7 28.9 1.0 OP1 B:G222 2.9 28.1 1.0 P B:C223 4.1 29.8 1.0 P B:G222 4.2 31.5 1.0 O5' B:G222 4.3 18.7 1.0 N2 B:G221 4.5 23.3 1.0 N7 B:G224 4.6 2.2 1.0 OP1 B:C223 4.6 11.3 1.0 N7 B:A695 4.8 26.7 1.0 O5' B:C223 4.9 15.0 1.0 C5' B:G221 5.0 23.4 1.0

Potassium binding site 2 out of 4 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:K902 b:30.0 occ:1.00 N7 B:A424 4.0 26.8 1.0 O6 B:G425 4.1 21.7 1.0 OP1 B:U423 4.1 40.8 1.0 O3' B:A422 4.5 40.5 1.0 C8 B:A424 4.6 24.7 1.0 O3' A:C81 4.6 10.2 1.0 O2' B:A422 4.6 33.0 1.0 OP2 A:U82 4.8 23.0 1.0 O6 B:G222 4.8 6.6 1.0 C5' B:U423 4.8 39.0 1.0 O2' A:C81 4.9 22.9 1.0 N4 B:C223 4.9 0.5 1.0 P B:U423 4.9 52.1 1.0

Potassium binding site 3 out of 4 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K201 b:30.0 occ:1.00 OP2 A:G61 2.8 28.8 1.0 OP2 A:A60 2.9 30.1 1.0 O6 B:G696 3.1 22.4 1.0 O5' A:G83 3.2 8.8 1.0 O4' A:G83 3.3 14.8 1.0 OP1 A:G83 3.5 7.9 1.0 P A:A60 3.7 35.5 1.0 C5' A:G61 4.0 14.6 1.0 OP1 A:A60 4.0 23.7 1.0 P A:G83 4.0 15.3 1.0 C6 B:G696 4.1 7.2 1.0 O5' A:A60 4.1 29.1 1.0 C4' A:G83 4.1 11.6 1.0 N6 B:A697 4.1 6.8 1.0 P A:G61 4.1 20.4 1.0 C5' A:G83 4.2 0.0 1.0 N7 B:G696 4.2 14.0 1.0 MG A:MG203 4.2 30.0 1.0 C1' A:G83 4.3 2.5 1.0 O5' A:G61 4.5 19.1 1.0 C5 B:G696 4.5 9.5 1.0 O4' A:G61 4.7 27.4 1.0 MG A:MG206 4.8 30.0 1.0 O3' A:U82 4.8 23.2 1.0 C6 B:A697 4.9 9.9 1.0 C8 A:G61 4.9 10.8 1.0 C3' A:A60 5.0 24.2 1.0 N9 A:G83 5.0 4.2 1.0 C4' A:G61 5.0 17.2 1.0 C8 A:G83 5.0 0.0 1.0

Potassium binding site 4 out of 4 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K202 b:30.0 occ:1.00 O6 A:G83 2.3 19.3 1.0 OP2 A:G86 2.4 16.5 1.0 C6 A:G83 3.2 15.8 1.0 N7 A:G83 3.5 2.3 1.0 C5 A:G83 3.7 2.4 1.0 P A:G86 3.9 22.2 1.0 O4' B:G696 4.0 22.9 1.0 O5' A:C85 4.2 26.4 1.0 OP1 A:C85 4.4 18.7 1.0 N1 A:G83 4.4 8.7 1.0 C1' B:G696 4.5 6.2 1.0 OP2 A:C85 4.6 10.4 1.0 O3' A:C85 4.7 14.8 1.0 OP1 A:G86 4.7 22.5 1.0 P A:C85 4.7 24.4 1.0 O5' A:G86 4.7 35.5 1.0 C8 A:G83 4.7 0.0 1.0 C3' A:C85 4.8 15.0 1.0 O5' B:G696 5.0 18.9 1.0 N9 B:G696 5.0 8.5 1.0 C4 A:G83 5.0 6.4 1.0

L.Wang, J.Xie, C.Zhang, J.Zou, Z.Huang, S.Shang, X.Chen, Y.Yang, J.Liu, H.Dong, D.Huang, Z.Su. Structural Basis of Circularly Permuted Group II Intron Self-Splicing. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 39890981
DOI: 10.1038/S41594-025-01484-X