Potassium in PDB 8xts: Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State

The structure of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State (pdb code 8xts). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State, PDB code: 8xts:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K901 b:14.3 occ:1.00 OP2 A:A60 2.6 19.8 1.0 O5' A:G83 3.0 5.2 1.0 OP2 A:G61 3.1 11.4 1.0 O6 A:G696 3.2 14.4 1.0 O4' A:G83 3.3 4.2 1.0 OP1 A:G83 3.4 6.8 1.0 P A:A60 3.5 16.3 1.0 O5' A:A60 3.8 21.3 1.0 P A:G83 3.8 10.7 1.0 OP1 A:A60 3.9 17.8 1.0 C5' A:G83 4.0 12.0 1.0 C4' A:G83 4.0 7.4 1.0 C5' A:G61 4.1 4.8 1.0 C6 A:G696 4.2 13.7 1.0 N7 A:G696 4.3 17.5 1.0 MG A:MG907 4.3 9.9 1.0 P A:G61 4.4 22.5 1.0 C1' A:G83 4.4 4.1 1.0 O5' A:G61 4.6 14.1 1.0 N6 A:A697 4.6 14.6 1.0 C5 A:G696 4.7 11.8 1.0 O3' A:U82 4.8 3.8 1.0 C8 A:G83 4.9 8.3 1.0 C5' A:A60 4.9 20.4 1.0 OP2 A:G83 4.9 11.9 1.0 N9 A:G83 5.0 4.4 1.0

Potassium binding site 2 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K902 b:23.9 occ:1.00 OP2 A:A695 2.7 41.5 1.0 OP2 A:G224 2.7 3.7 1.0 OP1 A:A695 3.2 40.4 1.0 P A:A695 3.3 43.5 1.0 P A:G224 4.1 10.8 1.0 O3' A:G694 4.1 16.4 1.0 C3' A:G694 4.2 8.9 1.0 C8 A:G224 4.5 2.6 1.0 O5' A:G224 4.6 5.0 1.0 N7 A:G224 4.6 6.0 1.0 O2' A:G694 4.7 12.5 1.0 O5' A:A695 4.7 37.0 1.0 C2' A:G694 4.9 6.1 1.0 OP1 A:G224 4.9 8.6 1.0

Potassium binding site 3 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K903 b:58.9 occ:1.00 OP2 A:G86 2.7 7.8 1.0 O6 A:G83 2.9 11.2 1.0 P A:G86 3.8 9.3 1.0 O4' A:G696 3.9 13.2 1.0 C6 A:G83 4.0 7.9 1.0 OP1 A:G86 4.1 6.0 1.0 OP1 A:G696 4.2 20.8 1.0 N7 A:G83 4.3 7.8 1.0 O5' A:G696 4.4 16.0 1.0 O5' A:G86 4.5 6.3 1.0 C5 A:G83 4.5 5.9 1.0 C1' A:G696 4.6 17.4 1.0 OP2 A:C87 4.6 10.7 1.0 C4' A:G696 4.8 14.6 1.0 P A:G696 4.9 28.9 1.0

Potassium binding site 4 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K904 b:19.8 occ:1.00 O2' A:C81 2.9 6.1 1.0 O6 A:G425 3.1 4.6 1.0 O3' A:C81 3.3 3.7 1.0 N7 A:A424 3.7 5.5 1.0 OP2 A:U82 3.8 2.8 1.0 C8 A:A424 4.0 6.3 1.0 C2' A:C81 4.0 3.9 1.0 C3' A:C81 4.1 5.2 1.0 C6 A:G425 4.1 5.0 1.0 P A:U82 4.1 2.9 1.0 N7 A:G425 4.2 5.7 1.0 C4' A:C81 4.3 5.9 1.0 C5 A:G425 4.5 2.4 1.0 N4 A:C223 4.6 4.5 1.0 OP1 A:U82 4.8 6.6 1.0 C5 A:A424 4.8 4.5 1.0

Potassium binding site 5 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K905 b:56.4 occ:1.00 O6 A:G230 3.1 5.7 1.0 C6 A:G230 4.2 5.1 1.0 OP2 A:G228 4.4 5.3 1.0 OP2 A:U229 4.6 4.2 1.0 C5 A:U229 4.6 5.7 1.0 C5 A:G230 4.9 2.6 1.0 N7 A:G230 5.0 4.9 1.0 OP2 A:U627 5.0 10.3 1.0 O4 A:U229 5.0 5.2 1.0

Potassium binding site 6 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K906 b:54.6 occ:1.00 O6 A:G800 2.9 4.7 1.0 O4 A:U703 3.1 1.8 1.0 O4 A:U801 3.8 1.6 1.0 N6 A:A702 3.9 5.0 1.0 C6 A:G800 4.0 1.9 1.0 N1 A:G704 4.0 4.6 1.0 N2 A:G704 4.0 2.3 1.0 C4 A:U703 4.0 5.3 1.0 N3 A:U703 4.1 3.3 1.0 C2 A:G704 4.2 5.8 1.0 N7 A:G800 4.6 4.4 1.0 C5 A:G800 4.6 2.1 1.0 C6 A:G704 4.7 3.7 1.0 C4 A:U801 4.7 4.1 1.0 C6 A:A702 4.9 5.0 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