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

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

Magnesium

(Mg)

30 atoms

The binding sites of Potassium atom in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 2S State (pdb code 8xtr). 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 2S State, PDB code: 8xtr:
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 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K301 b:30.0 occ:1.00 OP2 A:A60 2.3 17.6 1.0 O5' A:G83 3.1 9.2 1.0 O6 B:G696 3.2 7.7 1.0 P A:A60 3.3 22.4 1.0 OP2 A:G61 3.4 5.1 1.0 OP1 A:G83 3.4 11.0 1.0 O4' A:G83 3.5 8.0 1.0 OP1 A:A60 3.6 18.7 1.0 O5' A:A60 3.8 18.3 1.0 P A:G83 3.9 0.5 1.0 N7 B:G696 4.1 9.3 1.0 C5' A:G83 4.2 5.1 1.0 C6 B:G696 4.2 9.8 1.0 C4' A:G83 4.3 0.1 1.0 C5' A:G61 4.5 0.0 1.0 C5 B:G696 4.6 9.3 1.0 C1' A:G83 4.6 0.7 1.0 MG A:MG305 4.6 30.0 1.0 O3' A:U59 4.7 2.8 1.0 O3' A:U82 4.7 1.3 1.0 P A:G61 4.7 11.4 1.0 N6 B:A697 4.8 4.5 1.0 C8 A:G83 4.8 0.5 1.0 O5' A:G61 4.9 9.7 1.0 C5' A:A60 5.0 15.5 1.0

Potassium binding site 2 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K302 b:30.0 occ:1.00 OP2 A:G86 2.2 14.6 1.0 O6 A:G83 3.0 0.5 1.0 P A:G86 3.6 15.0 1.0 N7 A:G83 3.8 0.0 1.0 C6 A:G83 3.8 0.0 1.0 OP1 A:C85 4.0 0.0 1.0 O4' B:G696 4.0 3.7 1.0 OP1 A:G86 4.1 13.8 1.0 C5 A:G83 4.1 0.0 1.0 O3' A:C85 4.4 0.0 1.0 OP2 A:C85 4.4 14.3 1.0 O5' A:C85 4.4 8.0 1.0 P A:C85 4.5 2.5 1.0 O5' A:G86 4.7 13.3 1.0 C3' A:C85 4.8 1.1 1.0 C1' B:G696 4.9 2.6 1.0 C8 A:G83 5.0 0.5 1.0 C5' A:C85 5.0 0.9 1.0

Potassium binding site 3 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K303 b:30.0 occ:1.00 O6 B:G425 2.8 0.8 1.0 O2' A:C81 3.2 1.1 1.0 O3' A:C81 3.5 1.7 1.0 C6 B:G425 3.8 8.7 1.0 OP2 A:U82 3.9 1.2 1.0 N7 B:A424 4.1 4.3 1.0 N7 B:G425 4.2 4.8 1.0 P A:U82 4.3 0.0 1.0 C3' A:C81 4.3 1.6 1.0 C2' A:C81 4.3 7.2 1.0 N4 B:C223 4.4 1.9 1.0 C8 B:A424 4.4 3.1 1.0 C5 B:G425 4.4 5.6 1.0 C4' A:C81 4.5 0.0 1.0 OP1 A:U82 4.9 0.0 1.0

Potassium binding site 4 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:K304 b:30.0 occ:1.00 O4 A:U67 2.6 15.0 1.0 C4 A:U67 3.8 5.5 1.0 C5 A:U67 4.6 0.0 1.0 N3 A:U67 4.7 7.8 1.0 N7 A:G66 4.9 0.0 1.0 O6 A:G66 4.9 3.0 1.0

Potassium binding site 5 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 2S 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:K901 b:30.0 occ:1.00 O6 B:G221 2.4 42.8 1.0 OP2 B:G224 2.6 4.2 1.0 C6 B:G221 3.2 46.8 1.0 N7 B:G221 3.6 48.0 1.0 C5 B:G221 3.7 43.9 1.0 P B:G224 3.7 1.3 1.0 O3' B:C223 4.1 0.6 1.0 OP1 B:G224 4.2 2.5 1.0 OP1 B:C223 4.4 7.3 1.0 C3' B:C223 4.4 4.0 1.0 N1 B:G221 4.4 44.4 1.0 O5' B:C223 4.6 2.0 1.0 OP2 B:C223 4.7 3.5 1.0 P B:C223 4.7 1.6 1.0 C8 B:G221 4.8 43.5 1.0 C8 B:G224 4.8 3.5 1.0 N7 B:G224 4.9 9.9 1.0 C4 B:G221 5.0 45.8 1.0 OP1 B:A695 5.0 57.4 1.0

Potassium binding site 6 out of 6 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 2S 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:K902 b:30.0 occ:1.00 O6 B:G230 2.9 4.3 1.0 C6 B:G230 4.0 1.9 1.0 OP2 B:U627 4.4 2.0 1.0 OP2 B:G228 4.7 9.7 1.0 N1 B:G230 4.9 0.8 1.0 C5 B:G230 4.9 0.2 1.0 C5 B:U229 5.0 8.4 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