Magnesium 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:

Potassium

(K)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 38 binding sites of Magnesium where determined in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State, PDB code: 8xtp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg903 b:30.0 occ:1.00 OP1 B:A225 2.9 26.7 1.0 O4' B:A628 3.4 23.5 1.0 P B:A225 4.2 23.8 1.0 C1' B:A628 4.3 17.1 1.0 O2' A:C85 4.3 14.8 1.0 N9 B:A628 4.3 12.9 1.0 N3 B:A628 4.4 13.8 1.0 C4 B:A628 4.4 15.9 1.0 C4' B:A628 4.5 15.8 1.0 OP2 B:C226 4.5 29.4 1.0 O3' B:G224 4.5 24.6 1.0 C5' B:A628 4.9 18.3 1.0 OP2 B:A225 4.9 23.6 1.0

Magnesium binding site 2 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg904 b:30.0 occ:1.00 OP2 B:C426 2.3 19.3 1.0 OP1 B:G425 3.2 16.1 1.0 P B:C426 3.7 18.9 1.0 O5' B:G425 3.9 16.6 1.0 OP2 B:U427 4.1 17.7 1.0 P B:G425 4.2 20.0 1.0 OP1 B:C426 4.3 14.5 1.0 O5' B:C426 4.4 6.6 1.0 O3' B:G425 4.7 18.9 1.0

Magnesium binding site 3 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg905 b:30.0 occ:1.00 OP2 B:U423 2.5 42.5 1.0 OP2 B:A422 3.3 26.5 1.0 O2' B:C421 3.5 43.4 1.0 O3' B:C421 3.8 37.8 1.0 P B:U423 3.8 52.1 1.0 O5' B:U423 3.9 35.3 1.0 P B:A422 4.2 46.3 1.0 C2' B:C421 4.5 41.0 1.0 C5' B:A422 4.7 24.0 1.0 OP1 B:U423 4.7 40.8 1.0 C3' B:C421 4.7 36.4 1.0 O3' B:A422 4.9 40.5 1.0 O5' B:A422 5.0 29.5 1.0 C4' B:A422 5.0 23.0 1.0

Magnesium binding site 4 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg906 b:30.0 occ:1.00 N7 B:G440 3.9 37.3 1.0 O6 B:G441 3.9 32.2 1.0 O6 B:G440 4.1 32.6 1.0 OP2 B:C439 4.3 37.8 1.0 C5 B:G440 4.6 33.5 1.0 C6 B:G440 4.7 36.6 1.0 N7 B:G441 4.8 38.4 1.0 C8 B:G440 4.9 37.3 1.0 C6 B:G441 4.9 30.8 1.0

Magnesium binding site 5 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 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:Mg907 b:30.0 occ:1.00 OP2 B:U616 3.7 32.1 1.0 O4 B:U274 3.7 33.8 1.0 OP2 B:A617 4.1 29.4 1.0 O6 B:G273 4.1 41.4 1.0 O6 B:G618 4.2 24.6 1.0 N4 B:C619 4.6 35.8 1.0 N2 B:G275 4.8 19.4 1.0 C4 B:U274 4.8 32.6 1.0 N1 B:G275 4.9 25.4 1.0 P B:U616 4.9 40.1 1.0

Magnesium binding site 6 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 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:Mg908 b:30.0 occ:1.00 N7 B:G236 4.2 11.9 1.0 N7 B:G235 4.2 11.6 1.0 O6 B:G236 4.3 14.6 1.0 O6 B:G260 4.5 20.3 1.0 O6 B:G235 4.7 10.4 1.0 OP2 B:C234 4.9 27.1 1.0 C5 B:G235 4.9 9.4 1.0 C5 B:G236 5.0 11.4 1.0 N4 B:C237 5.0 20.1 1.0

Magnesium binding site 7 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 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:Mg909 b:30.0 occ:1.00 O4 B:U558 2.3 49.0 1.0 OP2 B:A557 2.4 49.6 1.0 C4 B:U558 3.3 50.1 1.0 P B:A557 3.8 49.4 1.0 C5 B:U558 3.9 48.2 1.0 OP1 B:A557 4.3 37.2 1.0 N6 B:A565 4.4 55.9 1.0 N3 B:U558 4.4 52.7 1.0 N1 B:A566 4.6 43.5 1.0 O3' B:A556 4.6 39.4 1.0 C3' B:A556 4.6 29.9 1.0 O5' B:A557 4.8 42.3 1.0 C5' B:A556 4.8 35.3 1.0 OP2 B:A556 5.0 37.8 1.0

Magnesium binding site 8 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 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:Mg910 b:30.0 occ:1.00 OP2 B:G568 2.3 60.5 1.0 OP2 B:G523 2.5 51.4 1.0 P B:G523 3.2 51.0 1.0 OP1 B:G523 3.3 43.7 1.0 O5' B:G523 3.6 46.6 1.0 P B:G568 3.7 66.1 1.0 OP1 B:A565 4.2 60.5 1.0 O3' B:A567 4.2 54.3 1.0 O2' B:A567 4.3 43.8 1.0 OP2 B:A566 4.4 48.9 1.0 O5' B:G568 4.6 59.1 1.0 O3' B:A522 4.7 64.0 1.0 OP1 B:G568 4.7 66.0 1.0 C5' B:G523 4.8 43.1 1.0

Magnesium binding site 9 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 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:Mg911 b:30.0 occ:1.00 OP2 B:C569 2.1 77.3 1.0 OP1 B:A566 2.2 47.8 1.0 OP1 B:G568 2.4 66.0 1.0 P B:C569 3.5 80.1 1.0 P B:A566 3.6 53.3 1.0 P B:G568 3.8 66.1 1.0 OP1 B:C569 4.2 79.6 1.0 O3' B:G568 4.2 68.1 1.0 OP2 B:A566 4.3 48.9 1.0 O3' B:A565 4.5 53.2 1.0 C3' B:G568 4.5 67.6 1.0 O5' B:G568 4.5 59.1 1.0 O5' B:C569 4.5 81.5 1.0 C5' B:G568 4.5 61.4 1.0 OP2 B:G568 4.5 60.5 1.0 O5' B:A566 4.6 55.2 1.0 C3' B:A567 4.8 44.4 1.0 O3' B:A567 4.9 54.3 1.0 C5' B:A566 4.9 48.9 1.0

Magnesium binding site 10 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Post- 2S State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 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:Mg912 b:30.0 occ:1.00 OP2 B:G417 2.5 25.5 1.0 O3' B:G366 2.9 19.7 1.0 OP2 B:A367 3.5 13.6 1.0 P B:A367 3.7 33.1 1.0 C3' B:G366 3.9 18.0 1.0 P B:G417 3.9 23.4 1.0 OP1 B:G366 4.2 19.6 1.0 OP2 B:G366 4.4 21.1 1.0 OP2 B:C416 4.4 26.7 1.0 O5' B:A367 4.4 13.7 1.0 OP1 B:G417 4.6 18.5 1.0 O5' B:C416 4.6 23.0 1.0 C5' B:A367 4.6 13.1 1.0 O5' B:G417 4.7 8.9 1.0 P B:G366 4.7 29.5 1.0 P B:C416 4.9 24.1 1.0 O3' B:C416 4.9 18.2 1.0 C3' B:C416 4.9 4.6 1.0 OP1 B:C416 5.0 11.3 1.0 C2' B:G366 5.0 12.3 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