Magnesium 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:

Potassium

(K)

6 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 30 binding sites of Magnesium where determined in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 2S State, PDB code: 8xtr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:30.0 occ:1.00 OP1 A:A60 2.2 18.7 1.0 OP2 A:C134 2.4 57.9 1.0 OP1 A:G83 2.5 11.0 1.0 P A:C134 3.5 63.9 1.0 OP2 A:G61 3.5 5.1 1.0 P A:A60 3.7 22.4 1.0 OP1 A:C134 3.7 58.0 1.0 P A:G83 3.8 0.5 1.0 C5' A:A60 4.2 15.5 1.0 O5' A:A60 4.2 18.3 1.0 C2' A:U133 4.2 122.8 1.0 OP1 A:G61 4.2 12.0 1.0 OP2 A:G83 4.3 4.0 1.0 MG A:MG306 4.3 30.0 1.0 O2' A:U133 4.4 117.0 1.0 P A:G61 4.4 11.4 1.0 OP2 A:A60 4.5 17.6 1.0 O3' A:U133 4.6 123.5 1.0 K A:K301 4.6 30.0 1.0 O5' A:C134 4.6 44.1 1.0 O3' A:U59 4.7 2.8 1.0 C3' A:U133 4.7 122.3 1.0 O5' A:G83 4.7 9.2 1.0 O3' A:U82 4.8 1.3 1.0

Magnesium binding site 2 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:30.0 occ:1.00 OP2 A:G83 2.3 4.0 1.0 O3' A:U219 2.5 3.6 1.0 OP1 A:C81 2.6 5.1 1.0 P A:G83 3.5 0.5 1.0 OP1 A:C134 3.6 58.0 1.0 P A:C81 3.8 0.2 1.0 C3' A:U219 3.8 3.8 1.0 OP1 A:G61 3.8 12.0 1.0 OP1 A:G83 3.9 11.0 1.0 OP2 A:C81 4.1 0.0 1.0 C4' A:U219 4.2 9.0 1.0 MG A:MG305 4.3 30.0 1.0 O2' A:U219 4.4 4.0 1.0 O5' A:G83 4.4 9.2 1.0 P A:C134 4.5 63.9 1.0 O3' A:G80 4.5 0.0 1.0 OP2 A:C134 4.6 57.9 1.0 C5' A:U219 4.7 3.9 1.0 O3' A:U82 4.7 1.3 1.0 C2' A:U219 4.7 0.2 1.0 O5' A:C134 4.7 44.1 1.0 P A:G61 4.8 11.4 1.0 OP2 A:G61 4.9 5.1 1.0

Magnesium binding site 3 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:30.0 occ:1.00 OP2 A:G80 2.6 18.9 1.0 OP1 A:C62 3.1 6.2 1.0 P A:G80 3.9 8.1 1.0 OP1 A:G80 4.3 2.5 1.0 P A:C62 4.4 40.2 1.0 C5' A:G80 4.6 0.0 1.0 OP2 A:C62 4.8 15.5 1.0 O5' A:G80 4.8 5.6 1.0 O3' A:G79 5.0 1.2 1.0

Magnesium binding site 4 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:30.0 occ:1.00 O6 A:G78 4.1 0.0 1.0 N6 A:A77 4.5 3.4 1.0 O4 A:U71 4.6 0.0 1.0 OP2 A:U76 4.7 14.0 1.0 N7 A:G78 4.7 2.6 1.0 N7 A:A77 4.8 14.4 1.0 OP1 A:U76 5.0 6.8 1.0

Magnesium binding site 5 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:30.0 occ:1.00 OP2 B:C226 3.5 8.0 1.0 O4' B:A628 4.5 2.3 1.0 P B:C226 4.6 3.7 1.0 OP1 B:A225 4.6 13.4 1.0 OP1 B:C226 4.6 1.5 1.0

Magnesium binding site 6 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:30.0 occ:1.00 O6 B:G692 2.8 2.8 1.0 C6 B:G692 4.0 7.2 1.0 N1 B:G692 4.8 5.2 1.0 N1 B:G693 4.9 1.3 1.0 O6 B:G693 5.0 1.6 1.0

Magnesium binding site 7 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:30.0 occ:1.00 OP2 B:C426 2.7 0.6 1.0 OP1 B:G425 3.0 1.0 1.0 O5' B:G425 3.6 6.7 1.0 P B:G425 4.0 0.9 1.0 P B:C426 4.1 7.4 1.0 O3' B:G425 4.7 0.1 1.0 OP1 B:C426 4.7 8.0 1.0 OP2 B:U427 4.8 3.2 1.0 O3' B:A424 4.9 7.3 1.0 C5' B:G425 4.9 3.6 1.0

Magnesium binding site 8 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg906 b:30.0 occ:1.00 OP1 A:U218 2.5 7.6 1.0 OP2 B:A422 2.5 2.3 1.0 OP2 B:U423 2.9 11.4 1.0 OP1 B:U423 3.6 9.6 1.0 P B:U423 3.8 18.8 1.0 P B:A422 3.9 3.9 1.0 P A:U218 3.9 0.3 1.0 OP1 B:A422 4.3 6.7 1.0 C5' A:U218 4.5 1.1 1.0 O5' A:U218 4.5 2.9 1.0 C4' B:A422 4.7 3.0 1.0 O5' B:A422 4.8 5.3 1.0 C5' B:A422 4.8 5.0 1.0 OP2 A:U218 4.8 6.8 1.0 O3' A:G217 4.8 8.0 1.0 O3' B:C421 4.9 13.8 1.0 O5' B:U423 4.9 15.5 1.0 O3' B:A422 4.9 0.4 1.0

Magnesium binding site 9 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg907 b:30.0 occ:1.00 O6 B:G440 2.9 5.3 1.0 O4 B:U458 2.9 7.4 1.0 O6 B:G459 3.4 3.4 1.0 O6 B:G441 3.7 3.0 1.0 C4 B:U458 3.7 0.9 1.0 N3 B:U458 3.8 4.5 1.0 C6 B:G459 3.8 9.7 1.0 N1 B:G459 3.9 2.1 1.0 N4 B:C457 4.0 1.7 1.0 C6 B:G440 4.0 7.4 1.0 OP2 B:C439 4.2 3.5 1.0 MG B:MG908 4.3 30.0 1.0 C6 B:G441 4.6 5.8 1.0 N7 B:G440 4.7 0.2 1.0 C5 B:G440 4.7 4.4 1.0 C5 B:G459 4.8 2.2 1.0 C2 B:G459 4.9 1.7 1.0

Magnesium binding site 10 out of 30 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron 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 2S State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg908 b:30.0 occ:1.00 MG B:MG907 4.3 30.0 1.0 OP2 B:G440 4.9 5.5 1.0 O6 B:G441 4.9 3.0 1.0 OP2 B:C439 4.9 3.5 1.0 N7 B:G440 4.9 0.2 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