Magnesium 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:

Potassium

(K)

6 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 Pre-1S State (pdb code 8xts). 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 Pre-1S State, PDB code: 8xts:
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 Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:9.9 occ:1.00 OP1 A:G83 2.2 6.8 1.0 OP1 A:A60 2.2 17.8 1.0 OP2 A:G220 2.8 79.6 1.0 OP2 A:G61 3.3 11.4 1.0 P A:G83 3.4 10.7 1.0 P A:A60 3.6 16.3 1.0 OP2 A:G83 3.9 11.9 1.0 O5' A:A60 4.1 21.3 1.0 C5' A:A60 4.1 20.4 1.0 OP1 A:G61 4.2 8.8 1.0 P A:G220 4.2 71.8 1.0 P A:G61 4.3 22.5 1.0 OP2 A:A60 4.3 19.8 1.0 MG A:MG908 4.3 6.6 1.0 K A:K901 4.3 14.3 1.0 O5' A:G83 4.4 5.2 1.0 O3' A:U82 4.5 3.8 1.0 O3' A:U59 4.7 19.1 1.0 OP1 A:G220 4.9 71.8 1.0

Magnesium binding site 2 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:6.6 occ:1.00 OP2 A:G83 2.0 11.9 1.0 OP1 A:C81 2.7 5.2 1.0 OP2 A:G220 3.2 79.6 1.0 O3' A:U219 3.2 10.6 1.0 P A:G83 3.3 10.7 1.0 OP1 A:G61 3.4 8.8 1.0 P A:C81 3.7 2.8 1.0 P A:G220 3.9 71.8 1.0 OP2 A:C81 3.9 6.2 1.0 OP1 A:G83 3.9 6.8 1.0 O5' A:G83 4.1 5.2 1.0 MG A:MG907 4.3 9.9 1.0 P A:G61 4.3 22.5 1.0 O2' A:U219 4.3 8.6 1.0 C3' A:U219 4.4 7.5 1.0 O3' A:G80 4.5 2.0 1.0 O3' A:U82 4.5 3.8 1.0 OP2 A:G61 4.5 11.4 1.0 O5' A:G61 4.5 14.1 1.0 C5' A:G83 4.6 12.0 1.0 C4' A:U219 4.7 8.1 1.0 C3' A:U82 4.8 8.5 1.0 OP1 A:G220 4.9 71.8 1.0 C2' A:U219 5.0 8.2 1.0

Magnesium binding site 3 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:6.7 occ:1.00 OP1 A:A225 2.4 7.2 1.0 OP2 A:C226 2.7 5.8 1.0 P A:C226 3.8 8.9 1.0 P A:A225 3.9 5.3 1.0 OP1 A:C226 4.1 2.9 1.0 C5' A:A225 4.5 5.3 1.0 O3' A:A225 4.6 9.0 1.0 O5' A:A225 4.6 6.1 1.0 O3' A:G224 4.7 8.8 1.0 OP2 A:A225 4.7 12.2 1.0 C3' A:A225 5.0 4.8 1.0 O4' A:A628 5.0 1.4 1.0

Magnesium binding site 4 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg910 b:16.3 occ:1.00 O6 A:G692 2.5 4.0 1.0 C6 A:G692 3.7 3.8 1.0 O6 A:G693 4.3 3.8 1.0 N1 A:G693 4.3 3.2 1.0 C5 A:G692 4.5 10.9 1.0 N7 A:G692 4.5 3.4 1.0 N1 A:G692 4.7 9.2 1.0 C6 A:G693 4.7 5.7 1.0

Magnesium binding site 5 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg911 b:12.7 occ:1.00 OP1 A:G425 2.8 4.6 1.0 OP2 A:C426 3.2 11.7 1.0 OP1 A:C426 3.2 6.3 1.0 P A:C426 3.7 3.7 1.0 P A:G425 4.2 3.1 1.0 C5' A:G425 4.3 6.7 1.0 O5' A:G425 4.5 7.8 1.0 O3' A:G425 4.6 6.5 1.0 OP2 A:U427 4.8 3.6 1.0 O5' A:C426 5.0 7.4 1.0

Magnesium binding site 6 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg912 b:5.5 occ:1.00 OP1 A:U218 2.7 6.4 1.0 OP1 A:U423 2.7 1.2 1.0 OP2 A:A422 2.9 15.9 1.0 P A:U423 3.8 15.3 1.0 P A:A422 4.0 22.4 1.0 OP2 A:U423 4.0 13.7 1.0 OP1 A:A422 4.1 7.0 1.0 P A:U218 4.1 7.8 1.0 O3' A:A422 4.7 5.8 1.0 C4' A:A422 4.7 6.9 1.0 OP2 A:U218 4.7 11.5 1.0 O5' A:U218 4.7 5.8 1.0

Magnesium binding site 7 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg913 b:5.2 occ:1.00 O6 A:G440 2.9 7.0 1.0 O6 A:G459 3.5 6.7 1.0 O4 A:U458 3.5 6.1 1.0 O6 A:G441 3.6 4.5 1.0 C6 A:G440 3.9 5.5 1.0 N4 A:C457 4.0 3.6 1.0 C6 A:G459 4.0 3.4 1.0 N3 A:U458 4.0 4.5 1.0 MG A:MG914 4.0 30.0 1.0 N1 A:G459 4.1 3.5 1.0 OP2 A:C439 4.2 15.6 1.0 C4 A:U458 4.3 3.8 1.0 N7 A:G440 4.3 7.2 1.0 C5 A:G440 4.5 2.9 1.0 C6 A:G441 4.5 4.7 1.0

Magnesium binding site 8 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg914 b:30.0 occ:1.00 MG A:MG913 4.0 5.2 1.0 OP2 A:G440 4.5 3.6 1.0 N7 A:G440 4.6 7.2 1.0 OP2 A:C439 4.6 15.6 1.0 OP1 A:C439 5.0 1.9 1.0 O6 A:G441 5.0 4.5 1.0

Magnesium binding site 9 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg915 b:8.7 occ:1.00 O4 A:U274 2.7 8.9 1.0 O6 A:G618 2.9 5.0 1.0 O6 A:G273 3.4 8.7 1.0 N4 A:C619 3.5 10.4 1.0 C4 A:U274 3.7 7.3 1.0 N2 A:G275 4.0 6.2 1.0 C6 A:G618 4.0 3.7 1.0 N3 A:U274 4.1 6.0 1.0 C2 A:G275 4.2 8.6 1.0 N1 A:G275 4.2 9.5 1.0 C6 A:G273 4.4 6.0 1.0 N7 A:G618 4.5 2.8 1.0 OP2 A:A617 4.5 15.6 1.0 OP2 A:U616 4.5 17.7 1.0 C4 A:C619 4.6 2.6 1.0 C5 A:G618 4.6 3.7 1.0 N3 A:G275 4.8 8.5 1.0 C6 A:G275 5.0 10.0 1.0

Magnesium binding site 10 out of 38 in the Comamonas Testosteroni Kf-1 Circularly Permuted Group II Intron Pre-1S 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 Pre-1S State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg916 b:20.3 occ:1.00 O6 A:G236 3.2 1.4 1.0 O6 A:G235 3.3 4.0 1.0 C6 A:G235 4.0 4.2 1.0 N7 A:G235 4.1 4.8 1.0 C6 A:G236 4.1 2.7 1.0 N7 A:G236 4.3 4.6 1.0 C5 A:G235 4.4 4.3 1.0 C5 A:G236 4.6 3.1 1.0 N4 A:C262 4.6 3.7 1.0 N4 A:C263 4.7 2.9 1.0 O6 A:G260 4.7 3.9 1.0 OP2 A:C234 5.0 9.9 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