Magnesium in PDB 8oly: Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B

The structure of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B, PDB code: 8oly was solved by I.Silvestri, M.Marcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.02 / 3.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.518, 94.686, 222.874, 90, 90, 90
R / Rfree (%)	20 / 23.7

The structure of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B also contains other interesting chemical elements:

Potassium

(K)

19 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 Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B (pdb code 8oly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 30 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B, PDB code: 8oly:
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 Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:131.0 occ:1.00 O A:HOH519 1.7 101.7 1.0 O A:HOH516 1.8 146.7 1.0 OP1 A:C377 1.9 115.2 1.0 OP1 A:C358 1.9 132.9 1.0 OP2 A:G359 2.0 131.5 1.0 P A:C377 2.8 113.9 1.0 P A:G359 3.1 102.8 1.0 OP2 A:C377 3.3 115.6 1.0 OP1 A:G359 3.3 101.3 1.0 P A:C358 3.3 119.4 1.0 O5' A:C377 3.4 100.9 1.0 MG A:MG431 3.4 107.9 1.0 K A:K441 3.6 114.8 1.0 O5' A:C358 3.9 118.3 1.0 O3' A:C358 4.0 111.4 1.0 N7 A:G1 4.1 180.8 1.0 O3' A:A376 4.2 105.2 1.0 C5' A:C358 4.2 114.2 1.0 O3' B:U0 4.3 112.8 1.0 OP2 A:C358 4.3 119.5 1.0 O A:HOH528 4.3 79.6 1.0 OP2 A:G1 4.3 240.2 1.0 C8 A:G1 4.3 205.0 1.0 O5' A:G359 4.3 108.1 1.0 O3' A:C357 4.4 117.0 1.0 C5' A:C377 4.8 104.1 1.0 C3' A:C358 4.9 124.0 1.0

Magnesium binding site 2 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:117.2 occ:1.00 OP2 A:U4 3.2 106.3 1.0 P A:U4 4.2 109.8 1.0 N1 A:A376 4.3 108.2 1.0 N7 A:G5 4.3 106.1 1.0 OP1 A:U4 4.4 125.5 1.0 OP2 A:G5 4.6 99.3 1.0 C2 A:A376 4.7 109.3 1.0 C8 A:G5 4.8 97.2 1.0 O5' A:U4 4.8 95.4 1.0

Magnesium binding site 3 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:132.5 occ:1.00 O6 A:G386 3.5 132.4 1.0 O6 A:G385 3.7 134.4 1.0 OP2 A:A290 3.8 118.1 1.0 O3' A:C289 4.1 142.6 1.0 C6 A:G385 4.4 129.8 1.0 C6 A:G386 4.5 131.8 1.0 N7 A:G386 4.5 167.0 1.0 P A:A290 4.6 141.0 1.0 O2 A:C289 4.8 159.7 1.0 N7 A:G385 4.8 135.4 1.0 C5 A:G385 4.9 133.1 1.0 C5 A:G386 4.9 145.8 1.0 C1' A:C289 4.9 136.0 1.0 C5' A:A290 5.0 139.7 1.0

Magnesium binding site 4 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:87.9 occ:1.00 O4 A:U379 4.2 129.4 1.0 O4 A:U363 4.2 134.5 1.0 O6 A:G362 4.5 153.6 1.0 N7 A:G362 4.5 128.8 1.0 OP1 A:G378 4.5 116.0 1.0 N4 A:C361 4.7 142.9 1.0 N6 A:A380 4.8 152.2 1.0 C5 A:C361 4.8 129.4 1.0 C4 A:C361 4.8 128.3 1.0 N6 A:A364 4.9 129.0 1.0

Magnesium binding site 5 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:127.4 occ:1.00 O A:HOH511 1.7 127.7 1.0 OP2 A:G374 3.6 101.2 1.0 OP2 A:G373 3.8 118.8 1.0 OP1 A:C360 3.8 123.3 1.0 OP2 A:C361 4.4 138.0 1.0 O5' A:G373 4.5 105.8 1.0 P A:G373 4.6 112.3 1.0 OP1 A:C361 4.7 113.3 1.0 N7 A:G374 4.7 98.8 1.0 P A:C360 4.8 125.6 1.0 O5' A:C360 4.9 119.1 1.0 C8 A:G374 4.9 95.3 1.0

Magnesium binding site 6 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:131.0 occ:1.00 OP2 A:U26 2.1 139.9 1.0 P A:U26 3.4 128.0 1.0 O4 A:U65 3.7 118.7 1.0 O5' A:U26 4.0 109.1 1.0 OP1 A:U26 4.2 104.8 1.0 C4 A:U65 4.4 99.3 1.0 C5 A:U65 4.4 92.6 1.0 C5 A:U26 4.5 106.3 1.0 C6 A:U26 4.6 94.5 1.0 O3' A:A25 4.6 119.2 1.0 O6 A:G41 4.8 126.6 1.0

Magnesium binding site 7 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:154.7 occ:1.00 O A:HOH532 1.7 129.1 1.0 O A:HOH503 1.7 151.3 1.0 O6 A:G325 2.3 167.5 1.0 C6 A:G325 3.5 181.8 1.0 OP2 A:C323 3.9 138.2 1.0 N7 A:G324 4.0 183.5 1.0 O6 A:G324 4.0 156.1 1.0 C5 A:G325 4.4 200.4 1.0 N1 A:G325 4.4 171.6 1.0 N7 A:G325 4.6 220.9 1.0 C6 A:G324 4.7 164.0 1.0 C5 A:G324 4.7 179.5 1.0 P A:C323 4.8 157.4 1.0 OP2 A:G324 4.9 143.6 1.0

Magnesium binding site 8 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:135.3 occ:1.00 O A:HOH531 1.7 133.0 1.0 K A:K451 2.9 146.3 1.0 O6 A:G46 3.1 114.4 1.0 O4 A:U47 3.1 108.6 1.0 OP2 A:U59 3.3 84.4 1.0 N7 A:G46 3.7 93.3 1.0 C6 A:G46 3.9 111.3 1.0 C5 A:G46 4.1 98.7 1.0 C4 A:U47 4.1 96.9 1.0 O2' A:G58 4.3 102.1 1.0 O4 A:U45 4.3 127.3 1.0 N6 A:A61 4.3 101.7 1.0 N1 A:G48 4.4 82.6 1.0 P A:U59 4.4 91.9 1.0 OP1 A:U59 4.5 86.8 1.0 C5 A:U47 4.6 110.3 1.0 O6 A:G48 4.6 97.5 1.0 C6 A:G48 4.7 84.3 1.0 C4 A:U45 4.8 106.2 1.0 C8 A:G46 4.8 105.5 1.0

Magnesium binding site 9 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:97.3 occ:1.00 O A:HOH505 1.7 92.3 1.0 OP1 A:G107 2.2 92.2 1.0 OP2 A:A106 3.5 106.1 1.0 OP2 A:A105 3.5 97.3 1.0 P A:G107 3.6 104.7 1.0 C8 A:A105 3.7 106.3 1.0 N7 A:A105 3.8 102.6 1.0 O3' A:A106 3.9 104.2 1.0 OP2 A:G107 4.4 100.0 1.0 O5' A:G107 4.8 84.6 1.0 C5' A:A106 4.8 107.7 1.0 C5' A:G107 4.8 96.2 1.0 P A:A106 4.8 122.7 1.0 P A:A105 4.8 106.2 1.0 O5' A:A106 4.8 108.6 1.0 C3' A:A106 4.9 99.6 1.0 C3' A:A105 4.9 115.2 1.0 O5' A:A105 5.0 105.1 1.0

Magnesium binding site 10 out of 30 in the Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron Post First Step of Splicing in the Presence of K+, MG2+ and Intronistat B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:100.6 occ:1.00 O A:HOH510 1.7 93.2 1.0 OP2 A:C372 2.2 132.4 1.0 O6 A:G373 3.5 99.8 1.0 P A:C372 3.5 120.9 1.0 N7 A:G373 3.8 113.0 1.0 O5' A:C372 4.0 100.2 1.0 C6 A:G373 4.3 99.1 1.0 OP1 A:C372 4.3 133.4 1.0 OP1 A:A371 4.4 129.2 1.0 O6 A:G374 4.4 95.1 1.0 C5 A:G373 4.5 105.1 1.0 OP2 A:A371 4.6 130.7 1.0 C5 A:C372 4.6 115.6 1.0 N7 A:G374 4.7 98.8 1.0 O3' A:A371 4.7 105.9 1.0 P A:A371 4.8 119.9 1.0 O5' A:A371 4.9 118.8 1.0 C6 A:C372 4.9 117.7 1.0 C3' A:A371 4.9 101.4 1.0 C8 A:G373 5.0 117.5 1.0

I.Silvestri, J.Manigrasso, A.Andreani, N.Brindani, C.Mas, J.B.Reiser, P.Vidossich, G.Martino, A.Mccarthy, M.De Vivo, M.Marcia. Targeting the Conserved Active Site of Splicing Machines with Specific and Selective Small Molecule Modulators Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48697-0