Magnesium in PDB 8ruh: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon, PDB code: 8ruh 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)	89.23 / 4.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.204, 96.484, 231.693, 90, 90, 90
R / Rfree (%)	18.4 / 25.8

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon also contains other interesting chemical elements:

Potassium

(K)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon (pdb code 8ruh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon, PDB code: 8ruh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:197.4 occ:1.00 OP1 A:C358 2.0 208.3 1.0 OP1 A:C377 2.0 178.4 1.0 OP2 A:G359 2.0 198.5 1.0 O A:HOH521 2.1 116.2 1.0 O B:HOH101 2.4 84.2 1.0 P A:C377 2.9 158.3 1.0 OP2 A:C377 2.9 152.5 1.0 O A:HOH522 3.0 116.6 1.0 P A:G359 3.3 182.3 1.0 P A:C358 3.4 203.2 1.0 O A:HOH502 3.5 123.1 1.0 MG A:MG429 3.6 141.5 1.0 OP1 A:G359 3.7 171.1 1.0 O5' A:C377 3.7 142.8 1.0 C5' A:C358 3.9 214.5 1.0 K A:K438 4.0 174.0 1.0 O5' A:C358 4.0 214.3 1.0 O3' A:A376 4.2 171.5 1.0 O3' A:C358 4.2 199.8 1.0 O3' A:C357 4.3 196.2 1.0 O5' A:G359 4.3 184.2 1.0 OP2 A:C358 4.5 199.6 1.0 O3' B:U0 4.6 186.7 1.0 C4' A:C358 4.9 213.3 1.0 C3' A:C358 4.9 213.2 1.0

Magnesium binding site 2 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:122.0 occ:1.00 O6 A:G386 2.8 181.5 1.0 O6 A:G385 2.9 189.9 1.0 N7 A:G386 3.3 202.5 1.0 C6 A:G385 3.3 189.8 1.0 C6 A:G386 3.6 198.8 1.0 C5 A:G385 3.7 196.1 1.0 N7 A:G385 3.7 209.4 1.0 C5 A:G386 3.8 200.5 1.0 N1 A:G385 4.3 181.7 1.0 C8 A:G386 4.5 213.4 1.0 C8 A:G385 4.7 194.8 1.0 C4 A:G385 4.7 187.3 1.0 O4 A:U387 4.8 178.7 1.0 N1 A:G386 5.0 218.5 1.0

Magnesium binding site 3 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:109.6 occ:1.00 O4 A:U379 3.3 204.7 1.0 N4 A:C361 3.8 256.2 1.0 O4 A:U363 4.0 203.9 1.0 O6 A:G362 4.0 280.2 1.0 N6 A:A380 4.2 217.3 1.0 OP1 A:G378 4.2 166.0 1.0 C5 A:C361 4.3 229.6 1.0 C4 A:C361 4.4 238.3 1.0 C4 A:U379 4.5 207.7 1.0 N7 A:G362 4.7 245.7 1.0 N6 A:A364 4.7 174.6 1.0 C6 A:G362 4.8 268.1 1.0

Magnesium binding site 4 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:72.7 occ:1.00 OP2 A:G373 2.8 210.3 1.0 O A:HOH501 3.3 33.5 1.0 P A:G373 3.9 194.8 1.0 OP1 A:C361 4.2 214.7 1.0 N7 A:G374 4.3 149.8 1.0 O5' A:G373 4.3 148.6 1.0 MG A:MG409 4.4 160.3 1.0 OP1 A:G373 4.5 217.8 1.0 O A:HOH515 4.5 89.3 1.0 OP2 A:C361 4.7 200.2 1.0 N7 A:G373 4.7 146.7 1.0 OP1 A:C360 4.8 174.2 1.0 C8 A:G374 4.9 146.4 1.0 C8 A:G373 5.0 148.2 1.0

Magnesium binding site 5 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:121.7 occ:1.00 OP2 A:U26 2.0 145.1 1.0 P A:U26 3.4 148.2 1.0 O3' A:A25 3.8 153.9 1.0 OP1 A:U26 4.2 148.7 1.0 O2' A:A25 4.3 180.1 1.0 O5' A:U26 4.5 122.5 1.0 OP2 A:G64 4.8 171.2 1.0 O6 A:G41 5.0 174.2 1.0 C5' A:U26 5.0 126.7 1.0

Magnesium binding site 6 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:162.5 occ:1.00 O6 A:G325 2.0 210.9 1.0 C6 A:G325 3.2 213.1 1.0 O6 A:G324 3.4 192.7 1.0 O A:HOH536 3.7 81.0 1.0 OP2 A:C323 3.7 220.5 1.0 N1 A:G325 3.8 189.9 1.0 N7 A:G324 3.9 235.3 1.0 C6 A:G324 4.3 204.4 1.0 C5 A:G325 4.4 242.4 1.0 C5 A:G324 4.5 228.6 1.0 N7 A:G325 4.9 279.7 1.0 P A:C323 4.9 207.9 1.0

Magnesium binding site 7 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:103.4 occ:1.00 O A:HOH524 2.0 50.8 1.0 K A:K446 2.5 189.2 1.0 O4 A:U45 3.5 177.0 1.0 O6 A:G46 3.7 110.7 1.0 OP2 A:U59 3.9 112.8 1.0 C4 A:U45 4.0 163.9 1.0 N7 A:G46 4.0 147.6 1.0 C5 A:U45 4.1 170.9 1.0 C6 A:G46 4.5 111.0 1.0 O4 A:U47 4.5 110.2 1.0 OP1 A:U59 4.6 128.0 1.0 C5 A:G46 4.6 127.8 1.0 O2' A:G58 4.6 164.4 1.0 P A:U59 4.8 126.3 1.0

Magnesium binding site 8 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:160.6 occ:1.00 OP1 A:G107 2.0 172.7 1.0 O A:HOH512 2.5 59.5 1.0 P A:G107 3.3 154.0 1.0 OP2 A:A106 3.4 149.9 1.0 OP2 A:A105 3.8 146.1 1.0 O3' A:A106 3.8 162.0 1.0 C8 A:A105 3.9 171.7 1.0 OP2 A:G107 4.1 138.6 1.0 N7 A:A105 4.1 173.9 1.0 O5' A:A105 4.4 179.1 1.0 O5' A:G107 4.6 142.9 1.0 P A:A106 4.7 166.7 1.0 P A:A105 4.7 162.6 1.0 C3' A:A106 4.7 161.3 1.0 O5' A:A106 4.8 152.0 1.0 C5' A:G107 4.8 138.6 1.0 C3' A:A105 4.8 173.7 1.0

Magnesium binding site 9 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:160.3 occ:1.00 O A:HOH515 1.8 89.3 1.0 OP2 A:C372 2.0 183.6 1.0 P A:C372 3.0 184.4 1.0 OP1 A:C372 3.2 186.2 1.0 O5' A:C372 3.8 169.1 1.0 OP1 A:A371 4.2 177.8 1.0 MG A:MG404 4.4 72.7 1.0 O3' A:A371 4.4 178.9 1.0 O6 A:G373 4.5 129.2 1.0 OP2 A:A371 4.5 162.7 1.0 O6 A:G374 4.7 137.0 1.0 P A:A371 4.7 179.3 1.0 N7 A:G373 4.7 146.7 1.0 OP2 A:G373 4.9 210.3 1.0 O5' A:A371 4.9 184.9 1.0

Magnesium binding site 10 out of 28 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+ and 5'-Exon


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 in the Presence of K+, MG2+ and 5'-Exon within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:121.3 occ:1.00 OP1 A:G239 2.0 121.1 1.0 OP1 A:C119 2.0 171.8 1.0 O A:HOH506 3.1 36.9 1.0 P A:G239 3.3 133.6 1.0 O3' A:U238 3.5 138.8 1.0 P A:C119 3.5 165.8 1.0 OP1 A:A174 3.6 136.1 1.0 C5' A:C119 4.1 154.4 1.0 O3' A:G118 4.1 134.2 1.0 OP2 A:G239 4.2 122.4 1.0 O5' A:C119 4.3 155.0 1.0 O5' A:G239 4.4 143.7 1.0 OP2 A:C119 4.5 161.5 1.0 C3' A:U238 4.9 141.9 1.0 C5' A:G239 5.0 147.4 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