Magnesium in PDB 8ruj: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking, PDB code: 8ruj 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)	49.52 / 3.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.57, 95.098, 227.801, 90, 90, 90
R / Rfree (%)	19.6 / 23.6

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Potassium	(K)	18 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking (pdb code 8ruj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking, PDB code: 8ruj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:119.2 occ:1.00 O32 A:VTR401 2.0 154.9 1.0 OP2 A:C377 2.0 116.4 1.0 OP1 A:U375 2.0 131.9 1.0 O01 A:VTR401 2.0 143.9 1.0 C31 A:VTR401 2.4 149.2 1.0 C02 A:VTR401 2.5 149.8 1.0 P A:C377 3.4 119.2 1.0 P A:U375 3.4 120.5 1.0 C29 A:VTR401 3.7 155.4 1.0 C03 A:VTR401 3.9 162.5 1.0 MG A:MG403 3.9 132.4 1.0 C18 A:VTR401 3.9 202.8 1.0 OP1 A:G359 4.1 185.3 1.0 OP2 A:U375 4.1 120.7 1.0 OP1 A:C377 4.1 134.7 1.0 O5' A:C377 4.2 128.7 1.0 O3' A:G374 4.2 136.4 1.0 C19 A:VTR401 4.2 208.2 1.0 C4' A:A376 4.3 110.8 1.0 O3' A:A376 4.4 118.7 1.0 O30 A:VTR401 4.4 157.2 1.0 C5' A:A376 4.4 105.5 1.0 C3' A:A376 4.5 117.2 1.0 O5' A:U375 4.5 105.4 1.0 C27 A:VTR401 4.7 170.3 1.0 C5' A:U375 4.8 106.7 1.0 C05 A:VTR401 4.9 166.2 1.0 BR04 A:VTR401 5.0 192.2 1.0

Magnesium binding site 2 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:132.4 occ:1.00 O30 A:VTR401 2.0 157.2 1.0 O32 A:VTR401 2.0 154.9 1.0 OP1 A:C377 2.0 134.7 1.0 OP2 A:G359 2.0 207.1 1.0 OP1 A:C358 2.0 138.0 1.0 OP1 A:G359 2.1 185.3 1.0 P A:G359 2.5 157.6 1.0 C29 A:VTR401 2.7 155.4 1.0 C31 A:VTR401 2.8 149.2 1.0 P A:C377 2.9 119.2 1.0 OP2 A:C377 3.2 116.4 1.0 P A:C358 3.3 132.0 1.0 O5' A:C377 3.5 128.7 1.0 O5' A:G359 3.6 140.4 1.0 K A:K435 3.7 134.3 1.0 O3' A:C358 3.8 134.1 1.0 O5' A:C358 3.8 135.3 1.0 MG A:MG402 3.9 119.2 1.0 OP2 A:C358 3.9 128.9 1.0 C27 A:VTR401 4.0 170.3 1.0 C5' A:C358 4.1 143.0 1.0 C02 A:VTR401 4.1 149.8 1.0 O3' A:A376 4.4 118.7 1.0 C3' A:C358 4.5 144.0 1.0 O3' A:C357 4.6 143.2 1.0 C5' A:G359 4.7 147.4 1.0 C4' A:C358 4.7 143.0 1.0 BR28 A:VTR401 4.8 219.4 1.0 C5' A:C377 4.8 125.7 1.0 O01 A:VTR401 4.8 143.9 1.0

Magnesium binding site 3 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:125.0 occ:1.00 OP2 A:U4 2.0 143.2 1.0 P A:U4 3.5 116.5 1.0 OP1 A:G3 3.6 163.3 1.0 OP1 A:U4 4.2 141.0 1.0 C2 A:A376 4.2 153.4 1.0 N1 A:A376 4.3 143.0 1.0 O3' A:G3 4.5 101.3 1.0 O5' A:U4 4.5 108.2 1.0 O5' A:G3 4.5 151.8 1.0 P A:G3 4.6 169.8 1.0 N7 A:G5 4.8 130.8 1.0

Magnesium binding site 4 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:117.6 occ:1.00 O A:HOH516 1.9 119.5 1.0 OP2 A:G374 2.0 134.7 1.0 OP1 A:C360 2.0 142.4 1.0 P A:C360 3.3 135.5 1.0 P A:G374 3.4 130.4 1.0 OP2 A:C360 3.8 132.8 1.0 OP1 A:G374 3.9 130.9 1.0 O5' A:C360 4.2 143.1 1.0 C5' A:G374 4.3 119.2 1.0 O5' A:G374 4.4 126.6 1.0 O3' A:G373 4.4 126.8 1.0 O3' A:G359 4.4 137.1 1.0 O5' A:G373 4.5 126.3 1.0 C5' A:C360 4.6 150.0 1.0 OP2 A:G373 4.6 127.9 1.0 C3' A:G373 4.6 133.9 1.0 OP1 A:G373 4.7 137.6 1.0 P A:G373 4.8 134.6 1.0

Magnesium binding site 5 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:141.5 occ:1.00 O6 A:G325 2.0 182.8 1.0 O A:HOH521 2.2 150.8 1.0 N7 A:G324 3.1 178.2 1.0 C6 A:G325 3.1 160.3 1.0 O6 A:G324 3.4 140.4 1.0 C5 A:G324 3.9 169.4 1.0 C6 A:G324 4.0 158.4 1.0 N1 A:G325 4.0 153.5 1.0 C5 A:G325 4.1 165.0 1.0 C8 A:G324 4.2 184.7 1.0 N7 A:G325 4.5 172.6 1.0 OP2 A:C323 4.5 170.2 1.0 OP2 A:G324 4.8 137.8 1.0

Magnesium binding site 6 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:123.0 occ:1.00 OP1 A:U59 3.1 108.1 1.0 O6 A:G46 3.3 115.5 1.0 O4 A:U45 3.9 129.1 1.0 O4 A:U47 4.2 95.4 1.0 P A:U59 4.2 111.4 1.0 OP2 A:U59 4.2 108.2 1.0 C6 A:G46 4.4 125.6 1.0 C4 A:U45 4.6 135.5 1.0 C5 A:U45 4.8 136.2 1.0 O2' A:G58 4.8 103.5 1.0 N7 A:G46 4.9 117.3 1.0

Magnesium binding site 7 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:100.2 occ:1.00 O A:HOH503 1.9 112.1 1.0 OP1 A:G107 2.0 107.2 1.0 P A:G107 3.4 115.6 1.0 OP1 A:G108 3.6 97.7 1.0 C5' A:G107 3.9 100.3 1.0 O3' A:A106 4.2 114.8 1.0 N7 A:A105 4.2 146.4 1.0 O5' A:G107 4.3 101.4 1.0 OP2 A:G107 4.5 122.3 1.0 C5 A:C261 4.6 114.4 1.0 C8 A:A105 4.6 139.6 1.0

Magnesium binding site 8 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:122.5 occ:1.00 O A:HOH531 1.7 126.3 1.0 OP2 A:C372 2.0 154.2 1.0 OP2 A:A371 3.4 133.4 1.0 P A:C372 3.5 125.7 1.0 O6 A:G373 3.7 126.4 1.0 OP1 A:A371 3.8 129.6 1.0 P A:A371 4.0 126.2 1.0 O5' A:A371 4.1 124.1 1.0 O3' A:A371 4.2 108.3 1.0 O5' A:C372 4.3 114.6 1.0 C5 A:C372 4.3 146.4 1.0 N7 A:G373 4.4 126.5 1.0 OP1 A:C372 4.4 118.6 1.0 C3' A:A371 4.4 107.8 1.0 C5' A:A371 4.6 119.0 1.0 C6 A:G373 4.6 122.6 1.0 C6 A:C372 4.7 138.0 1.0 C5 A:G373 4.9 114.0 1.0

Magnesium binding site 9 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:114.6 occ:1.00 O4 A:U379 3.7 143.9 1.0 O6 A:G362 3.8 132.2 1.0 O4 A:U363 4.4 155.4 1.0 OP1 A:G378 4.5 111.1 1.0 C5 A:C361 4.5 135.4 1.0 N7 A:G362 4.5 136.2 1.0 N6 A:A380 4.6 148.6 1.0 C6 A:G362 4.7 142.2 1.0 N4 A:C361 4.7 140.8 1.0 C4 A:C361 4.8 139.0 1.0 C4 A:U379 4.9 151.8 1.0 C5 A:G362 5.0 140.6 1.0

Magnesium binding site 10 out of 21 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of K+, MG2+, 5'-Exon, and ARN25850 After 1H Soaking


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+, 5'-Exon, and ARN25850 After 1H Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:107.4 occ:1.00 OP1 A:G239 2.0 132.3 1.0 OP1 A:A174 2.1 109.6 1.0 OP1 A:C119 3.1 106.1 1.0 P A:G239 3.2 117.4 1.0 O3' A:U238 3.4 118.5 1.0 P A:A174 3.5 112.5 1.0 C5' A:G239 3.8 105.4 1.0 O5' A:G239 3.8 106.8 1.0 O3' A:G173 4.3 124.8 1.0 C5' A:A174 4.5 113.0 1.0 OP2 A:G239 4.5 111.8 1.0 OP2 A:A174 4.6 114.4 1.0 O5' A:A174 4.6 110.1 1.0 P A:C119 4.6 109.8 1.0 C3' A:U238 4.8 107.7 1.0 C4' A:G239 5.0 107.6 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