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Magnesium in PDB 8ruk: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850, PDB code: 8ruk 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) 48.55 / 4.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.845, 95.144, 225.535, 90, 90, 90
R / Rfree (%) 19.1 / 24.3

Other elements in 8ruk:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850 also contains other interesting chemical elements:

Sodium (Na) 4 atoms
Bromine (Br) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 10 in 8ruk

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Magnesium binding site 1 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:39.3
occ:1.00
 O6 A:G46 3.4 97.6 1.0
OP2 A:U59 3.4 92.2 1.0
OP1 A:U59 4.0 94.5 1.0
O4 A:U47 4.1 94.0 1.0
P A:U59 4.2 93.7 1.0
C6 A:G46 4.3 91.9 1.0
N7 A:G46 4.6 97.9 1.0
O2' A:G58 4.6 93.9 1.0
O6 A:G48 4.6 92.0 1.0
O4 A:U45 4.7 118.2 1.0
C5 A:G46 4.8 94.8 1.0
N6 A:A61 4.8 86.9 1.0
N1 A:G48 4.9 88.1 1.0

Magnesium binding site 2 out of 10 in 8ruk

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Magnesium binding site 2 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:87.2
occ:1.00
 OP1 A:G107 2.0 155.9 1.0
P A:G107 3.5 160.9 1.0
N7 A:A105 3.8 165.8 1.0
C8 A:A105 4.1 163.7 1.0
OP2 A:A105 4.1 131.7 1.0
O5' A:G107 4.2 146.8 1.0
C5' A:G107 4.3 138.8 1.0
OP2 A:G107 4.3 152.6 1.0
O3' A:A106 4.5 155.9 1.0
OP1 A:G108 4.7 133.6 1.0
C5 A:C261 4.8 150.3 1.0
OP1 A:A109 4.9 122.7 1.0
C5' A:A106 5.0 151.1 1.0

Magnesium binding site 3 out of 10 in 8ruk

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Magnesium binding site 3 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:85.7
occ:1.00
 OP1 A:G239 2.0 133.3 1.0
OP1 A:C119 2.9 130.6 1.0
P A:G239 3.4 133.7 1.0
OP1 A:A174 4.0 128.8 1.0
O3' A:U238 4.0 137.7 1.0
P A:C119 4.4 124.4 1.0
O5' A:G239 4.4 127.7 1.0
OP2 A:G239 4.4 133.8 1.0
OP2 A:A120 4.5 95.2 1.0
C5' A:C119 4.6 109.1 1.0
C5' A:G239 4.8 123.1 1.0
O5' A:C119 4.9 116.0 1.0
OP1 A:U238 4.9 137.8 1.0

Magnesium binding site 4 out of 10 in 8ruk

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Magnesium binding site 4 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:81.5
occ:1.00
 OP1 A:A105 3.3 130.5 1.0
P A:A105 4.8 137.2 1.0

Magnesium binding site 5 out of 10 in 8ruk

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Magnesium binding site 5 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:100.1
occ:1.00
 OP2 A:U66 2.0 155.0 1.0
OP1 A:A67 2.0 118.1 1.0
P A:A67 3.4 102.1 1.0
P A:U66 3.5 151.2 1.0
O3' A:U66 3.8 103.4 1.0
O5' A:U66 4.1 124.5 1.0
O5' A:A67 4.3 92.3 1.0
O3' A:U65 4.4 136.2 1.0
OP2 A:A67 4.4 92.4 1.0
OP1 A:U66 4.4 142.7 1.0
C5' A:A67 4.6 90.7 1.0
C3' A:U66 5.0 102.3 1.0

Magnesium binding site 6 out of 10 in 8ruk

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Magnesium binding site 6 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:53.8
occ:1.00
 O A:HOH507 2.8 51.6 1.0
OP1 A:U96 4.4 104.9 1.0
OP2 A:U96 4.4 99.7 1.0
OP1 A:G284 4.7 119.6 1.0
P A:U96 5.0 104.6 1.0

Magnesium binding site 7 out of 10 in 8ruk

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Magnesium binding site 7 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:44.1
occ:1.00
 OP2 A:A67 2.0 92.4 1.0
O6 A:G68 2.7 130.0 1.0
N7 A:G68 2.8 113.4 1.0
C6 A:G68 3.3 112.4 1.0
P A:A67 3.3 102.1 1.0
C5 A:G68 3.3 110.3 1.0
O5' A:U66 3.7 124.5 1.0
C5' A:U66 4.0 104.5 1.0
OP1 A:A67 4.0 118.1 1.0
C8 A:G68 4.0 119.3 1.0
C3' A:U66 4.2 102.3 1.0
O3' A:U66 4.2 103.4 1.0
N1 A:A120 4.4 95.4 1.0
OP1 A:U65 4.5 95.9 1.0
O5' A:A67 4.5 92.3 1.0
N1 A:G68 4.6 107.2 1.0
C4 A:G68 4.6 111.1 1.0
C4' A:U66 4.7 104.1 1.0
N6 A:A120 4.9 105.8 1.0
N9 A:G68 5.0 118.4 1.0

Magnesium binding site 8 out of 10 in 8ruk

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Magnesium binding site 8 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:86.8
occ:1.00
 OP2 A:A283 2.0 129.1 1.0
O A:HOH501 3.0 86.6 1.0
P A:A283 3.1 127.1 1.0
OP1 A:A283 3.5 123.7 1.0
O5' A:A283 3.8 126.3 1.0
O3' A:A282 4.5 122.0 1.0
C3' A:A282 4.9 118.0 1.0
O6 A:G284 4.9 132.2 1.0
O5' A:A282 5.0 132.4 1.0

Magnesium binding site 9 out of 10 in 8ruk

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Magnesium binding site 9 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:133.6
occ:1.00
 O32 A:VTR401 2.0 196.6 1.0
O01 A:VTR401 2.0 203.0 1.0
OP1 A:U375 2.0 162.1 1.0
OP2 A:C377 2.0 171.4 1.0
C31 A:VTR401 2.6 209.4 1.0
C02 A:VTR401 2.6 214.1 1.0
P A:U375 3.3 147.5 1.0
P A:C377 3.4 162.6 1.0
OP2 A:U375 3.8 141.8 1.0
MG A:MG411 3.8 131.4 1.0
C29 A:VTR401 4.0 212.7 1.0
C4' A:A376 4.0 149.9 1.0
C03 A:VTR401 4.0 221.7 1.0
OP1 A:C377 4.0 172.0 1.0
O3' A:A376 4.1 162.6 1.0
C3' A:A376 4.1 157.1 1.0
C5' A:A376 4.2 143.1 1.0
O3' A:G374 4.3 155.6 1.0
C18 A:VTR401 4.3 320.0 1.0
OP1 A:G359 4.4 169.1 1.0
O5' A:U375 4.4 139.6 1.0
O5' A:C377 4.5 153.3 1.0
C19 A:VTR401 4.6 311.3 1.0
O30 A:VTR401 4.6 204.7 1.0
C5' A:U375 4.6 135.0 1.0
C5' A:C377 4.9 152.1 1.0
BR04 A:VTR401 5.0 219.2 1.0
C27 A:VTR401 5.0 221.6 1.0

Magnesium binding site 10 out of 10 in 8ruk

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Magnesium binding site 10 out of 10 in the Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+, and ARN25850


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 Na+, MG2+, and ARN25850 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:131.4
occ:1.00
 OP1 A:C358 2.0 168.1 1.0
O32 A:VTR401 2.0 196.6 1.0
OP1 A:C377 2.0 172.0 1.0
O30 A:VTR401 2.0 204.7 1.0
C29 A:VTR401 2.7 212.7 1.0
C31 A:VTR401 2.7 209.4 1.0
OP2 A:G359 2.7 162.4 1.0
P A:C377 2.9 162.6 1.0
P A:C358 2.9 157.9 1.0
OP2 A:C377 3.1 171.4 1.0
O5' A:C358 3.2 158.5 1.0
P A:G359 3.3 165.3 1.0
OP1 A:G359 3.3 169.1 1.0
OP2 A:C358 3.7 149.8 1.0
O5' A:C377 3.7 153.3 1.0
O3' A:C358 3.8 164.7 1.0
MG A:MG410 3.8 133.6 1.0
C5' A:C358 3.9 161.0 1.0
C02 A:VTR401 4.0 214.1 1.0
C27 A:VTR401 4.0 221.6 1.0
O3' A:C357 4.2 159.0 1.0
O3' A:A376 4.3 162.6 1.0
C3' A:C358 4.5 166.9 1.0
C4' A:C358 4.7 165.4 1.0
O01 A:VTR401 4.7 203.0 1.0
O5' A:G359 4.8 154.4 1.0

Reference:

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
Page generated: Fri Aug 15 14:09:36 2025

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