Magnesium in PDB 8om0: Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in the Presence of Na+, MG2+ and Intronistat B, PDB code: 8om0 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) 47.35 / 3.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.813, 94.282, 223.875, 90, 90, 90
R / Rfree (%) 23.8 / 29.6

Other elements in 8om0:

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

Sodium (Na) 5 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 Intronistat B (pdb code 8om0). 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 Intronistat B, PDB code: 8om0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:155.6
occ:1.00
 OP1 A:A356 2.4 239.3 1.0
OP1 A:A290 3.2 223.0 1.0
P A:A356 3.3 298.0 1.0
O3' A:A355 3.4 284.4 1.0
O5' A:A355 3.7 229.3 1.0
OP2 A:A356 3.8 249.9 1.0
O5' A:C289 4.2 222.7 1.0
OP1 A:A355 4.3 325.1 1.0
OP2 A:G291 4.3 236.0 1.0
C3' A:C289 4.4 180.9 1.0
P A:A355 4.4 282.3 1.0
OP1 A:C289 4.4 261.3 1.0
C3' A:A355 4.6 246.8 1.0
P A:A290 4.6 198.0 1.0
OP2 A:A355 4.6 267.1 1.0
C8 A:A290 4.7 217.8 1.0
C5' A:A355 4.8 224.7 1.0
O5' A:A356 4.8 324.9 1.0
C2' A:C289 4.8 182.9 1.0
N7 A:A290 4.8 206.1 1.0
P A:C289 4.8 243.7 1.0
OP2 A:C289 4.9 229.8 1.0
C4' A:A355 4.9 236.9 1.0

Magnesium binding site 2 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:180.7
occ:1.00
 OP1 A:G107 2.0 224.7 1.0
N4 A:C261 2.7 242.3 1.0
O6 A:G3 2.8 263.5 1.0
P A:G107 3.1 198.7 1.0
OP2 A:G107 3.2 194.8 1.0
C2' A:A105 3.6 188.6 1.0
C4 A:C261 3.7 223.8 1.0
N9 A:A105 3.8 215.4 1.0
C8 A:A105 3.8 217.1 1.0
C1' A:A105 3.8 195.9 1.0
O2' A:A105 4.0 177.4 1.0
C6 A:G3 4.0 199.7 1.0
O3' A:A106 4.1 195.1 1.0
C3' A:A106 4.1 201.3 1.0
C5 A:C261 4.1 205.4 1.0
C4 A:A105 4.4 224.8 1.0
C2' A:A106 4.4 200.4 1.0
N7 A:A105 4.4 220.1 1.0
O5' A:G107 4.4 179.4 1.0
C5 A:G107 4.6 186.9 1.0
N7 A:G107 4.6 187.8 1.0
C5 A:A105 4.7 218.9 1.0
C6 A:G107 4.8 189.0 1.0
N3 A:C261 4.8 209.6 1.0
C3' A:A105 4.9 203.5 1.0
N1 A:G3 5.0 185.6 1.0
O6 A:G107 5.0 194.0 1.0
C5 A:G3 5.0 186.0 1.0

Magnesium binding site 3 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:188.0
occ:1.00
 O6 A:G382 2.0 222.2 1.0
N4 A:C381 2.0 243.7 1.0
N7 A:G382 2.4 241.6 1.0
C6 A:G382 2.7 207.9 1.0
C4 A:C381 2.8 246.9 1.0
C5 A:G382 2.8 214.5 1.0
MG A:MG415 2.8 160.3 1.0
N3 A:C381 3.0 239.1 1.0
C8 A:G382 3.7 242.6 1.0
C5 A:C381 3.9 255.9 1.0
N1 A:G382 4.0 196.4 1.0
C4 A:G382 4.2 203.7 1.0
O6 A:G362 4.2 207.9 1.0
N7 A:G383 4.2 226.9 1.0
C2 A:C381 4.2 231.9 1.0
O6 A:G383 4.3 274.1 1.0
N9 A:G382 4.6 219.9 1.0
N1 A:G362 4.8 205.4 1.0
C6 A:G362 4.8 213.1 1.0
C5 A:G383 4.9 226.8 1.0
C6 A:G383 4.9 240.7 1.0
C6 A:C381 4.9 251.2 1.0
O2 A:C381 5.0 209.1 1.0

Magnesium binding site 4 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:238.2
occ:1.00
 OP1 A:G284 3.1 158.9 1.0
OP2 A:G284 3.6 144.3 1.0
P A:G284 3.8 164.7 1.0
OP1 A:A95 4.0 207.4 1.0
O3' A:A283 4.4 186.2 1.0
OP2 A:U96 4.7 154.6 1.0
OP1 A:U96 4.7 182.5 1.0
OP1 A:G81 4.7 227.7 1.0

Magnesium binding site 5 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:225.0
occ:1.00
 N1 A:G155 1.9 302.8 1.0
N9 A:G156 2.2 319.8 1.0
C6 A:G155 2.3 306.3 1.0
C4 A:G156 2.4 329.1 1.0
C1' A:G156 2.4 287.4 1.0
O6 A:G155 2.6 310.3 1.0
C2 A:G155 2.7 298.3 1.0
N3 A:G156 2.8 302.1 1.0
O4' A:G156 3.0 276.8 1.0
C8 A:G156 3.0 327.7 1.0
C5 A:G155 3.2 315.0 1.0
C5 A:G156 3.3 324.9 1.0
N2 A:G155 3.3 294.1 1.0
N3 A:G155 3.6 309.4 1.0
N7 A:G156 3.6 331.4 1.0
C4 A:G155 3.7 320.8 1.0
C2 A:G156 3.7 273.4 1.0
C2' A:G156 3.8 282.2 1.0
O2 A:C180 3.9 258.6 1.0
C6 A:G156 4.2 290.9 1.0
N1 A:G156 4.3 277.2 1.0
N7 A:G155 4.3 310.3 1.0
O2' A:G156 4.4 271.7 1.0
C4' A:G156 4.4 276.0 1.0
C2 A:C180 4.4 267.5 1.0
N2 A:G156 4.6 246.5 1.0
O5' A:G156 4.7 267.5 1.0
C3' A:G156 4.8 283.8 1.0
N1 A:A222 4.9 347.3 1.0
N9 A:G155 4.9 319.5 1.0
N3 A:C180 4.9 272.6 1.0

Magnesium binding site 6 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:186.2
occ:1.00
 O3' A:A282 2.5 290.1 1.0
N7 A:A283 2.6 166.9 1.0
N7 A:G284 2.9 171.5 1.0
OP1 A:A283 2.9 340.9 1.0
C5 A:G284 3.0 152.8 1.0
P A:A283 3.1 320.3 1.0
C6 A:G284 3.1 152.6 1.0
O6 A:G284 3.2 156.5 1.0
OP2 A:A283 3.3 319.4 1.0
C8 A:A283 3.4 157.4 1.0
C5 A:A283 3.7 164.9 1.0
C3' A:A282 3.7 297.9 1.0
C8 A:G284 3.8 172.2 1.0
C4 A:G284 3.9 156.3 1.0
N6 A:A283 3.9 191.7 1.0
N1 A:G284 4.0 156.8 1.0
C6 A:A283 4.2 180.1 1.0
N9 A:G284 4.3 175.1 1.0
O5' A:A283 4.7 265.7 1.0
N3 A:G284 4.7 151.0 1.0
C2 A:G284 4.7 160.3 1.0
N9 A:A283 4.7 155.9 1.0
C4' A:A282 4.8 288.1 1.0
C4 A:A283 4.8 161.9 1.0
C5' A:A282 4.9 299.4 1.0
C2' A:A282 4.9 255.8 1.0

Magnesium binding site 7 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg413

b:179.2
occ:1.00
 OP1 A:C358 1.9 205.0 1.0
OAE A:GDE401 2.0 119.6 1.0
OAC A:GDE401 2.1 117.5 1.0
OP1 A:C377 2.2 185.0 1.0
CAL A:GDE401 2.9 119.2 1.0
CAI A:GDE401 3.0 123.1 1.0
OP2 A:G359 3.2 203.1 1.0
P A:C377 3.2 182.8 1.0
P A:C358 3.4 207.4 1.0
OP2 A:C377 3.4 188.0 1.0
OP1 A:G359 3.4 225.5 1.0
P A:G359 3.7 232.4 1.0
MG A:MG414 3.7 164.9 1.0
O3' A:C357 4.0 222.8 1.0
CAJ A:GDE401 4.1 112.9 1.0
C5' A:C358 4.2 215.5 1.0
O5' A:C377 4.2 199.0 1.0
OP2 A:C358 4.3 203.0 1.0
O5' A:C358 4.3 215.0 1.0
O3' A:C358 4.3 211.3 1.0
CAF A:GDE401 4.3 134.4 1.0
O3' A:A376 4.5 187.7 1.0
OAD A:GDE401 4.7 114.6 1.0
C3' A:C358 4.8 200.0 1.0
OP1 A:U375 4.9 222.0 1.0
C4' A:C358 5.0 211.4 1.0

Magnesium binding site 8 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg414

b:164.9
occ:1.00
 OP1 A:U375 1.7 222.0 1.0
OP2 A:C377 1.7 188.0 1.0
OAD A:GDE401 2.1 114.6 1.0
OAE A:GDE401 2.1 119.6 1.0
P A:U375 2.7 230.4 1.0
CAL A:GDE401 2.9 119.2 1.0
CAJ A:GDE401 2.9 112.9 1.0
OP1 A:G359 2.9 225.5 1.0
O3' A:G374 3.0 213.9 1.0
P A:C377 3.1 182.8 1.0
OP2 A:U375 3.6 230.4 1.0
O5' A:C377 3.7 199.0 1.0
MG A:MG413 3.7 179.2 1.0
OP1 A:C377 3.8 185.0 1.0
O5' A:U375 4.0 225.2 1.0
CAI A:GDE401 4.2 123.1 1.0
C5' A:U375 4.2 223.9 1.0
CAG A:GDE401 4.3 130.3 1.0
P A:G359 4.3 232.4 1.0
O3' A:A376 4.3 187.7 1.0
C3' A:G374 4.4 216.7 1.0
C3' A:A376 4.5 189.0 1.0
OAC A:GDE401 4.6 117.5 1.0
C4' A:A376 4.6 212.9 1.0
C5' A:A376 4.7 208.9 1.0
C5' A:C377 4.8 215.2 1.0
OP2 A:G359 4.8 203.1 1.0
O5' A:A376 5.0 185.5 1.0

Magnesium binding site 9 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg415

b:160.3
occ:1.00
 MG A:MG404 2.8 188.0 1.0
O6 A:G383 3.3 274.1 1.0
O6 A:G382 3.7 222.2 1.0
N7 A:G383 3.8 226.9 1.0
N7 A:G382 4.1 241.6 1.0
C6 A:G383 4.2 240.7 1.0
C6 A:G382 4.3 207.9 1.0
O4 A:U384 4.3 256.1 1.0
C5 A:G383 4.4 226.8 1.0
N4 A:C381 4.4 243.7 1.0
C5 A:G382 4.5 214.5 1.0
N2 A:G288 4.5 197.0 1.0
N3 A:G288 4.9 211.7 1.0
C8 A:G383 5.0 219.1 1.0

Magnesium binding site 10 out of 10 in 8om0

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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 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 in the Presence of Na+, MG2+ and Intronistat B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg416

b:166.8
occ:1.00
 O4 A:U379 3.3 209.8 1.0
O4 A:U363 3.4 228.6 1.0
O6 A:G362 3.8 207.9 1.0
N7 A:G362 3.9 206.2 1.0
N6 A:A380 4.1 200.3 1.0
N6 A:A364 4.1 198.0 1.0
C6 A:G362 4.3 213.1 1.0
C5 A:G362 4.4 211.3 1.0
C4 A:U379 4.5 225.8 1.0
C4 A:U363 4.5 208.5 1.0
C8 A:G362 4.9 214.4 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 Oct 4 14:57:47 2024

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