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Magnesium in PDB 3igi: Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron

Protein crystallography data

The structure of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron, PDB code: 3igi was solved by N.Toor, K.S.Keating, O.Fedorova, K.Rajashankar, J.Wang, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 3.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.092, 94.969, 225.972, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.8

Other elements in 3igi:

The structure of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron also contains other interesting chemical elements:

Potassium (K) 22 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Magnesium atom in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron (pdb code 3igi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 44 binding sites of Magnesium where determined in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron, PDB code: 3igi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 44 in 3igi

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Magnesium binding site 1 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg413

b:57.0
occ:1.00
O3' B:U6 2.2 0.8 1.0
OP1 A:U375 2.2 83.2 1.0
OP2 A:C377 2.3 76.5 1.0
O2' B:U6 2.9 0.1 1.0
OP1 B:A7 3.1 84.6 1.0
P A:U375 3.1 66.2 1.0
C3' B:U6 3.1 0.1 1.0
P B:A7 3.2 0.1 1.0
C4' B:U6 3.4 0.9 1.0
O3' A:G374 3.4 78.4 1.0
P A:C377 3.5 74.1 1.0
OP2 A:U375 3.5 56.3 1.0
C2' B:U6 3.5 0.7 1.0
OP1 A:G359 3.9 68.8 1.0
OP1 A:C377 4.0 72.5 1.0
O5' A:C377 4.0 56.2 1.0
OP2 B:A7 4.2 0.9 1.0
O5' B:A7 4.3 0.6 1.0
O4' B:U6 4.4 88.4 1.0
C5' B:U6 4.4 0.4 1.0
OP2 A:G359 4.5 65.5 1.0
O5' A:U375 4.5 66.0 1.0
C5' B:A7 4.6 0.5 1.0
C1' B:U6 4.6 0.4 1.0
MG A:MG414 4.6 71.9 1.0
C3' A:G374 4.6 76.2 1.0
C5' A:C377 4.7 59.2 1.0
P A:G359 4.7 75.9 1.0
O3' A:A376 4.8 54.5 1.0
C5' A:G374 5.0 78.7 1.0

Magnesium binding site 2 out of 44 in 3igi

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Magnesium binding site 2 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg414

b:71.9
occ:1.00
OP1 B:A7 2.2 84.6 1.0
OP1 A:C358 2.3 90.9 1.0
OP1 A:C377 2.3 72.5 1.0
OP2 B:A7 2.7 0.9 1.0
P B:A7 2.8 0.1 1.0
OP2 A:G359 3.0 65.5 1.0
P A:C377 3.6 74.1 1.0
P A:C358 3.7 77.5 1.0
O5' B:A7 3.9 0.6 1.0
OP2 A:C377 4.1 76.5 1.0
O3' B:U6 4.1 0.8 1.0
P A:G359 4.4 75.9 1.0
O5' A:C358 4.4 62.9 1.0
O3' A:A376 4.4 54.5 1.0
C5' A:C358 4.5 63.6 1.0
C5' B:A7 4.6 0.5 1.0
O3' A:C357 4.6 90.8 1.0
MG A:MG413 4.6 57.0 1.0
OP2 A:C358 4.7 89.8 1.0
O5' A:C377 4.7 56.2 1.0
OP1 A:G359 5.0 68.8 1.0

Magnesium binding site 3 out of 44 in 3igi

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Magnesium binding site 3 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg415

b:84.9
occ:1.00
OP2 A:U4 2.6 84.5 1.0
O A:HOH533 2.7 79.8 1.0
O A:HOH565 3.4 86.8 1.0
OP1 A:G3 3.5 0.5 1.0
P A:U4 4.0 76.5 1.0
OP1 A:U4 4.5 88.0 1.0
O3' A:G3 4.7 56.0 1.0
P A:G3 4.7 0.6 1.0
O5' A:G3 4.8 83.8 1.0

Magnesium binding site 4 out of 44 in 3igi

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Magnesium binding site 4 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg416

b:91.6
occ:1.00
O6 A:G15 2.8 98.8 1.0
O4 A:U256 3.2 0.9 1.0
O6 A:G14 3.7 99.4 1.0
C6 A:G15 4.0 88.9 1.0
O4 A:U255 4.0 0.0 1.0
C4 A:U256 4.3 0.4 1.0
C6 A:G14 4.5 82.5 1.0
N3 A:U256 4.5 1.0 1.0
N7 A:G15 4.6 83.6 1.0
C5 A:G15 4.7 83.5 1.0
O6 A:G16 4.8 97.4 1.0

Magnesium binding site 5 out of 44 in 3igi

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Magnesium binding site 5 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg417

b:75.0
occ:1.00
O6 A:G244 3.6 0.8 1.0
O6 A:G243 3.8 91.0 1.0
O6 A:G242 4.0 0.2 1.0
N7 A:G243 4.1 84.9 1.0
N7 A:G242 4.2 85.5 1.0
C6 A:G244 4.5 93.0 1.0
O A:HOH546 4.5 84.5 1.0
C6 A:G242 4.6 96.9 1.0
C6 A:G243 4.6 90.6 1.0
C5 A:G242 4.6 82.3 1.0
C5 A:G243 4.8 88.4 1.0

Magnesium binding site 6 out of 44 in 3igi

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Magnesium binding site 6 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg418

b:91.5
occ:1.00
O A:HOH546 2.6 84.5 1.0
OP1 A:C39 4.0 90.4 1.0
OP2 A:G243 4.3 0.4 1.0
O3' A:C38 4.5 72.2 1.0
OP1 A:C38 4.7 56.9 1.0
P A:C39 4.8 86.6 1.0
O6 A:G244 4.8 0.8 1.0
C5' A:C38 5.0 72.4 1.0

Magnesium binding site 7 out of 44 in 3igi

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Magnesium binding site 7 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg419

b:0.3
occ:1.00
O6 A:G385 2.9 77.6 1.0
O6 A:G386 3.1 90.0 1.0
MG A:MG421 3.4 99.2 1.0
C6 A:G385 3.7 75.3 1.0
N7 A:G385 3.8 90.2 1.0
C5 A:G385 4.0 83.1 1.0
C6 A:G386 4.0 90.4 1.0
N7 A:G386 4.2 86.8 1.0
O2 A:C289 4.4 95.5 1.0
C5 A:G386 4.5 89.4 1.0
N4 A:C358 4.5 65.2 1.0
N1 A:G385 4.8 73.5 1.0
N4 A:C357 4.9 80.8 1.0
C8 A:G385 4.9 91.0 1.0
O6 A:G359 4.9 90.6 1.0

Magnesium binding site 8 out of 44 in 3igi

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Magnesium binding site 8 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg420

b:84.2
occ:1.00
O A:HOH501 2.5 88.3 1.0
OP1 A:G135 3.8 76.6 1.0
OP1 A:G373 3.9 66.9 1.0
O3' A:A134 4.3 69.9 1.0
OP1 A:U132 4.4 74.7 1.0
OP1 A:G133 4.6 73.9 1.0
P A:G135 4.7 85.8 1.0
P A:G373 4.9 72.2 1.0
OP2 A:G133 4.9 62.3 1.0
O2' A:A134 4.9 94.7 1.0

Magnesium binding site 9 out of 44 in 3igi

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Magnesium binding site 9 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg421

b:99.2
occ:1.00
OP2 A:A290 3.0 69.2 1.0
O6 A:G386 3.2 90.0 1.0
MG A:MG419 3.4 0.3 1.0
O4 A:U387 3.7 79.5 1.0
C6 A:G386 4.1 90.4 1.0
N7 A:G386 4.3 86.8 1.0
P A:A290 4.3 87.1 1.0
C5 A:G386 4.5 89.4 1.0
O6 A:G388 4.7 96.4 1.0
O5' A:A290 4.7 91.3 1.0
O3' A:C289 4.8 89.7 1.0
C5' A:A290 4.8 85.1 1.0
C4 A:U387 4.8 73.2 1.0
N4 A:C357 4.8 80.8 1.0
O2' A:C289 4.9 81.8 1.0

Magnesium binding site 10 out of 44 in 3igi

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Magnesium binding site 10 out of 44 in the Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg422

b:86.6
occ:1.00
OP2 A:G374 2.5 64.7 1.0
O A:HOH536 2.8 74.1 1.0
OP1 A:C360 3.0 81.5 1.0
OP2 A:G373 3.7 76.4 1.0
P A:G374 4.0 76.3 1.0
O5' A:G373 4.1 51.8 1.0
P A:G373 4.2 72.2 1.0
OP1 A:G373 4.3 66.9 1.0
P A:C360 4.4 79.7 1.0
C3' A:G373 4.5 57.9 1.0
O3' A:G373 4.5 54.6 1.0
OP1 A:G374 4.9 85.1 1.0
O5' A:G374 4.9 78.8 1.0
O5' A:C360 4.9 77.8 1.0
C5' A:G374 5.0 78.7 1.0
C8 A:G374 5.0 62.6 1.0

Reference:

N.Toor, K.S.Keating, O.Fedorova, K.Rajashankar, J.Wang, A.M.Pyle. Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron. Rna V. 16 57 2010.
ISSN: ISSN 1355-8382
PubMed: 19952115
DOI: 10.1261/RNA.1844010
Page generated: Mon Dec 14 08:16:57 2020

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