Magnesium in PDB 6t3s: Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3s was solved by M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.89 / 3.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.890, 95.240, 227.896, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23

Other elements in 6t3s:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon (pdb code 6t3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon, PDB code: 6t3s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in 6t3s

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Magnesium binding site 1 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:0.4
occ:1.00
O6 A:G325 2.5 0.7 1.0
O6 A:G324 2.9 0.3 1.0
N7 A:G324 3.0 0.6 1.0
C6 A:G325 3.4 0.8 1.0
C6 A:G324 3.5 0.7 1.0
C5 A:G324 3.6 0.5 1.0
N7 A:G325 4.0 0.8 1.0
C5 A:G325 4.0 0.1 1.0
C8 A:G324 4.2 0.1 1.0
N1 A:G325 4.5 0.4 1.0
OP2 A:C323 4.8 0.4 1.0
N1 A:G324 4.8 0.7 1.0
C4 A:G324 4.8 0.7 1.0

Magnesium binding site 2 out of 20 in 6t3s

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Magnesium binding site 2 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:97.7
occ:1.00
O6 A:G46 3.0 75.1 1.0
O4 A:U45 3.7 72.5 1.0
N7 A:G46 3.8 80.5 1.0
C6 A:G46 3.9 78.1 1.0
C5 A:G46 4.2 76.5 1.0
C4 A:U45 4.2 69.8 1.0
O4 A:U47 4.3 69.0 1.0
C5 A:U45 4.4 70.9 1.0
OP2 A:U59 4.6 80.7 1.0
C8 A:G46 5.0 81.3 1.0

Magnesium binding site 3 out of 20 in 6t3s

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Magnesium binding site 3 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:73.3
occ:1.00
OP1 A:G107 2.4 74.3 1.0
P A:G107 3.8 83.0 1.0
N7 A:A105 3.9 0.4 1.0
OP1 A:G108 4.1 85.5 1.0
C8 A:A105 4.1 1.0 1.0
OP2 A:A105 4.3 76.9 1.0
C5' A:G107 4.3 79.3 1.0
O5' A:G107 4.3 76.7 1.0
O3' A:A106 4.6 88.5 1.0
OP2 A:G107 4.9 85.8 1.0

Magnesium binding site 4 out of 20 in 6t3s

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Magnesium binding site 4 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:82.5
occ:1.00
OP2 A:C372 2.0 0.3 1.0
P A:C372 3.4 96.5 1.0
N7 A:G373 3.8 94.3 1.0
O6 A:G373 3.9 81.3 1.0
O5' A:C372 4.1 89.5 1.0
OP1 A:C372 4.2 0.5 1.0
OP2 A:A371 4.2 81.8 1.0
OP1 A:A371 4.3 92.1 1.0
O6 A:G374 4.4 69.8 1.0
O3' A:A371 4.5 78.8 1.0
P A:A371 4.6 87.6 1.0
C5 A:G373 4.6 81.4 1.0
C6 A:G373 4.6 77.0 1.0
O5' A:A371 4.6 90.7 1.0
C3' A:A371 4.8 79.2 1.0
C5 A:C372 4.8 75.7 1.0
C8 A:G373 4.9 96.6 1.0
N7 A:G374 4.9 78.3 1.0
OP2 A:G373 5.0 96.4 1.0

Magnesium binding site 5 out of 20 in 6t3s

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Magnesium binding site 5 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:81.3
occ:1.00
O4 A:U379 3.6 0.1 1.0
OP1 A:G378 4.2 95.9 1.0
O4 A:U363 4.3 0.9 1.0
O6 A:G362 4.5 0.0 1.0
N7 A:G362 4.7 0.2 1.0
C4 A:U379 4.7 0.5 1.0
N6 A:A380 4.8 0.1 1.0
N6 A:A364 4.8 0.9 1.0
N4 A:C361 4.8 0.5 1.0
N7 A:G378 4.9 0.4 1.0

Magnesium binding site 6 out of 20 in 6t3s

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Magnesium binding site 6 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:65.2
occ:1.00
OP1 A:G239 1.9 79.9 1.0
OP1 A:C119 2.2 81.9 1.0
P A:G239 3.3 73.8 1.0
OP1 A:A174 3.6 61.9 1.0
P A:C119 3.7 83.4 1.0
O3' A:U238 3.7 68.1 1.0
C5' A:C119 4.0 76.7 1.0
O5' A:G239 4.2 68.1 1.0
OP1 A:U238 4.4 63.3 1.0
C5' A:G239 4.4 71.7 1.0
O5' A:C119 4.4 71.9 1.0
O3' A:G118 4.4 76.4 1.0
OP2 A:G239 4.4 70.7 1.0
OP2 A:C119 4.7 92.5 1.0

Magnesium binding site 7 out of 20 in 6t3s

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Magnesium binding site 7 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:0.5
occ:1.00
OP1 A:A105 2.3 79.5 1.0
P A:A105 3.6 79.8 1.0
O5' A:A105 3.9 75.1 1.0
C5' A:A105 4.2 84.5 1.0
C3' A:G104 4.3 84.9 1.0
O3' A:G104 4.4 89.5 1.0
N1 A:A77 4.5 99.8 1.0
OP2 A:A105 4.8 76.9 1.0
C2' A:G104 5.0 82.5 1.0
O6 A:G111 5.0 96.5 1.0

Magnesium binding site 8 out of 20 in 6t3s

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Magnesium binding site 8 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:72.9
occ:1.00
OP2 A:U66 2.1 95.4 1.0
OP1 A:A67 2.4 1.0 1.0
P A:U66 3.5 0.4 1.0
P A:A67 3.6 96.8 1.0
O3' A:U66 3.8 83.9 1.0
OP1 A:U66 4.1 0.1 1.0
OP2 A:A67 4.4 84.0 1.0
O3' A:U65 4.4 0.7 1.0
O5' A:U66 4.5 91.3 1.0
O5' A:A67 4.7 82.8 1.0
C5' A:A67 4.9 82.4 1.0

Magnesium binding site 9 out of 20 in 6t3s

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Magnesium binding site 9 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:78.4
occ:1.00
OP1 A:G284 3.4 89.1 1.0
OP2 A:U96 4.2 85.5 1.0
OP1 A:A95 4.3 89.8 1.0
OP1 A:U96 4.5 83.2 1.0
P A:G284 4.6 95.2 1.0
OP2 A:G284 4.8 96.1 1.0
P A:U96 4.9 91.3 1.0

Magnesium binding site 10 out of 20 in 6t3s

Go back to Magnesium Binding Sites List in 6t3s
Magnesium binding site 10 out of 20 in the Structure of Oceanobacillus Iheyensis Group II Intron U-Mutant (C289U/C358U/G385A) in the Presence of Na+, 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 U-Mutant (C289U/C358U/G385A) in the Presence of Na+, MG2+ and 5'-Exon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:0.3
occ:1.00
OP2 A:A154 2.0 0.5 1.0
N7 A:G155 2.5 0.7 1.0
O6 A:G155 3.1 0.3 1.0
C5 A:G155 3.3 0.6 1.0
P A:A154 3.4 0.9 1.0
C6 A:G155 3.5 0.7 1.0
C8 A:G155 3.6 0.6 1.0
O5' A:A154 4.1 0.8 1.0
OP1 A:A154 4.1 0.4 1.0
OP2 A:G155 4.2 0.4 1.0
N7 A:G156 4.4 0.1 1.0
O3' A:G153 4.5 0.1 1.0
C4 A:G155 4.5 0.8 1.0
O6 A:G156 4.6 0.4 1.0
N9 A:G155 4.7 0.9 1.0
N1 A:G155 4.9 0.8 1.0
O4 A:U221 5.0 0.8 1.0

Reference:

J.Manigrasso, I.Chillon, V.Genna, S.Somarowthu, A.M.Pyle, M.De Vivo, M.Marcia. Visualizing Group II Intron Dynamics Between the First and Second Steps of Splicing To Be Published.
Page generated: Tue Dec 15 00:07:38 2020

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