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Magnesium in PDB 4e8p: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+

Protein crystallography data

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p 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) 48.16 / 3.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.987, 95.024, 223.492, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.4

Other elements in 4e8p:

The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ also contains other interesting chemical elements:

Rubidium (Rb) 18 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+ (pdb code 4e8p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+, PDB code: 4e8p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in 4e8p

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Magnesium binding site 1 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:82.0
occ:1.00
O3' A:C286 2.3 0.6 1.0
O5' A:A287 2.6 0.7 1.0
P A:A287 2.9 0.6 1.0
OP1 A:A287 3.3 0.2 1.0
C3' A:C286 3.5 0.5 1.0
C5' A:A287 3.8 0.4 1.0
C4' A:C286 4.0 0.2 1.0
OP2 A:G321 4.2 93.7 1.0
OP2 A:A287 4.2 0.8 1.0
OP1 A:G288 4.3 0.2 1.0
O2' A:C286 4.3 0.1 1.0
OP1 A:G321 4.3 97.6 1.0
C1' A:C286 4.3 97.5 1.0
C2' A:C286 4.3 0.3 1.0
OP2 A:G288 4.5 1.0 1.0
O4' A:C286 4.5 96.3 1.0
P A:G321 4.6 0.5 1.0
P A:G288 4.6 0.2 1.0
O3' A:G320 4.7 86.8 1.0
O3' A:A287 4.7 0.0 1.0
C3' A:A287 4.8 1.0 1.0
C4' A:A287 4.8 0.5 1.0

Magnesium binding site 2 out of 27 in 4e8p

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Magnesium binding site 2 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:66.0
occ:1.00
OP1 A:U375 2.1 91.5 1.0
OP2 A:C377 2.4 78.0 1.0
O A:HOH924 2.5 51.4 1.0
P A:C377 3.4 83.9 1.0
P A:U375 3.5 96.9 1.0
OP1 A:C377 3.6 84.5 1.0
O3' A:G374 3.9 87.4 1.0
MG A:MG403 4.2 64.8 1.0
OP1 A:G359 4.3 0.7 1.0
OP2 A:U375 4.4 99.4 1.0
OP2 A:G359 4.5 94.9 1.0
O5' A:C377 4.6 86.8 1.0
O3' A:A376 4.6 87.7 1.0
O5' A:U375 4.7 83.0 1.0
C3' A:A376 4.8 95.1 1.0
C5' A:U375 4.9 79.9 1.0
C5' A:A376 4.9 87.0 1.0
O A:HOH921 4.9 80.2 1.0
C4' A:A376 4.9 92.5 1.0
P A:G359 5.0 0.7 1.0

Magnesium binding site 3 out of 27 in 4e8p

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Magnesium binding site 3 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:64.8
occ:1.00
OP1 A:C377 1.4 84.5 1.0
OP1 A:C358 1.9 96.1 1.0
OP2 A:G359 2.0 94.9 1.0
O A:HOH921 2.4 80.2 1.0
P A:C377 2.8 83.9 1.0
O A:HOH924 2.8 51.4 1.0
P A:C358 2.9 94.4 1.0
O5' A:C358 2.9 97.0 1.0
P A:G359 3.4 0.7 1.0
O5' A:C377 3.4 86.8 1.0
RB A:RB437 3.5 93.0 1.0
RB A:RB428 3.5 54.0 0.3
OP2 A:C377 3.7 78.0 1.0
O3' A:A376 3.8 87.7 1.0
C5' A:C358 3.9 0.7 1.0
OP2 A:C358 3.9 98.4 1.0
O5' A:G359 4.1 99.5 1.0
O3' A:C357 4.1 95.2 1.0
OP1 A:G359 4.2 0.7 1.0
MG A:MG402 4.2 66.0 1.0
O3' A:C358 4.4 0.8 1.0
C3' A:C358 4.7 0.0 1.0
C5' A:C377 4.8 86.2 1.0
C4' A:C358 4.9 0.4 1.0

Magnesium binding site 4 out of 27 in 4e8p

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Magnesium binding site 4 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:77.3
occ:1.00
OP2 A:U4 2.2 88.2 1.0
OP1 A:G3 2.3 0.8 1.0
P A:U4 3.7 92.3 1.0
P A:G3 3.8 0.7 1.0
O3' A:G3 4.5 92.9 1.0
O3' A:U2 4.5 0.3 1.0
OP1 A:U4 4.5 94.5 1.0
O5' A:G3 4.5 0.4 1.0
O6 A:G5 4.6 85.6 1.0
C5' A:G3 4.7 98.5 1.0
O5' A:U4 4.7 80.2 1.0
OP2 A:G3 4.7 0.4 1.0
C3' A:G3 4.9 95.1 1.0
C2 A:A376 4.9 95.7 1.0

Magnesium binding site 5 out of 27 in 4e8p

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Magnesium binding site 5 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:85.1
occ:1.00
O6 A:G386 3.1 0.7 1.0
OP2 A:A290 3.7 0.2 1.0
O3' A:C289 4.1 0.3 1.0
C6 A:G386 4.2 0.6 1.0
O6 A:G385 4.3 0.7 1.0
P A:A290 4.4 0.0 1.0
C5' A:A290 4.4 0.6 1.0
N7 A:G386 4.7 0.4 1.0
C5 A:G386 4.9 0.8 1.0

Magnesium binding site 6 out of 27 in 4e8p

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Magnesium binding site 6 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:70.9
occ:1.00
OP2 A:G374 2.5 96.7 1.0
OP1 A:C360 3.1 95.0 1.0
OP2 A:G373 3.6 0.3 1.0
OP2 A:C360 3.9 89.3 1.0
P A:G374 4.0 0.9 1.0
P A:C360 4.0 0.3 1.0
P A:G373 4.3 0.3 1.0
OP1 A:G373 4.4 99.7 1.0
O5' A:G373 4.4 93.2 1.0
OP1 A:G374 4.7 0.3 1.0
C3' A:G373 4.8 97.8 1.0
O5' A:C360 4.8 1.0 1.0
C5' A:G374 4.8 86.8 1.0
O3' A:G373 4.9 96.0 1.0
O5' A:G374 4.9 95.4 1.0

Magnesium binding site 7 out of 27 in 4e8p

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Magnesium binding site 7 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:79.3
occ:1.00
O6 A:G325 2.4 0.1 1.0
N7 A:G324 3.1 0.4 1.0
C6 A:G325 3.5 0.2 1.0
O6 A:G324 3.6 0.0 1.0
C5 A:G324 3.9 0.9 1.0
OP2 A:G324 4.0 0.5 1.0
C8 A:G324 4.1 0.8 1.0
C6 A:G324 4.1 0.7 1.0
C5 A:G325 4.3 0.3 1.0
N1 A:G325 4.4 0.9 1.0
N7 A:G325 4.5 0.1 1.0
OP2 A:C323 4.5 0.0 1.0

Magnesium binding site 8 out of 27 in 4e8p

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Magnesium binding site 8 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:61.9
occ:1.00
O6 A:G46 3.6 67.8 1.0
O4 A:U47 3.9 66.5 1.0
OP1 A:U59 3.9 65.7 1.0
RB A:RB441 4.0 0.3 1.0
N7 A:G46 4.2 69.5 1.0
OP2 A:U59 4.4 68.7 1.0
C6 A:G46 4.5 68.5 1.0
O4 A:U45 4.5 79.5 1.0
C5 A:G46 4.7 67.9 1.0
P A:U59 4.7 65.8 1.0
O6 A:G48 4.9 57.6 1.0
C4 A:U47 4.9 67.1 1.0
C5 A:U45 4.9 78.0 1.0
O2' A:G58 4.9 72.9 1.0
C4 A:U45 4.9 74.8 1.0

Magnesium binding site 9 out of 27 in 4e8p

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Magnesium binding site 9 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:75.3
occ:1.00
OP1 A:G239 2.2 78.0 1.0
OP1 A:C119 2.9 81.4 1.0
O3' A:U238 3.1 73.6 1.0
OP1 A:A174 3.2 75.7 1.0
P A:G239 3.2 76.2 1.0
O5' A:G239 4.2 74.8 1.0
C5' A:C119 4.2 61.8 1.0
C5' A:G239 4.2 74.5 1.0
P A:C119 4.3 80.7 1.0
C3' A:U238 4.4 73.9 1.0
OP2 A:G239 4.5 81.8 1.0
O5' A:U238 4.5 70.8 1.0
O5' A:C119 4.6 68.8 1.0
P A:A174 4.6 92.0 1.0
O3' A:G118 4.7 80.3 1.0
C5' A:A174 4.9 80.1 1.0
C4' A:U238 4.9 73.7 1.0

Magnesium binding site 10 out of 27 in 4e8p

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Magnesium binding site 10 out of 27 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Rb+ and MG2+


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 A Ligand-Free State in the Presence of Rb+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:61.8
occ:1.00
OP1 A:G107 2.1 81.5 1.0
P A:G107 3.6 84.2 1.0
N7 A:A105 3.8 94.9 1.0
OP2 A:A105 4.0 78.5 1.0
C8 A:A105 4.1 95.2 1.0
O3' A:A106 4.2 91.4 1.0
OP2 A:G107 4.3 82.9 1.0
OP1 A:G108 4.6 92.3 1.0
O5' A:G107 4.7 73.5 1.0
OP2 A:A106 4.8 96.2 1.0
C5' A:A106 4.8 84.5 1.0

Reference:

M.Marcia, A.M.Pyle. Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033
Page generated: Mon Dec 14 13:44:33 2020

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