Magnesium in PDB 5j01: Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+.

The structure of Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+., PDB code: 5j01 was solved by M.Costa, H.Walbott, D.Monachello, E.Westhof, F.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.76 / 3.39
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.930, 262.580, 69.040, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.4

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 - 42;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. (pdb code 5j01). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 42 binding sites of Magnesium where determined in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+., PDB code: 5j01:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:0.9 occ:1.00 O2' A:U419 1.8 98.8 1.0 OP1 A:C377 1.9 94.8 1.0 O3' A:U419 1.9 99.4 1.0 OP2 A:G359 2.0 0.8 1.0 OP1 A:C358 2.0 89.9 1.0 O A:HOH622 2.1 89.1 1.0 C2' A:U419 2.6 0.5 1.0 C3' A:U419 2.6 0.1 1.0 P A:C377 3.1 91.2 1.0 C1' A:U419 3.3 0.3 1.0 P A:G359 3.4 0.6 1.0 P A:C358 3.4 91.8 1.0 OP2 A:C377 3.6 87.5 1.0 O5' A:C358 3.9 95.7 1.0 C5' A:C358 3.9 97.7 1.0 C4' A:U419 3.9 0.1 1.0 O5' A:C377 4.0 85.7 1.0 OP1 A:G359 4.0 0.1 1.0 O4' A:U419 4.2 99.0 1.0 O3' A:A376 4.3 73.7 1.0 OP2 A:C358 4.3 88.7 1.0 O2 A:U419 4.3 0.9 1.0 O3' A:C358 4.3 90.0 1.0 O5' A:G359 4.3 74.8 1.0 O3' A:C357 4.5 94.1 1.0 N1 A:U419 4.5 0.5 1.0 C2 A:U419 4.8 0.1 1.0 C3' A:C358 4.8 96.1 1.0 C4' A:C358 4.9 99.5 1.0

Magnesium binding site 2 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:97.3 occ:1.00 O A:HOH673 2.1 78.5 1.0 O A:HOH666 2.1 92.5 1.0 O A:HOH656 2.1 71.9 1.0 O A:HOH645 2.1 0.1 1.0 O A:HOH752 2.1 0.2 1.0 OP2 A:U4 3.2 93.4 1.0 N7 A:G5 4.2 75.5 1.0 P A:U4 4.4 95.3 1.0 OP2 A:U2 4.5 0.7 1.0 N7 A:A287 4.5 95.2 1.0 N1 A:A376 4.6 84.5 1.0 OP1 A:U4 4.7 95.5 1.0 O A:HOH706 4.8 0.7 1.0 OP1 A:A287 4.8 93.2 1.0 C8 A:G5 4.9 74.9 1.0 O2 A:U2 4.9 0.6 1.0 C2 A:A376 4.9 83.3 1.0 C5' A:U2 4.9 0.4 1.0 O5' A:U4 5.0 73.7 1.0

Magnesium binding site 3 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:85.5 occ:1.00 O A:HOH641 2.1 0.9 1.0 O A:HOH615 2.1 0.6 1.0 O A:HOH725 2.1 89.7 1.0 O4 A:U4 2.3 91.6 1.0 OP1 A:G3 2.3 92.1 1.0 C4 A:U4 3.4 96.0 1.0 OP2 A:A376 3.5 82.4 1.0 O6 A:G5 3.5 75.6 1.0 P A:G3 3.6 97.1 1.0 OP2 A:G3 4.0 96.7 1.0 C5 A:U4 4.1 99.6 1.0 N7 A:G3 4.2 92.4 1.0 C6 A:G5 4.2 76.3 1.0 N1 A:G5 4.4 79.3 1.0 C2' A:U2 4.5 0.8 1.0 N3 A:U4 4.5 98.4 1.0 O3' A:U2 4.6 0.6 1.0 O5' A:G3 4.6 85.2 1.0 O3' A:U375 4.6 81.9 1.0 C3' A:U2 4.6 0.1 1.0 P A:A376 4.7 81.8 1.0 C8 A:G3 4.7 89.4 1.0

Magnesium binding site 4 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:0.8 occ:1.00 O A:HOH689 2.1 0.2 1.0 O A:HOH700 2.1 0.8 1.0 O A:HOH749 2.1 0.3 1.0 O A:HOH751 2.1 0.4 1.0 O A:HOH738 2.1 77.8 1.0 O4 A:U379 3.7 99.8 1.0 O4 A:U363 4.2 0.3 1.0 OP1 A:G378 4.6 94.2 1.0 N6 A:A364 4.7 0.3 1.0 N7 A:G362 4.8 0.1 1.0 C4 A:U379 4.8 95.9 1.0 O6 A:G362 4.8 0.5 1.0 C5 A:C361 4.9 0.1 1.0 N4 A:C361 4.9 0.1 1.0 N7 A:G378 5.0 86.0 1.0

Magnesium binding site 5 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:0.6 occ:1.00 O A:HOH680 2.1 0.5 1.0 O A:HOH647 2.1 0.4 1.0 O A:HOH711 2.1 0.3 1.0 O A:HOH708 2.1 0.8 1.0 OP2 A:A355 2.2 1.0 1.0 OP2 A:A356 2.3 0.8 1.0 P A:A355 3.3 0.6 1.0 O5' A:A355 3.4 0.9 1.0 P A:A356 3.7 0.6 1.0 OP1 A:A355 4.1 0.9 1.0 N7 A:A356 4.3 0.2 1.0 O5' A:A356 4.3 0.1 1.0 OP1 A:A290 4.4 0.8 1.0 OP1 A:A356 4.4 0.3 1.0 C8 A:A356 4.6 0.5 1.0 O3' A:G354 4.6 0.0 1.0 C5' A:A355 4.6 0.7 1.0 O3' A:A355 4.8 0.6 1.0 O5' A:C289 4.8 0.8 1.0 C3' A:C289 4.8 0.3 1.0 C2' A:C289 4.9 0.9 1.0 C3' A:A355 5.0 1.0 1.0

Magnesium binding site 6 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:0.4 occ:1.00 O A:HOH688 2.1 0.8 1.0 O A:HOH687 2.1 0.2 1.0 O A:HOH667 2.1 0.8 1.0 O A:HOH710 2.1 0.1 1.0 OP1 A:C368 2.1 0.5 1.0 OP1 A:U71 2.1 0.2 1.0 P A:C368 3.3 0.4 1.0 P A:U71 3.4 0.1 1.0 O3' A:C367 3.5 93.2 1.0 O3' A:C70 3.8 95.5 1.0 OP2 A:U71 4.2 0.6 1.0 OP2 A:C368 4.3 0.8 1.0 O5' A:C368 4.4 94.5 1.0 C5' A:C368 4.4 94.5 1.0 O5' A:U71 4.6 0.6 1.0 C3' A:C367 4.9 92.0 1.0 C5' A:U71 4.9 0.6 1.0

Magnesium binding site 7 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:0.9 occ:1.00 O A:HOH697 2.1 0.2 1.0 O A:HOH665 2.1 60.6 1.0 O A:HOH604 2.1 0.6 1.0 O A:HOH619 2.1 82.2 1.0 O A:HOH702 2.1 76.0 1.0 OP2 A:G113 3.8 0.0 1.0 N7 A:G114 4.0 0.6 1.0 OP2 A:U71 4.1 0.6 1.0 OP2 A:C112 4.1 0.3 1.0 O6 A:G114 4.5 0.7 1.0 N7 A:G113 4.8 0.0 1.0 C5 A:G114 4.9 0.7 1.0 C8 A:G114 5.0 0.2 1.0

Magnesium binding site 8 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:0.1 occ:1.00 OP2 A:A106 2.0 95.9 1.0 OP1 A:G107 2.0 89.1 1.0 O A:HOH626 2.1 0.7 1.0 O A:HOH644 2.1 69.4 1.0 O A:HOH653 2.1 0.6 1.0 O A:HOH664 2.1 88.8 1.0 P A:G107 3.2 86.9 1.0 O3' A:A106 3.3 0.6 1.0 P A:A106 3.4 97.4 1.0 OP1 A:G108 4.1 76.5 1.0 OP2 A:G107 4.1 85.4 1.0 C5' A:A106 4.1 0.2 1.0 C3' A:A106 4.2 0.5 1.0 OP1 A:A106 4.2 93.2 1.0 O5' A:A106 4.3 0.6 1.0 O3' A:A105 4.3 0.2 1.0 O5' A:G107 4.3 72.5 1.0 C5 A:C261 4.5 92.8 1.0 C4' A:A106 4.6 0.5 1.0 C5' A:G107 4.7 75.0 1.0 OP1 A:A109 4.8 84.8 1.0 C3' A:A105 4.9 98.5 1.0

Magnesium binding site 9 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:0.4 occ:1.00 OP2 A:A105 1.7 0.5 1.0 O A:HOH670 2.1 71.3 1.0 O A:HOH603 2.1 58.9 1.0 P A:A105 2.9 0.9 1.0 OP1 A:A106 3.4 93.2 1.0 OP1 A:A105 3.5 0.1 1.0 O3' A:G104 3.6 0.3 1.0 O6 A:G111 3.9 86.8 1.0 O5' A:A105 4.2 89.8 1.0 C5' A:A105 4.6 92.5 1.0 O A:HOH662 4.7 0.6 1.0 C3' A:G104 4.7 99.3 1.0 N1 A:A77 4.9 0.1 1.0 P A:A106 4.9 97.4 1.0 N4 A:C76 5.0 0.2 1.0 C6 A:G111 5.0 85.9 1.0

Magnesium binding site 10 out of 42 in the Structure of the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ 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 the Lariat Form of A Chimeric Derivative of the Oceanobacillus Iheyensis Group II Intron in the Presence of NH4+ and MG2+. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:0.2 occ:1.00 O A:HOH743 2.1 1.0 1.0 O A:HOH614 2.1 0.4 1.0 O A:HOH660 2.1 0.1 1.0 O A:HOH712 2.1 0.2 1.0 O A:HOH635 2.1 0.1 1.0 OP1 A:G111 2.2 93.4 1.0 P A:G111 3.5 92.8 1.0 O5' A:G111 3.6 90.3 1.0 OP1 A:C112 3.8 0.3 1.0 O2' A:A110 4.1 97.2 1.0 C3' A:A110 4.1 97.3 1.0 O2 A:U13 4.2 0.5 1.0 O3' A:A110 4.2 95.5 1.0 P A:C112 4.4 0.5 1.0 OP2 A:C112 4.4 0.3 1.0 C2' A:A110 4.4 97.1 1.0 O3' A:G111 4.5 92.6 1.0 O2' A:U13 4.6 0.5 1.0 OP2 A:G111 4.7 88.7 1.0 O3' A:U13 4.7 0.8 1.0

M.Costa, H.Walbott, D.Monachello, E.Westhof, F.Michel. Crystal Structures of A Group II Intron Lariat Primed For Reverse Splicing. Science V. 354 2016.
ISSN: ESSN 1095-9203
PubMed: 27934709
DOI: 10.1126/SCIENCE.AAF9258