Magnesium in PDB 3eoh: Refined Group II Intron Structure

The structure of Refined Group II Intron Structure, PDB code: 3eoh was solved by N.Toor, K.Rajashankar, K.S.Keating, 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 (%)	20.8 / 23.7

The structure of Refined Group II Intron Structure also contains other interesting chemical elements:

Potassium

(K)

9 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Refined Group II Intron Structure (pdb code 3eoh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 31 binding sites of Magnesium where determined in the Refined Group II Intron Structure, PDB code: 3eoh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:63.1 occ:1.00 OP1 A:G239 2.3 64.8 1.0 OP1 A:C119 2.5 65.1 1.0 O3' A:U238 3.2 56.3 1.0 P A:G239 3.3 47.1 1.0 MG A:MG424 3.3 83.9 1.0 OP1 A:A174 3.6 56.9 1.0 P A:C119 3.9 60.5 1.0 OP1 A:U238 3.9 64.2 1.0 C5' A:C119 4.0 60.3 1.0 OP2 A:G239 4.3 44.5 1.0 O5' A:C119 4.4 60.1 1.0 O3' A:G118 4.4 61.9 1.0 O5' A:G239 4.5 51.2 1.0 C3' A:U238 4.5 56.5 1.0 C5' A:G239 4.6 54.0 1.0

Magnesium binding site 2 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:53.8 occ:1.00 OP1 A:C358 2.4 84.6 1.0 OP2 A:G359 2.4 69.5 1.0 OP1 B:U5 2.4 93.9 1.0 OP1 A:C377 2.8 72.1 1.0 OP2 A:C377 2.8 68.2 1.0 OP2 B:U5 2.9 91.6 1.0 P B:U5 3.0 0.6 1.0 P A:C377 3.2 63.8 1.0 P A:C358 3.6 75.4 1.0 P A:G359 3.7 64.5 1.0 O5' A:C377 3.8 74.1 1.0 MG B:MG7 4.0 50.1 1.0 OP2 A:C358 4.0 69.3 1.0 O3' B:U4 4.0 99.5 1.0 MG A:MG436 4.1 57.3 1.0 OP1 A:G359 4.2 64.5 1.0 O5' A:C358 4.3 75.0 1.0 O5' B:U5 4.3 0.9 1.0 C5' A:C358 4.5 68.6 1.0 O5' A:G359 4.5 66.5 1.0 O3' A:A376 4.7 79.3 1.0 C5' B:U5 4.8 0.6 1.0 O3' A:C357 4.8 78.3 1.0 O3' A:C358 4.8 71.6 1.0 C5' A:C377 4.9 75.8 1.0

Magnesium binding site 3 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:56.3 occ:1.00 OP1 A:G107 2.4 48.6 1.0 P A:G107 3.8 53.9 1.0 O3' A:A106 4.2 61.0 1.0 OP1 A:G108 4.2 65.8 1.0 C5' A:G107 4.3 56.5 1.0 OP2 A:A105 4.4 71.9 1.0 N7 A:A105 4.5 72.5 1.0 O5' A:G107 4.5 52.8 1.0 C8 A:A105 4.5 73.7 1.0 OP2 A:A106 4.7 54.3 1.0 OP2 A:G107 5.0 57.8 1.0

Magnesium binding site 4 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:62.0 occ:1.00 O3' A:A110 2.6 68.1 1.0 OP1 A:G111 3.4 69.5 1.0 P A:G111 3.5 59.4 1.0 C3' A:A110 3.6 65.0 1.0 O5' A:G111 3.9 69.9 1.0 OP2 A:C112 4.2 65.6 1.0 OP1 A:C112 4.3 84.6 1.0 C2' A:A110 4.6 63.8 1.0 P A:C112 4.6 88.3 1.0 C4' A:A110 4.7 63.0 1.0 O2' A:A110 4.8 65.6 1.0 O2 A:U13 4.9 90.3 1.0 OP2 A:G111 4.9 72.2 1.0

Magnesium binding site 5 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:67.5 occ:1.00 OP2 A:C372 2.5 79.5 1.0 OP1 A:A371 3.8 87.2 1.0 P A:C372 3.9 80.1 1.0 O6 A:G373 4.2 64.0 1.0 OP2 A:A371 4.3 76.0 1.0 P A:A371 4.3 74.7 1.0 O5' A:A371 4.3 69.5 1.0 O3' A:A371 4.6 63.0 1.0 O6 A:G374 4.6 73.8 1.0 N7 A:G373 4.7 64.1 1.0 OP1 A:C372 4.7 82.7 1.0 C3' A:A371 4.8 65.4 1.0 O5' A:C372 4.9 65.1 1.0 C5' A:A371 4.9 74.3 1.0

Magnesium binding site 6 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg418 b:65.8 occ:1.00 O4 A:U363 4.0 84.7 1.0 O4 A:U379 4.0 84.8 1.0 OP1 A:G378 4.1 81.6 1.0 O6 A:G362 4.2 87.8 1.0 N6 A:A380 4.5 93.7 1.0 N7 A:G362 4.6 82.5 1.0 N6 A:A364 4.8 76.8 1.0 N4 A:C361 4.8 84.1 1.0 C4 A:C361 5.0 84.0 1.0 C6 A:G362 5.0 87.1 1.0

Magnesium binding site 7 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg419 b:75.4 occ:1.00 OP1 A:G284 3.6 72.8 1.0 OP1 A:A95 3.9 59.7 1.0 OP2 A:U96 4.3 58.7 1.0 OP1 A:U96 4.4 64.6 1.0 P A:G284 4.5 74.2 1.0 OP2 A:G284 4.8 65.0 1.0 P A:U96 4.8 64.6 1.0 O3' A:A283 5.0 67.1 1.0

Magnesium binding site 8 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg420 b:89.1 occ:1.00 O6 A:G46 3.6 75.5 1.0 O4 A:U45 4.0 66.9 1.0 OP1 A:U59 4.1 49.3 1.0 N7 A:G46 4.3 64.2 1.0 OP2 A:U59 4.5 54.2 1.0 O4 A:U47 4.5 60.7 1.0 C6 A:G46 4.6 71.2 1.0 C4 A:U45 4.6 68.4 1.0 C5 A:U45 4.8 74.2 1.0 P A:U59 4.8 55.4 1.0 C5 A:G46 4.8 64.7 1.0

Magnesium binding site 9 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg421 b:0.9 occ:1.00 OP2 A:A61 2.7 43.2 1.0 P A:A61 3.9 47.1 1.0 O5' A:A61 4.0 48.8 1.0 OP2 A:C62 4.3 55.0 1.0 N7 A:A61 4.4 47.3 1.0 C8 A:A61 4.5 46.4 1.0 OP1 A:A61 4.8 57.9 1.0 C5 A:C62 4.8 58.5 1.0

Magnesium binding site 10 out of 31 in the Refined Group II Intron Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Refined Group II Intron Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg422 b:56.0 occ:1.00 OP2 A:U66 2.6 74.0 1.0 OP1 A:A67 2.6 60.1 1.0 P A:A67 4.0 62.7 1.0 P A:U66 4.0 79.0 1.0 O3' A:U66 4.4 63.0 1.0 O3' A:U65 4.7 74.6 1.0 OP1 A:U66 4.7 71.2 1.0 OP2 A:A67 4.9 66.9 1.0 O5' A:U66 4.9 68.0 1.0

N.Toor, K.Rajashankar, K.S.Keating, A.M.Pyle. Structural Basis For Exon Recognition By A Group II Intron. Nat.Struct.Mol.Biol. V. 15 1221 2008.
ISSN: ISSN 1545-9993
PubMed: 18953333
DOI: 10.1038/NSMB.1509