Magnesium in PDB 3eog: Co-Crystallization Showing Exon Recognition By A Group II Intron

The structure of Co-Crystallization Showing Exon Recognition By A Group II Intron, PDB code: 3eog 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)	48.42 / 3.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.485, 95.078, 225.043, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.3

The structure of Co-Crystallization Showing Exon Recognition By A Group II Intron also contains other interesting chemical elements:

Potassium

(K)

11 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 Co-Crystallization Showing Exon Recognition By A Group II Intron (pdb code 3eog). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 31 binding sites of Magnesium where determined in the Co-Crystallization Showing Exon Recognition By A Group II Intron, PDB code: 3eog:
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 Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:53.1 occ:1.00 OP1 A:G239 2.1 56.8 1.0 OP1 A:C119 2.5 53.7 1.0 P A:G239 3.2 58.7 1.0 O3' A:U238 3.3 54.7 1.0 OP1 A:A174 3.7 55.0 1.0 P A:C119 3.8 53.7 1.0 C5' A:C119 4.0 54.0 1.0 MG A:MG425 4.1 0.1 1.0 O5' A:C119 4.2 53.7 1.0 O5' A:G239 4.2 59.9 1.0 C5' A:G239 4.4 60.4 1.0 OP2 A:G239 4.4 59.3 1.0 O3' A:G118 4.6 57.8 1.0 C3' A:U238 4.6 55.0 1.0 OP1 A:U238 4.9 54.7 1.0

Magnesium binding site 2 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:53.7 occ:1.00 OP2 A:C377 2.3 58.6 1.0 OP1 A:U375 2.4 61.6 1.0 O3' B:U4 2.5 84.0 1.0 O2' B:U4 2.5 81.5 1.0 OP1 B:U5 2.8 89.9 1.0 P B:U5 3.2 0.9 1.0 P A:U375 3.2 61.4 1.0 C3' B:U4 3.2 85.4 1.0 O5' A:C377 3.3 66.3 1.0 C2' B:U4 3.4 84.5 1.0 P A:C377 3.4 62.9 1.0 OP2 A:U375 3.5 58.5 1.0 C4' B:U4 3.6 83.8 1.0 OP1 A:G359 3.7 63.0 1.0 MG A:MG415 3.7 53.7 1.0 O3' A:G374 3.8 71.0 1.0 OP2 A:G359 4.2 62.6 1.0 OP2 B:U5 4.3 96.3 1.0 O3' A:A376 4.3 73.3 1.0 O5' B:U5 4.3 97.0 1.0 P A:G359 4.4 63.8 1.0 O4' B:U4 4.5 77.1 1.0 C1' B:U4 4.6 81.8 1.0 OP1 A:C377 4.6 68.3 1.0 C5' B:U5 4.6 98.4 1.0 O5' A:U375 4.6 57.2 1.0 C5' A:C377 4.6 70.9 1.0 C5' B:U4 4.7 82.3 1.0 C5' A:A376 4.8 60.1 1.0

Magnesium binding site 3 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:53.7 occ:1.00 OP1 B:U5 2.3 89.9 1.0 OP1 A:C358 2.3 75.5 1.0 OP2 A:G359 2.5 62.6 1.0 OP2 A:C377 2.8 58.6 1.0 OP1 A:C377 2.9 68.3 1.0 P B:U5 3.1 0.9 1.0 P A:C377 3.1 62.9 1.0 OP2 B:U5 3.2 96.3 1.0 P A:C358 3.6 73.1 1.0 O5' A:C377 3.6 66.3 1.0 MG A:MG437 3.7 55.8 1.0 MG A:MG414 3.7 53.7 1.0 P A:G359 3.9 63.8 1.0 O3' B:U4 4.0 84.0 1.0 OP2 A:C358 4.0 71.0 1.0 O5' A:C358 4.2 66.9 1.0 O5' B:U5 4.4 97.0 1.0 OP1 A:G359 4.4 63.0 1.0 C5' A:C358 4.5 65.5 1.0 O5' A:G359 4.6 64.0 1.0 C5' B:U5 4.7 98.4 1.0 C5' A:C377 4.7 70.9 1.0 O3' A:A376 4.7 73.3 1.0 O3' A:C357 4.8 72.8 1.0

Magnesium binding site 4 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:46.0 occ:1.00 OP1 A:G107 2.4 53.2 1.0 P A:G107 3.8 57.8 1.0 OP2 A:A105 4.3 75.4 1.0 N7 A:A105 4.4 66.4 1.0 O5' A:G107 4.5 56.0 1.0 O3' A:A106 4.5 63.2 1.0 OP1 A:G108 4.5 64.8 1.0 C8 A:A105 4.5 67.0 1.0 C5' A:G107 4.6 56.4 1.0 OP2 A:A106 4.6 56.8 1.0 C5 A:C261 5.0 57.6 1.0 OP2 A:G107 5.0 55.2 1.0

Magnesium binding site 5 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:52.0 occ:1.00 O3' A:A110 2.8 67.3 1.0 OP1 A:G111 3.4 79.9 1.0 P A:G111 3.6 64.7 1.0 C3' A:A110 3.7 66.3 1.0 O5' A:G111 4.0 63.4 1.0 OP1 A:C112 4.2 71.4 1.0 OP2 A:C112 4.3 66.6 1.0 O2 A:U13 4.6 88.8 1.0 P A:C112 4.7 78.7 1.0 OP1 A:G14 4.8 77.5 1.0 O3' A:U13 4.8 95.4 1.0 C2' A:A110 4.8 66.0 1.0 O2' A:U13 4.8 91.3 1.0 C4' A:A110 4.8 67.9 1.0 OP2 A:G111 5.0 68.0 1.0 C5' A:A110 5.0 69.8 1.0

Magnesium binding site 6 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg418 b:57.1 occ:1.00 OP2 A:C372 2.4 81.9 1.0 OP1 A:A371 3.7 81.8 1.0 O6 A:G373 3.8 64.5 1.0 P A:C372 3.9 77.7 1.0 O6 A:G374 4.3 71.1 1.0 P A:A371 4.3 78.5 1.0 O5' A:A371 4.4 70.2 1.0 OP2 A:A371 4.4 69.2 1.0 OP1 A:C372 4.6 77.9 1.0 O5' A:C372 4.6 70.2 1.0 N7 A:G373 4.6 65.1 1.0 C6 A:G373 4.8 61.5 1.0 C5' A:A371 4.8 73.7 1.0 O3' A:A371 4.9 66.7 1.0

Magnesium binding site 7 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg419 b:63.1 occ:1.00 O4 A:U363 4.1 77.2 1.0 O6 A:G362 4.2 82.8 1.0 OP1 A:G378 4.4 75.0 1.0 N7 A:G362 4.4 74.7 1.0 N4 A:C361 4.4 72.2 1.0 O4 A:U379 4.4 87.7 1.0 C5 A:C361 4.4 66.7 1.0 N6 A:A380 4.5 77.2 1.0 C4 A:C361 4.5 70.7 1.0 N6 A:A364 4.6 70.4 1.0 C6 A:G362 4.8 82.4 1.0 C5 A:G362 4.9 80.7 1.0

Magnesium binding site 8 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg420 b:60.0 occ:1.00 OP2 A:U96 3.9 55.4 1.0 OP1 A:G284 3.9 60.2 1.0 OP1 A:A95 4.0 58.1 1.0 OP1 A:U96 4.1 58.9 1.0 P A:U96 4.4 58.2 1.0 P A:G284 4.7 61.4 1.0 OP2 A:G284 4.7 63.0 1.0 C5' A:A95 4.9 59.6 1.0 O3' A:A283 4.9 59.1 1.0

Magnesium binding site 9 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg421 b:63.5 occ:1.00 OP2 A:U59 3.8 53.0 1.0 O6 A:G46 3.9 69.6 1.0 O4 A:U45 4.1 73.2 1.0 OP1 A:U59 4.2 52.1 1.0 P A:U59 4.5 52.5 1.0 O4 A:U47 4.5 58.0 1.0 C4 A:U45 4.7 71.8 1.0 N7 A:G46 4.7 64.9 1.0 C6 A:G46 4.8 67.3 1.0 C5 A:U45 4.9 75.8 1.0

Magnesium binding site 10 out of 31 in the Co-Crystallization Showing Exon Recognition By A 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 Co-Crystallization Showing Exon Recognition By A Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg422 b:99.0 occ:1.00 OP2 A:A61 2.8 58.5 1.0 P A:A61 4.3 59.4 1.0 OP2 A:A60 4.3 52.0 1.0 OP1 A:A60 4.6 52.1 1.0 N7 A:A61 4.7 59.0 1.0 O5' A:A61 4.8 60.2 1.0 P A:A60 4.8 52.6 1.0 C8 A:A61 5.0 59.3 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