Magnesium in PDB 8tkj: Cryo-Em Structure of Rna Device 43, Apo State

The binding sites of Magnesium atom in the Cryo-Em Structure of Rna Device 43, Apo State (pdb code 8tkj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of Rna Device 43, Apo State, PDB code: 8tkj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:142.0 occ:1.00 OP2 A:A53 2.0 131.8 1.0 OP1 A:A53 2.2 138.2 1.0 P A:A53 2.2 135.7 1.0 O5' A:A53 2.8 136.4 1.0 OP2 A:G54 3.2 139.2 1.0 O3' A:G52 3.8 132.4 1.0 H3' A:A53 3.8 136.5 1.0 H8 A:A53 3.9 138.1 1.0 C5' A:A53 4.0 135.5 1.0 H5'' A:A53 4.1 136.8 1.0 H22 A:G66 4.1 133.4 1.0 H3' A:G52 4.2 140.3 1.0 C3' A:G52 4.6 133.2 1.0 C8 A:A53 4.6 141.1 1.0 H5' A:A53 4.7 136.4 1.0 P A:G54 4.7 132.6 1.0 C3' A:A53 4.7 131.7 1.0 C4' A:A53 4.9 131.8 1.0 N2 A:G66 4.9 131.7 1.0 OP2 A:A92 5.0 162.4 1.0

Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:99.6 occ:1.00 H5'' A:A35 3.4 124.1 1.0 H5' A:A35 4.1 124.0 1.0 N7 A:G11 4.2 178.1 1.0 C5' A:A35 4.2 124.3 1.0 O6 A:G12 4.2 153.3 1.0 N7 A:G12 4.7 141.6 1.0 H2' A:A35 4.7 123.6 1.0 H3' A:A35 4.7 123.8 1.0 O5' A:A35 4.8 122.4 1.0 OP2 A:G11 4.9 178.7 1.0 O6 A:G11 4.9 182.1 1.0 C8 A:G11 4.9 178.6 1.0 H8 A:A35 4.9 124.0 1.0 H8 A:G11 4.9 179.7 1.0 C5 A:G11 5.0 177.0 1.0

Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:80.9 occ:1.00 H5 A:U13 3.7 132.3 1.0 OP2 A:G12 3.7 150.9 1.0 O4 A:U13 4.2 139.3 1.0 C5 A:U13 4.4 134.0 1.0 H62 A:A14 4.6 137.3 1.0 C4 A:U13 4.7 133.2 1.0 P A:G12 4.9 163.4 1.0 OP2 A:A34 4.9 128.9 1.0

Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:101.4 occ:1.00 N7 A:G106 4.2 143.7 1.0 OP2 A:G106 4.8 155.8 1.0 O6 A:G106 4.9 145.2 1.0 N7 A:G107 4.9 142.2 1.0 H62 A:A108 4.9 150.7 1.0 H8 A:G107 5.0 153.8 1.0

Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:76.9 occ:1.00 O6 A:G27 4.1 143.5 1.0 H62 A:A20 4.3 150.8 1.0 N7 A:A20 4.4 142.2 1.0 O6 A:G21 4.5 142.9 1.0 N6 A:A20 4.9 154.4 1.0 N7 A:G21 5.0 133.3 1.0

Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:56.3 occ:1.00 HO2' A:A53 4.0 137.2 1.0 H4' A:A53 4.0 136.4 1.0 N7 A:G55 4.1 132.7 1.0 O2' A:A53 4.1 140.2 1.0 OP2 A:A67 4.3 133.2 1.0 H4' A:G66 4.5 133.8 1.0 H8 A:G55 4.6 136.9 1.0 OP2 A:G55 4.7 139.1 1.0 C8 A:G55 4.7 133.7 1.0 O3' A:A53 4.7 133.1 1.0 H62 A:A70 4.8 160.7 1.0 OP1 A:G54 4.9 142.3 1.0 H5 A:U56 4.9 149.9 1.0 O4 A:U56 4.9 146.6 1.0 C4' A:A53 4.9 131.8 1.0

Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:107.4 occ:1.00 O6 A:G76 3.9 158.8 1.0 N7 A:G75 4.1 158.7 1.0 O6 A:G75 4.3 164.6 1.0 H41 A:C77 4.6 168.6 1.0 N7 A:G76 4.7 156.7 1.0 C5 A:G75 4.7 156.1 1.0 C6 A:G75 4.8 157.1 1.0 H42 A:C87 4.9 156.9 1.0 C6 A:G76 4.9 151.9 1.0 C8 A:G75 5.0 158.2 1.0

Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Rna Device 43, Apo State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Rna Device 43, Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:70.8 occ:1.00 O6 A:G80 4.2 205.6 1.0 OP1 A:A82 4.5 238.0 1.0

J.R.Stagno, J.C.Deme, Y.-T.Lee, Y.-X.Wang, S.M.Lea. Cryo-Em Structure of Rna Device 43 Truncation Mutant, Apo State To Be Published.