Magnesium in PDB 4frg: Crystal Structure of the Cobalamin Riboswitch Aptamer Domain

The structure of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain, PDB code: 4frg was solved by F.E.Reyes, J.E.Johnson, J.T.Polaski, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 2.95
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.030, 142.030, 137.900, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 24.9

The structure of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Iridium	(Ir)	17 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain (pdb code 4frg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain, PDB code: 4frg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg111 b:63.8 occ:1.00 O2' B:A63 4.0 81.2 1.0 OP2 B:A63 4.1 85.6 1.0 O6 B:G58 4.1 87.4 1.0 C2' B:A63 4.2 82.0 1.0 O6 B:G57 4.3 84.5 1.0 OP2 B:C56 4.4 80.1 1.0 OP1 B:A63 4.4 84.9 1.0 C5 B:C56 4.5 80.6 1.0 OP2 B:A55 4.5 77.6 1.0 N7 B:G57 4.6 83.9 1.0 P B:A63 4.7 85.4 1.0 C3' B:A63 4.9 81.9 1.0 N4 B:C56 5.0 81.5 1.0

Magnesium binding site 2 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg112 b:79.7 occ:1.00 OP1 B:U35 3.1 94.8 1.0 O4 B:U38 3.4 0.4 1.0 N4 B:C39 4.2 0.7 1.0 O6 B:G37 4.3 0.5 1.0 N7 B:G37 4.3 0.8 1.0 OP2 B:C36 4.4 92.5 1.0 C4 B:U38 4.4 0.3 1.0 P B:U35 4.5 95.4 1.0 N6 B:A26 4.8 0.0 1.0 C5 B:U38 4.9 1.0 1.0 C6 B:G37 4.9 0.1 1.0 C5 B:G37 4.9 0.5 1.0 O6 B:G25 4.9 0.2 1.0 C5 B:C36 4.9 98.9 1.0

Magnesium binding site 3 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg113 b:96.6 occ:1.00 N4 B:C46 3.6 94.2 1.0 O6 B:G45 3.8 88.7 1.0 O6 B:G47 3.9 98.1 1.0 O4 B:U44 4.2 87.2 1.0 N7 B:G45 4.5 88.2 1.0 C6 B:G45 4.6 88.0 1.0 C4 B:U44 4.7 86.6 1.0 C5 B:U44 4.8 87.6 1.0 C4 B:C46 4.8 94.0 1.0 C6 B:G47 4.9 98.8 1.0 O6 B:G51 4.9 91.0 1.0 C5 B:G45 4.9 87.7 1.0

Magnesium binding site 4 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg114 b:88.4 occ:1.00 O6 B:G47 4.1 98.1 1.0 N7 B:G47 4.7 99.0 1.0 C6 B:G47 4.8 98.8 1.0

Magnesium binding site 5 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg115 b:85.3 occ:1.00 OP1 B:A7 3.2 92.6 1.0 OP2 B:A8 3.2 97.0 1.0 O6 B:G10 3.3 94.4 1.0 OP1 B:A6 3.5 88.8 1.0 P B:A8 4.3 99.1 1.0 C6 B:G10 4.4 93.4 1.0 N6 B:A9 4.5 92.8 1.0 P B:A6 4.6 88.2 1.0 OP1 B:A8 4.6 99.1 1.0 P B:A7 4.6 94.4 1.0 N7 B:A9 4.7 95.5 1.0 O5' B:A6 4.8 89.7 1.0 OP2 B:A6 4.9 86.6 1.0 IR B:IR3104 5.0 0.7 1.0

Magnesium binding site 6 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg116 b:56.1 occ:1.00 OP1 B:A14 3.4 92.3 1.0 OP2 B:G72 3.7 85.6 1.0 OP1 B:G72 4.0 84.9 1.0 P B:G72 4.3 84.3 1.0 O3' B:U13 4.3 92.1 1.0 O4 B:U16 4.5 0.3 1.0 P B:A14 4.5 92.0 1.0 IR B:IR3109 4.6 1.0 1.0 N7 B:G15 4.6 0.3 1.0 O6 B:G15 4.8 0.2 1.0 O3' B:U71 4.8 83.6 1.0

Magnesium binding site 7 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg117 b:90.2 occ:1.00 OP1 B:U13 3.2 88.7 1.0 OP2 B:A14 3.2 90.7 1.0 OP2 B:U5 3.7 83.3 1.0 OP2 B:A6 4.0 86.6 1.0 N7 B:A6 4.2 90.2 1.0 O5' B:U13 4.3 88.4 1.0 P B:U13 4.3 88.0 1.0 C5 B:U5 4.6 87.2 1.0 P B:A14 4.6 92.0 1.0 O5' B:U5 4.6 85.5 1.0 C8 B:A6 4.7 90.8 1.0 P B:U5 4.8 84.1 1.0 C6 B:U5 4.8 87.4 1.0

Magnesium binding site 8 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg110 b:68.1 occ:1.00 O6 X:G58 3.8 88.7 1.0 O2' X:A63 3.8 77.7 1.0 OP2 X:A63 4.0 81.4 1.0 O6 X:G57 4.1 87.4 1.0 C2' X:A63 4.1 78.3 1.0 OP1 X:A63 4.5 81.0 1.0 OP2 X:A55 4.5 77.6 1.0 C5 X:C56 4.6 83.8 1.0 N7 X:G57 4.6 87.5 1.0 P X:A63 4.7 81.3 1.0 OP2 X:C56 4.7 82.1 1.0 C3' X:A63 4.8 78.4 1.0 C6 X:G58 4.9 89.8 1.0 C6 X:G57 4.9 88.3 1.0 N4 X:C56 4.9 84.7 1.0

Magnesium binding site 9 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg111 b:83.7 occ:1.00 OP2 X:C64 3.1 78.4 1.0 OP1 X:A55 3.3 78.1 1.0 OP2 X:U54 4.2 78.9 1.0 OP1 X:U54 4.3 77.8 1.0 P X:C64 4.5 78.7 1.0 P X:U54 4.6 77.9 1.0 P X:A55 4.6 77.5 1.0 O5' X:U54 4.7 77.0 1.0 O5' X:A55 4.9 78.0 1.0 C5' X:A55 4.9 78.7 1.0

Magnesium binding site 10 out of 16 in the Crystal Structure of the Cobalamin Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Cobalamin Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg112 b:0.5 occ:1.00 OP1 B:G28 3.2 0.7 1.0 O3' X:A32 3.3 0.2 1.0 O2' X:A32 3.4 0.4 1.0 C5 X:U60 3.6 0.4 1.0 OP1 X:A33 3.6 0.8 1.0 C5' X:A33 3.9 99.6 1.0 P X:A33 4.0 0.6 1.0 C4 X:U60 4.0 0.5 1.0 C6 X:U60 4.1 0.2 1.0 O4 X:U60 4.2 1.0 1.0 C3' X:A32 4.3 0.5 1.0 C2' X:A32 4.3 0.3 1.0 O5' X:A33 4.4 0.6 1.0 P B:G28 4.7 0.8 1.0 C4' X:A32 4.9 0.1 1.0 N3 X:U60 4.9 0.9 1.0 N1 X:U60 5.0 0.7 1.0

J.E.Johnson, F.E.Reyes, J.T.Polaski, R.T.Batey. B12 Cofactors Directly Stabilize An Mrna Regulatory Switch. Nature V. 492 133 2012.
ISSN: ISSN 0028-0836
PubMed: 23064232
DOI: 10.1038/NATURE11607