Magnesium in PDB 3mei: Regulatory Motif From the Thymidylate Synthase Mrna

The structure of Regulatory Motif From the Thymidylate Synthase Mrna, PDB code: 3mei was solved by S.Dibrov, J.Mclean, T.Hermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.20 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.928, 38.564, 41.985, 90.00, 100.10, 90.00
R / Rfree (%)	17.6 / 23.8

The structure of Regulatory Motif From the Thymidylate Synthase Mrna also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Magnesium atom in the Regulatory Motif From the Thymidylate Synthase Mrna (pdb code 3mei). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Regulatory Motif From the Thymidylate Synthase Mrna, PDB code: 3mei:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Regulatory Motif From the Thymidylate Synthase Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Regulatory Motif From the Thymidylate Synthase Mrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg24 b:41.8 occ:1.00 O B:HOH28 2.1 45.7 1.0 O A:HOH33 2.1 28.3 1.0 O A:HOH31 2.1 32.1 1.0 O A:HOH131 2.2 49.5 1.0 O B:HOH27 2.3 29.6 1.0 O2 B:C14 4.0 26.8 1.0 O2 A:C9 4.1 28.8 1.0 O4' B:C15 4.2 29.3 1.0 N3 A:C9 4.5 26.6 1.0 C1' B:C15 4.5 30.8 1.0 O2 A:C10 4.5 25.6 1.0 O2 B:C15 4.7 29.8 1.0 C2 A:C9 4.7 27.5 1.0 C1' A:C10 5.0 33.3 1.0

Magnesium binding site 2 out of 5 in the Regulatory Motif From the Thymidylate Synthase Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Regulatory Motif From the Thymidylate Synthase Mrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:72.6 occ:1.00 O A:HOH109 2.0 49.6 1.0 O A:HOH26 2.2 37.5 1.0 N7 A:G19 3.2 26.1 1.0 OP2 A:G19 3.9 37.8 1.0 C4 A:U18 4.0 31.8 1.0 C8 A:G19 4.0 29.1 1.0 N7 A:G20 4.0 32.7 1.0 C5 A:U18 4.1 26.0 1.0 O4 A:U18 4.2 31.4 1.0 C5 A:G19 4.2 27.8 1.0 O6 A:G19 4.2 28.4 1.0 N3 A:U18 4.3 25.8 1.0 C6 A:U18 4.5 26.0 1.0 C6 A:G19 4.6 29.5 1.0 C2 A:U18 4.7 28.4 1.0 O6 A:G20 4.8 28.4 1.0 N1 A:U18 4.8 25.9 1.0 O A:HOH121 4.8 52.8 1.0 C8 A:G20 4.9 26.3 1.0

Magnesium binding site 3 out of 5 in the Regulatory Motif From the Thymidylate Synthase Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Regulatory Motif From the Thymidylate Synthase Mrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg24 b:80.1 occ:1.00 O B:HOH123 2.0 50.1 1.0 O A:HOH108 3.3 36.2 1.0 O6 B:G20 3.3 25.2 1.0 O6 B:G19 3.4 30.1 1.0 O B:HOH29 3.4 45.9 1.0 O4 B:U18 3.8 32.4 1.0 N7 B:G19 4.1 27.5 1.0 C4 B:U18 4.2 35.4 1.0 C6 B:G19 4.2 29.5 1.0 C6 B:G20 4.3 26.9 1.0 N7 B:G20 4.4 25.4 1.0 N3 B:U18 4.5 31.1 1.0 C5 B:G19 4.5 30.2 1.0 N4 A:C4 4.5 25.3 1.0 N4 A:C5 4.7 30.0 1.0 O B:HOH38 4.7 44.0 1.0 C5 B:G20 4.7 26.2 1.0 O A:HOH89 4.8 45.5 1.0 C5 B:U18 4.8 32.2 1.0

Magnesium binding site 4 out of 5 in the Regulatory Motif From the Thymidylate Synthase Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Regulatory Motif From the Thymidylate Synthase Mrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg25 b:66.2 occ:1.00 O B:HOH48 2.1 39.6 1.0 N7 B:G23 3.1 34.1 1.0 N7 B:G22 3.1 25.5 1.0 C8 B:G22 3.3 25.4 1.0 OP2 B:G23 3.5 38.8 1.0 C8 B:G23 3.6 26.1 1.0 C5 B:G22 3.8 25.6 1.0 N9 B:G22 4.0 25.5 1.0 OP2 B:G22 4.1 26.4 1.0 C3' B:G22 4.3 32.4 1.0 C4 B:G22 4.3 25.6 1.0 O5' B:G22 4.4 27.2 1.0 C5 B:G23 4.4 31.1 1.0 C6 B:G22 4.5 32.3 1.0 P B:G23 4.6 38.2 1.0 O5' B:G23 4.7 34.0 1.0 O6 B:G22 4.8 25.8 1.0 C2' B:G22 4.8 30.0 1.0 N9 B:G23 4.9 29.8 1.0 O3' B:G22 4.9 35.1 1.0 O6 B:G23 5.0 28.3 1.0 P B:G22 5.0 32.8 1.0 C1' B:G22 5.0 25.4 1.0

Magnesium binding site 5 out of 5 in the Regulatory Motif From the Thymidylate Synthase Mrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Regulatory Motif From the Thymidylate Synthase Mrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg26 b:72.6 occ:1.00 O B:HOH106 1.8 38.9 1.0 O B:HOH75 2.4 43.1 1.0 O A:HOH76 2.7 44.0 1.0 O B:HOH79 3.7 43.2 1.0 O B:HOH55 3.8 34.8 1.0 O B:HOH37 4.0 42.0 1.0 N4 B:C7 4.0 25.5 1.0 O A:HOH34 4.1 31.8 1.0 C5 B:C7 4.2 31.0 1.0 C4 B:C7 4.5 25.4 1.0 N7 B:G8 4.6 26.0 1.0 N3 A:C15 4.6 27.2 1.0 O6 B:G8 4.6 26.4 1.0 O2 A:C15 4.7 34.5 1.0 N4 B:C9 4.8 31.1 1.0 O B:HOH80 5.0 43.4 1.0

S.Dibrov, J.Mclean, T.Hermann. Structure of An Rna Dimer of A Regulatory Element From Human Thymidylate Synthase Mrna. Acta Crystallogr.,Sect.D V. 67 97 2011.
ISSN: ISSN 0907-4449
PubMed: 21245530
DOI: 10.1107/S0907444910050900