Magnesium in PDB 8joz: Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser

The structure of Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser, PDB code: 8joz was solved by J.Yoo, J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.74 / 2.22
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.614, 65.614, 584.532, 90, 90, 120
R / Rfree (%)	19.9 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser (pdb code 8joz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser, PDB code: 8joz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:35.1 occ:1.00 O B:HOH379 2.0 32.4 1.0 O B:HOH333 2.0 31.7 1.0 O B:HOH380 2.1 32.7 1.0 O B:HOH246 2.1 32.0 1.0 O B:HOH306 2.1 33.2 1.0 O B:HOH375 2.3 33.3 1.0 O B:HOH280 3.7 35.1 1.0 O B:HOH355 4.0 41.0 1.0 N7 B:G23 4.2 31.6 1.0 O B:HOH398 4.2 41.3 1.0 O B:HOH255 4.2 33.1 1.0 N7 B:G24 4.3 37.8 1.0 O6 B:G23 4.4 34.2 1.0 O B:HOH397 4.4 37.6 1.0 O B:HOH259 4.4 36.1 1.0 N4 B:C44 4.4 38.4 1.0 O6 B:G24 4.5 40.8 1.0 OP2 B:A22 4.6 30.7 1.0 C5 B:G23 4.8 33.2 1.0 C6 B:G23 4.8 34.0 1.0 N4 B:C25 4.9 41.0 1.0 OP2 B:G23 4.9 36.8 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:49.0 occ:1.00 O B:HOH277 1.9 35.8 1.0 O B:HOH402 2.0 42.5 1.0 O B:HOH405 2.1 43.0 1.0 O B:HOH400 2.2 39.3 1.0 O B:HOH245 2.2 39.6 1.0 O B:HOH298 2.3 38.6 1.0 O B:HOH232 3.8 37.8 1.0 O B:HOH263 4.1 38.8 1.0 N7 B:G42 4.2 37.3 1.0 O B:HOH330 4.2 40.2 1.0 O B:HOH372 4.3 44.7 1.0 O B:HOH355 4.4 41.0 1.0 O6 B:G43 4.4 40.5 1.0 N7 B:G43 4.6 39.0 1.0 O6 B:G42 4.6 37.6 1.0 C5 B:G42 5.0 35.7 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:46.7 occ:1.00 O B:HOH404 1.9 47.5 1.0 O B:HOH300 2.1 44.0 1.0 O B:HOH226 2.1 43.3 1.0 O B:HOH315 2.2 53.5 1.0 O B:HOH295 2.2 41.5 1.0 O B:HOH231 2.3 45.9 1.0 O B:HOH207 4.3 39.2 1.0 O6 B:G53 4.3 56.9 1.0 O2' B:A58 4.3 45.4 1.0 O B:HOH324 4.4 53.0 1.0 O B:HOH354 4.4 44.1 1.0 OP1 B:A58 4.4 43.3 1.0 OP1 B:U47K 4.5 41.9 1.0 O4 B:5MU54 4.5 62.1 1.0 C2' B:A58 4.7 47.4 1.0 N7 B:G53 4.7 59.4 1.0 OP2 B:A58 4.8 60.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:50.0 occ:1.00 O B:HOH229 1.9 42.3 1.0 O B:HOH273 2.0 37.0 1.0 O B:HOH224 2.1 41.0 1.0 O B:HOH219 2.1 37.5 1.0 O B:HOH307 2.1 41.1 1.0 O B:HOH251 2.3 41.4 1.0 OP2 B:G9 3.6 43.2 1.0 OP2 B:C12 3.7 41.7 1.0 O B:HOH257 3.9 42.1 1.0 N7 B:G13 4.2 37.4 1.0 OP1 B:4SU8 4.3 45.5 1.0 OP2 B:4SU8 4.3 50.9 1.0 O B:HOH310 4.5 46.5 1.0 C5' B:C12 4.5 40.0 1.0 OP2 B:G13 4.7 39.6 1.0 O6 B:G13 4.8 37.3 1.0 P B:4SU8 4.8 43.5 1.0 C6 B:C12 4.9 39.3 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:39.6 occ:1.00 O B:HOH265 1.9 36.8 1.0 O B:HOH321 2.0 37.1 1.0 O B:HOH264 2.1 39.5 1.0 OP1 B:C48 2.1 39.8 1.0 O B:HOH368 2.2 37.6 1.0 O B:HOH358 2.3 40.8 1.0 P B:C48 3.4 36.0 1.0 O B:HOH210 3.6 40.0 1.0 O3' B:U47K 3.6 33.2 1.0 OP2 B:A50 3.7 45.0 1.0 O B:HOH261 3.9 40.0 1.0 O B:HOH240 3.9 37.7 1.0 O B:HOH312 4.1 42.9 1.0 OP2 B:C48 4.2 34.3 1.0 O B:HOH327 4.3 40.5 1.0 O B:HOH222 4.3 45.5 1.0 N7 B:G51 4.4 44.8 1.0 N7 B:A50 4.4 43.5 1.0 OP1 B:C49 4.4 33.4 1.0 O B:HOH329 4.5 44.6 1.0 O5' B:C48 4.6 34.8 1.0 OP2 B:G51 4.6 44.8 1.0 C8 B:A50 4.7 42.7 1.0 C5' B:C48 4.9 35.4 1.0 C3' B:C48 4.9 35.0 1.0 C3' B:U47K 4.9 35.0 1.0 P B:A50 5.0 38.2 1.0 O5' B:A50 5.0 43.4 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:39.3 occ:1.00 O B:HOH341 2.0 35.8 1.0 O B:HOH253 2.0 33.5 1.0 O B:HOH214 2.2 29.4 1.0 O B:HOH281 2.2 35.5 1.0 O B:HOH344 2.3 34.6 1.0 O B:HOH384 2.5 38.8 1.0 OP1 B:G45 4.0 41.9 1.0 N7 B:G45 4.1 35.4 1.0 O B:HOH299 4.2 35.6 1.0 O2' B:G20B 4.3 36.8 1.0 OP2 B:G45 4.3 44.8 1.0 OP2 B:A21 4.4 36.7 1.0 O B:HOH247 4.4 42.2 1.0 O B:HOH272 4.5 38.8 1.0 C8 B:G45 4.6 37.8 1.0 O3' B:G20B 4.6 33.9 1.0 O B:HOH335 4.6 40.9 1.0 O B:HOH211 4.7 46.2 1.0 N2 B:G9 4.7 34.0 1.0 P B:G45 4.7 40.5 1.0 N3 B:G20B 4.8 34.7 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser


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 Cmom From E. Coli Complexed with Sinefungin and Cellularly Expressed Trna Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:42.4 occ:1.00 O B:HOH302 1.9 41.5 1.0 O B:HOH244 2.0 47.6 1.0 OP1 B:A59 2.0 40.4 1.0 O B:HOH360 2.1 51.5 1.0 O B:HOH266 2.1 42.6 1.0 O B:HOH340 2.2 47.7 1.0 P B:A59 3.4 41.0 1.0 O B:HOH387 3.9 44.9 1.0 OP2 B:A59 4.0 37.4 1.0 OP2 B:G20B 4.1 46.1 1.0 O B:HOH386 4.2 46.7 1.0 C4' B:A58 4.2 44.6 1.0 O3' B:A58 4.3 45.7 1.0 O2' B:H2U20A 4.4 41.4 1.0 O5' B:A59 4.4 38.3 1.0 OP2 B:H2U20 4.5 49.2 1.0 N7 B:A59 4.5 36.0 1.0 O4 B:U60 4.5 43.1 1.0 OP1 B:H2U20 4.5 42.9 1.0 C5' B:A58 4.6 48.8 1.0 O3' B:H2U20A 4.7 44.5 1.0 C3' B:A58 4.7 45.2 1.0 C8 B:A59 4.8 37.5 1.0

J.Yoo, J.Lee, J.Kim. Structural Basis For the Selective Methylation of 5-Carboxymethoxyuridine in Trna Modification. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37587716
DOI: 10.1093/NAR/GKAD668