Magnesium in PDB 354d: Structure of Loop E From E. Coli 5S Rrna

The structure of Structure of Loop E From E. Coli 5S Rrna, PDB code: 354d was solved by C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.184, 37.654, 32.944, 90.00, 105.90, 90.00
R / Rfree (%)	20.2 / 22.8

The binding sites of Magnesium atom in the Structure of Loop E From E. Coli 5S Rrna (pdb code 354d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Loop E From E. Coli 5S Rrna, PDB code: 354d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Loop E From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Loop E From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:52.4 occ:1.00 O B:HOH314 1.9 38.6 1.0 O A:HOH316 2.1 31.6 1.0 O B:HOH313 2.2 44.2 1.0 O A:HOH315 2.2 32.9 1.0 O A:HOH317 2.3 40.2 1.0 O A:HOH318 2.4 33.0 1.0 O6 A:G76 3.7 20.6 1.0 N7 A:G75 3.8 19.6 1.0 O B:HOH371 4.1 34.2 1.0 O B:HOH312 4.2 30.1 1.0 N7 A:G76 4.4 20.8 1.0 O A:HOH390 4.4 37.8 1.0 OP2 A:U74 4.5 24.8 1.0 O B:HOH330 4.6 22.1 1.0 C6 A:G76 4.6 20.5 1.0 O5' B:A99 4.6 23.1 1.0 O6 A:G75 4.6 20.2 1.0 C8 A:G75 4.7 21.9 1.0 OP2 B:A99 4.7 24.6 1.0 C5 A:G75 4.7 19.2 1.0 OP2 A:G75 4.8 27.1 1.0 C5 A:G76 4.9 19.6 1.0 C5 A:U74 5.0 16.6 1.0

Magnesium binding site 2 out of 5 in the Structure of Loop E From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Loop E From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg200 b:33.2 occ:1.00 O B:HOH301 1.9 31.0 1.0 O B:HOH303 2.0 31.5 1.0 O B:HOH305 2.1 35.4 1.0 O B:HOH302 2.2 36.4 1.0 O B:HOH304 2.3 28.6 1.0 O B:HOH300 2.3 29.6 1.0 O B:HOH341 4.0 27.7 1.0 O6 B:DG105 4.1 21.4 1.0 N7 B:DG105 4.2 20.8 1.0 O B:HOH347 4.5 28.7 1.0 O6 B:G46106 4.6 21.4 1.0 OP2 B:A104 4.7 21.8 1.0 C6 B:DG105 4.8 20.1 1.0 C5 B:DG105 4.8 19.3 1.0 N7 B:G46106 4.8 19.2 1.0 O B:HOH375 4.9 35.7 1.0

Magnesium binding site 3 out of 5 in the Structure of Loop E From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Loop E From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:31.4 occ:1.00 O B:HOH310 1.8 25.9 1.0 OP2 B:A101 2.1 23.8 1.0 O B:HOH306 2.1 29.1 1.0 O B:HOH309 2.2 26.1 1.0 O B:HOH307 2.3 39.0 1.0 O B:HOH308 2.5 24.6 1.0 MG B:MG202 2.7 32.0 1.0 P B:A101 3.4 20.8 1.0 OP2 B:G100 3.8 18.7 1.0 O5' B:A101 3.8 20.7 1.0 N7 B:A101 4.0 18.8 1.0 C8 B:A101 4.1 18.9 1.0 O5' B:G100 4.2 16.5 1.0 N7 B:G102 4.3 20.4 1.0 OP1 B:A101 4.4 22.4 1.0 P B:G100 4.4 19.0 1.0 O A:HOH358 4.4 33.0 1.0 O3' B:G100 4.5 19.4 1.0 O B:HOH339 4.6 28.0 1.0 OP1 B:G100 4.6 19.8 1.0 C3' B:G100 4.7 19.2 1.0 O6 B:G102 4.7 18.9 1.0 O B:HOH311 4.7 33.5 1.0 O B:HOH312 4.7 30.1 1.0

Magnesium binding site 4 out of 5 in the Structure of Loop E From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Loop E From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:32.0 occ:1.00 O B:HOH310 1.9 25.9 1.0 O B:HOH311 2.1 33.5 1.0 OP2 B:G100 2.1 18.7 1.0 O B:HOH309 2.2 26.1 1.0 O B:HOH308 2.4 24.6 1.0 O B:HOH312 2.7 30.1 1.0 MG B:MG201 2.7 31.4 1.0 P B:G100 3.4 19.0 1.0 O B:HOH371 4.0 34.2 1.0 O6 B:G102 4.0 18.9 1.0 OP1 B:G100 4.0 19.8 1.0 O5' B:G100 4.1 16.5 1.0 OP2 B:A101 4.2 23.8 1.0 O B:HOH306 4.4 29.1 1.0 O B:HOH307 4.4 39.0 1.0 N7 B:A101 4.5 18.8 1.0 O B:HOH330 4.6 22.1 1.0 O3' B:A99 4.6 17.6 1.0 O B:HOH410 4.8 42.5 1.0 O A:HOH358 4.8 33.0 1.0 O B:HOH314 4.9 38.6 1.0 C5' B:A99 5.0 20.2 1.0 C6 B:G102 5.0 18.2 1.0

Magnesium binding site 5 out of 5 in the Structure of Loop E From E. Coli 5S Rrna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Loop E From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:30.9 occ:1.00 O A:HOH319 2.0 31.2 1.0 O B:HOH321 2.2 33.4 1.0 O B:HOH320 2.3 25.6 1.0 O A:HOH323 2.3 28.0 1.0 O B:HOH322 2.3 30.8 1.0 O6 B:G98 2.6 24.9 1.0 C6 B:G98 3.6 21.0 1.0 N7 B:G98 4.0 20.0 1.0 O A:HOH331 4.1 23.6 1.0 C5 B:G98 4.2 17.0 1.0 O B:HOH337 4.2 27.6 1.0 OP2 B:C97 4.5 20.5 1.0 OP2 A:G76 4.7 31.1 1.0 N1 B:G98 4.8 20.2 1.0

C.C.Correll, B.Freeborn, P.B.Moore, T.A.Steitz. Metals, Motifs, and Recognition in the Crystal Structure of A 5S Rrna Domain. Cell(Cambridge,Mass.) V. 91 705 1997.
ISSN: ISSN 0092-8674
PubMed: 9393863
DOI: 10.1016/S0092-8674(00)80457-2