Magnesium in PDB 364d: 3.0 A Structure of Fragment I From E. Coli 5S Rrna

The structure of 3.0 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 364d 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 / 3.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.030, 59.030, 254.070, 90.00, 90.00, 120.00
R / Rfree (%)	27.2 / 32.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the 3.0 A Structure of Fragment I From E. Coli 5S Rrna (pdb code 364d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the 3.0 A Structure of Fragment I From E. Coli 5S Rrna, PDB code: 364d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the 3.0 A Structure of Fragment I 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 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:94.1 occ:1.00 O6 A:G6 4.1 0.4 1.0 O4 A:U5 4.4 0.0 1.0 O6 A:G7 4.7 0.5 1.0 C5 A:U5 4.8 0.2 1.0 C4 A:U5 4.8 0.6 1.0 N7 A:G6 5.0 0.6 1.0 N4 C:C113 5.0 0.9 1.0

Magnesium binding site 2 out of 12 in the 3.0 A Structure of Fragment I 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 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:0.4 occ:1.00 N2 A:G9 3.9 0.1 1.0 O4' A:G10 4.0 0.5 1.0 C1' A:G10 4.4 0.2 1.0 O2' C:G112 4.5 0.3 1.0 C4' A:G10 4.6 0.5 1.0 O2' A:G10 4.7 0.2 1.0 N3 A:G9 4.9 0.8 1.0 C2 A:G9 4.9 0.9 1.0

Magnesium binding site 3 out of 12 in the 3.0 A Structure of Fragment I 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 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:72.8 occ:1.00 OP2 B:G75 2.1 72.7 1.0 OP2 C:A99 2.3 85.3 1.0 P B:G75 3.5 74.2 1.0 P C:A99 3.5 82.6 1.0 O5' C:A99 3.6 81.5 1.0 N7 B:G76 3.7 95.4 1.0 O5' B:G75 3.9 73.0 1.0 N7 B:G75 3.9 87.4 1.0 C8 B:G75 4.1 83.7 1.0 O6 B:G76 4.2 97.9 1.0 O5' B:U74 4.4 69.7 1.0 OP2 B:U74 4.4 74.0 1.0 OP1 B:G75 4.4 71.8 1.0 C3' C:G98 4.4 80.3 1.0 O3' C:G98 4.5 81.0 1.0 OP2 B:G76 4.5 78.1 1.0 O3' B:U74 4.5 73.4 1.0 OP1 C:A99 4.6 83.4 1.0 OP1 B:U74 4.6 72.7 1.0 C5 B:G76 4.6 96.3 1.0 C3' B:U74 4.6 69.7 1.0 P B:U74 4.6 71.1 1.0 C8 B:G76 4.7 94.6 1.0 C2' C:G98 4.7 80.1 1.0 C5' C:A99 4.7 81.9 1.0 C6 B:G76 4.8 98.0 1.0 O4 B:U77 4.9 97.3 1.0

Magnesium binding site 4 out of 12 in the 3.0 A Structure of Fragment I 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 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg214 b:73.1 occ:1.00 MG C:MG216 3.0 83.2 1.0 O2 B:U77 3.2 92.3 1.0 O2' B:U77 3.7 84.6 1.0 C1' B:U77 4.0 88.8 1.0 N6 C:A99 4.0 87.6 1.0 N1 C:G100 4.1 94.6 1.0 C2 B:U77 4.3 92.8 1.0 C2' B:U77 4.3 87.2 1.0 O4' B:A78 4.5 0.3 1.0 N2 C:G100 4.6 0.0 1.0 O6 C:G100 4.6 93.2 1.0 N1 B:U77 4.7 92.9 1.0 C6 C:G100 4.7 92.2 1.0 N2 B:G76 4.7 96.9 1.0 C2 C:G100 4.8 96.0 1.0

Magnesium binding site 5 out of 12 in the 3.0 A Structure of Fragment I 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 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:71.3 occ:1.00 OP1 B:U74 2.2 72.7 1.0 OP1 C:A99 2.9 83.4 1.0 OP2 C:A99 3.2 85.3 1.0 P C:A99 3.3 82.6 1.0 P B:U74 3.7 71.1 1.0 O3' C:G98 3.8 81.0 1.0 OP1 C:G98 4.0 83.7 1.0 C5' B:U74 4.1 67.7 1.0 O5' B:U74 4.3 69.7 1.0 C3' C:G98 4.5 80.3 1.0 O3' B:A73 4.5 66.2 1.0 C5' C:G98 4.5 82.1 1.0 O5' C:G98 4.6 80.9 1.0 OP2 B:U74 4.6 74.0 1.0 OP2 B:G75 4.8 72.7 1.0 O5' C:A99 4.9 81.5 1.0 P C:G98 4.9 82.1 1.0

Magnesium binding site 6 out of 12 in the 3.0 A Structure of Fragment I 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 6 of 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg204 b:52.0 occ:1.00 OP2 C:G100 2.5 81.0 1.0 O6 C:G102 3.5 99.9 1.0 P C:G100 3.6 78.5 1.0 OP1 C:G100 4.0 78.9 1.0 N7 C:G102 4.1 99.0 1.0 N7 C:A101 4.3 89.7 1.0 C6 C:G102 4.4 98.0 1.0 O5' C:G100 4.4 81.9 1.0 N6 C:A101 4.5 87.7 1.0 OP2 C:A101 4.6 87.2 1.0 OP2 B:A73 4.6 81.7 1.0 C5 C:G102 4.6 96.1 1.0 C5' B:A73 4.7 71.0 1.0 C5 C:A101 4.8 86.7 1.0 O3' C:A99 4.8 76.5 1.0 C6 C:A101 5.0 87.0 1.0

Magnesium binding site 7 out of 12 in the 3.0 A Structure of Fragment I 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 7 of 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg205 b:71.6 occ:1.00 O6 C:G98 2.4 86.6 1.0 C6 C:G98 3.4 83.9 1.0 N7 C:G98 3.9 82.9 1.0 C5 C:G98 4.0 83.4 1.0 OP2 C:C97 4.0 87.2 1.0 OP1 B:G76 4.1 81.2 1.0 N1 C:G98 4.5 83.9 1.0 OP2 B:G76 4.9 78.1 1.0

Magnesium binding site 8 out of 12 in the 3.0 A Structure of Fragment I 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 8 of 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg208 b:90.5 occ:1.00 OP2 C:G107 3.3 0.2 1.0 N4 A:C11 3.5 0.6 1.0 N7 C:G107 3.9 0.1 1.0 N7 C:A108 3.9 1.0 1.0 N3 A:C11 4.2 0.1 1.0 C8 C:G107 4.3 0.7 1.0 C4 A:C11 4.3 0.6 1.0 N6 C:A109 4.4 0.2 1.0 N6 C:A108 4.6 0.3 1.0 P C:G107 4.7 0.1 1.0 N1 C:A109 4.8 0.7 1.0 C8 C:A108 4.8 0.9 1.0 C6 C:A109 4.9 0.3 1.0 O5' C:G107 4.9 0.1 1.0 C5 C:A108 4.9 0.4 1.0 OP2 C:A108 5.0 0.8 1.0

Magnesium binding site 9 out of 12 in the 3.0 A Structure of Fragment I 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 9 of 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg209 b:91.4 occ:1.00 N7 C:G106 3.1 0.8 1.0 O6 C:G106 3.2 0.5 1.0 O6 C:G105 3.8 0.4 1.0 C5 C:G106 3.8 0.5 1.0 C6 C:G106 3.9 0.2 1.0 O6 C:G107 4.1 0.6 1.0 C6 C:G105 4.2 1.0 1.0 C8 C:G106 4.2 0.1 1.0 N7 C:G105 4.3 0.6 1.0 C5 C:G105 4.4 0.2 1.0 C6 C:G107 4.8 0.9 1.0

Magnesium binding site 10 out of 12 in the 3.0 A Structure of Fragment I 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 10 of 3.0 A Structure of Fragment I From E. Coli 5S Rrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg211 b:0.8 occ:1.00 O4 C:U111 4.3 0.5 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