Magnesium in PDB 1y39: Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain

The structure of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain, PDB code: 1y39 was solved by M.S.Dunstan, D.Guhathakurta, D.E.Draper, G.L.Conn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	150.240, 150.240, 62.984, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.3

The structure of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Potassium	(K)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain (pdb code 1y39). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain, PDB code: 1y39:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg405 b:46.7 occ:1.00 OP2 C:A123 2.0 69.0 1.0 O4 C:U144 2.1 63.5 1.0 O6 C:G143 3.0 60.6 1.0 C4 C:U144 3.3 64.0 1.0 P C:A123 3.4 69.3 1.0 C6 C:G143 3.9 59.0 1.0 C3' C:C122 4.0 64.8 1.0 O3' C:C122 4.0 67.8 1.0 OP2 C:U147 4.1 64.6 1.0 C2' C:C122 4.1 63.5 1.0 C5 C:U144 4.2 65.0 1.0 OP1 C:A123 4.2 68.3 1.0 N3 C:U144 4.3 64.0 1.0 O5' C:A123 4.5 69.2 1.0 N1 C:G143 4.5 58.4 1.0 C5' C:A123 4.6 68.7 1.0 OP1 C:A146 4.6 63.5 1.0 C5 C:G143 4.8 58.9 1.0 O2' C:C122 5.0 65.6 1.0 C2 C:A119 5.0 63.4 1.0

Magnesium binding site 2 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg407 b:53.3 occ:1.00 OP1 C:U116 2.2 61.0 1.0 OP1 D:A336 2.4 57.2 1.0 P C:U116 3.4 61.2 1.0 O3' C:U115 3.4 61.8 1.0 P D:A336 3.7 56.3 1.0 O3' D:A335 3.9 55.4 1.0 OP2 C:U116 4.4 60.0 1.0 O5' C:U116 4.4 59.5 1.0 C5' C:U116 4.5 57.4 1.0 OP2 D:A336 4.7 54.8 1.0 O5' D:A336 4.7 56.0 1.0 C5' D:A336 4.8 55.0 1.0 C3' C:U115 4.8 61.3 1.0 O2' D:C354 4.9 60.7 1.0

Magnesium binding site 3 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg408 b:63.7 occ:1.00 OP2 C:G113 2.3 63.8 1.0 P C:G113 3.5 63.9 1.0 OP1 C:G113 4.1 64.0 1.0 O5' C:G113 4.1 64.3 1.0 OP2 C:C114 4.2 63.6 1.0 OP1 C:A120 4.2 65.1 1.0 C5 C:C114 4.4 50.9 1.0 O2' C:A111 4.7 67.3 1.0 O4 C:U115 4.7 63.8 1.0 O3' C:U112 4.8 63.3 1.0 N7 C:G113 4.9 61.2 1.0 O5' C:U112 4.9 66.8 1.0 C8 C:G113 5.0 61.6 1.0

Magnesium binding site 4 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg409 b:69.9 occ:1.00 O C:HOH806 2.2 58.1 1.0 N7 C:A104 3.4 81.0 1.0 O6 C:G106 3.4 67.5 1.0 N6 C:A104 3.7 80.0 1.0 N7 C:G105 3.9 67.4 1.0 C5 C:A104 4.0 80.7 1.0 C6 C:G106 4.2 67.0 1.0 C6 C:A104 4.2 80.5 1.0 C8 C:A104 4.3 81.8 1.0 O6 C:G105 4.5 65.0 1.0 N1 C:G106 4.8 66.5 1.0 OP2 C:C152 4.8 75.3 1.0 C8 C:G105 4.8 68.6 1.0 C5 C:G105 4.9 66.8 1.0 C5 C:G106 5.0 66.4 1.0

Magnesium binding site 5 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg415 b:63.5 occ:1.00 OP1 C:C122 2.0 61.6 1.0 OP2 C:A120 2.0 66.2 1.0 P C:C122 3.2 63.3 1.0 P C:A120 3.4 64.5 1.0 K C:K404 3.6 71.3 1.0 OP2 C:C122 3.8 64.8 1.0 O3' C:G121 3.8 62.8 1.0 O6 C:G113 3.9 62.4 1.0 OP1 C:A120 4.1 65.1 1.0 O6 C:G124 4.1 57.5 1.0 OP1 C:U112 4.2 68.4 1.0 O4 C:U112 4.2 55.6 1.0 O5' C:A120 4.3 64.9 1.0 O3' C:A119 4.4 64.8 1.0 C5' C:A120 4.4 66.6 1.0 O5' C:C122 4.5 61.6 1.0 C5 C:U112 4.6 57.3 1.0 N4 C:C125 4.6 58.0 1.0 N4 C:C114 4.7 51.7 1.0 C4 C:U112 4.8 57.3 1.0 C5' C:C122 4.9 62.3 1.0

Magnesium binding site 6 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg416 b:74.2 occ:1.00 N7 C:G121 3.7 58.3 1.0 O6 C:G121 4.0 58.2 1.0 C5 C:G121 4.5 58.8 1.0 N4 C:C150 4.6 75.5 1.0 C6 C:G121 4.6 58.6 1.0 C8 C:G121 4.7 59.1 1.0 OP2 C:G149 4.8 72.3 1.0 OP2 C:A148 4.9 70.3 1.0 O4 C:U151 4.9 71.5 1.0 N4 C:C122 5.0 60.3 1.0

Magnesium binding site 7 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg417 b:99.7 occ:1.00 N7 C:G106 4.4 67.7 1.0 OP2 C:G105 4.6 82.5 1.0 OP2 C:G106 4.7 73.6 1.0 O6 C:G106 4.9 67.5 1.0

Magnesium binding site 8 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg419 b:79.1 occ:1.00 OP2 C:C125 3.9 67.3 1.0 OP2 C:A126 4.1 66.4 1.0 N7 C:A126 4.6 64.8 1.0 P C:C125 4.9 67.6 1.0

Magnesium binding site 9 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg420 b:69.3 occ:1.00 O2 C:U110 3.2 64.2 1.0 O2' C:U110 4.1 65.5 1.0 O6 C:G109 4.3 57.5 1.0 C2 C:U110 4.3 64.1 1.0 O4 C:U108 4.5 57.5 1.0 C8 C:A138 4.6 53.5 1.0 N7 C:G109 4.7 58.8 1.0 C1' C:U110 4.9 65.0 1.0 C4 C:U108 5.0 59.1 1.0

Magnesium binding site 10 out of 18 in the Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Evolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg421 b:72.0 occ:1.00 O C:HOH807 2.4 27.9 1.0 O2' C:A136 2.8 68.2 1.0 O6 C:G137 2.9 62.2 1.0 O2' C:G106 3.2 70.8 1.0 N7 C:G137 3.3 61.0 1.0 O3' C:G106 3.4 72.3 1.0 OP2 C:A107 3.4 71.3 1.0 C6 C:G137 3.6 60.9 1.0 C2' C:A136 3.7 67.4 1.0 C5 C:G137 3.8 60.7 1.0 C2' C:G106 3.9 69.9 1.0 P C:A107 3.9 72.2 1.0 O6 C:G139 4.2 57.0 1.0 C6 C:G139 4.2 54.0 1.0 C3' C:G106 4.2 71.0 1.0 N7 C:A107 4.3 65.5 1.0 N1 C:G139 4.3 51.3 1.0 C8 C:A107 4.4 65.8 1.0 N6 C:A153 4.4 50.2 1.0 N1 C:A153 4.4 51.8 1.0 OP1 C:A107 4.5 70.7 1.0 C8 C:G137 4.5 61.4 1.0 OP2 C:G137 4.5 69.2 1.0 C1' C:A136 4.6 66.1 1.0 C5 C:G139 4.8 53.5 1.0 C6 C:A153 4.8 51.9 1.0 C2 C:G139 4.9 51.3 1.0 N1 C:G137 5.0 60.0 1.0 C3' C:A136 5.0 68.2 1.0 O3' C:A136 5.0 67.6 1.0

M.S.Dunstan, D.Guhathakurta, D.E.Draper, G.L.Conn. Coevolution of Protein and Rna Structures Within A Highly Conserved Ribosomal Domain Chem.Biol. V. 12 201 2005.
ISSN: ISSN 1074-5521
PubMed: 15734647
DOI: 10.1016/J.CHEMBIOL.2004.11.019