Magnesium in PDB 3cme: The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	210.786, 297.778, 572.588, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.5

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 93;

Binding sites:

The binding sites of Magnesium atom in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cme). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8025 b:39.9 occ:1.00 O 0:HOH5076 2.7 52.8 1.0 O 0:HOH4617 2.7 19.0 1.0 O A:HOH9110 2.7 74.6 1.0 OP1 0:U2115 2.8 29.0 1.0 O 0:HOH3905 2.8 25.7 1.0 O A:ALA196 3.0 32.8 1.0 O A:HOH9011 3.1 34.9 1.0 O A:HOH9002 3.6 50.8 1.0 P 0:U2115 3.9 29.5 1.0 C A:ALA196 4.1 31.4 1.0 O A:HOH8989 4.2 19.5 1.0 OP2 0:C2273 4.2 32.7 1.0 OP2 0:G2272 4.3 39.1 1.0 O A:VAL197 4.3 33.8 1.0 OP2 0:U2115 4.3 28.2 1.0 CA A:VAL197 4.4 31.9 1.0 C A:VAL197 4.4 31.9 1.0 O3' 0:C2114 4.5 29.1 1.0 O 0:HOH4679 4.5 64.0 1.0 OP1 0:C2273 4.6 33.4 1.0 CA A:GLY1 4.6 35.8 1.0 O A:HIS199 4.6 31.4 1.0 N A:VAL197 4.7 31.9 1.0 C A:HIS199 4.8 30.6 1.0 P 0:C2273 4.8 35.0 1.0 N A:GLY1 4.9 34.6 1.0 N A:HIS199 4.9 30.6 1.0 N A:PRO200 5.0 31.4 1.0

Magnesium binding site 2 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8044 b:51.4 occ:1.00 O 0:HOH9683 2.7 79.4 1.0 O2' 0:U2012 2.7 48.8 1.0 O A:GLN207 2.7 42.9 1.0 O 0:HOH5889 2.8 65.6 1.0 OP1 0:U1883 3.1 36.7 1.0 C A:GLN207 3.4 40.2 1.0 O3' 0:U2012 3.5 47.8 1.0 OP1 0:G2013 3.7 48.7 1.0 P 0:G2013 3.9 46.6 1.0 C2' 0:U2012 3.9 49.6 1.0 OP2 0:G2013 3.9 47.7 1.0 N A:HIS208 3.9 40.6 1.0 CA A:HIS208 3.9 40.7 1.0 CB A:GLN207 4.1 35.4 1.0 CB A:HIS208 4.1 40.5 1.0 C3' 0:U2012 4.2 48.4 1.0 CA A:GLN207 4.3 40.1 1.0 P 0:U1883 4.5 37.1 1.0 O 0:HOH9369 4.6 68.7 1.0 C4' 0:U2012 4.8 47.6 1.0 CG1 A:VAL192 4.9 36.1 1.0 N A:GLN207 4.9 42.8 1.0 O3' 0:C1882 4.9 32.9 1.0

Magnesium binding site 3 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8051 b:82.6 occ:1.00 C A:ASP26 2.6 66.4 1.0 N A:LEU27 2.8 65.4 1.0 OP2 0:G1873 2.8 36.5 1.0 NH2 A:ARG120 2.8 27.9 1.0 O 0:HOH4577 2.9 0.3 1.0 OP1 0:G1873 2.9 38.1 1.0 O A:ASP26 3.1 67.7 1.0 CA A:ASP26 3.1 66.2 1.0 P 0:G1873 3.1 37.3 1.0 O A:HOH9042 3.3 0.1 1.0 CA A:LEU27 3.4 64.6 1.0 NH1 A:ARG120 3.5 26.7 1.0 CZ A:ARG120 3.5 28.2 1.0 C A:LEU27 3.5 64.8 1.0 O3' 0:C1872 3.5 37.3 1.0 O A:LEU27 3.6 65.2 1.0 CB A:ASP26 3.6 67.8 1.0 CB A:LEU27 3.7 63.8 1.0 CG A:LEU27 3.9 61.7 1.0 O 0:HOH6057 4.1 20.2 1.0 N A:GLU28 4.3 65.8 1.0 N A:ASP26 4.4 66.3 1.0 CG A:ASP26 4.5 68.1 1.0 O A:ALA25 4.6 67.2 1.0 O5' 0:G1873 4.6 38.6 1.0 CD1 A:LEU27 4.7 61.5 1.0 NE A:ARG120 4.8 29.4 1.0 OD2 A:ASP26 4.8 68.3 1.0 CG A:GLU28 4.8 71.6 1.0 C3' 0:C1872 4.9 39.2 1.0 O A:HOH9040 5.0 37.6 1.0 C A:ALA25 5.0 65.6 1.0

Magnesium binding site 4 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg8043 b:29.5 occ:1.00 O B:HOH9013 2.4 71.5 1.0 O 0:HOH9636 2.6 59.9 1.0 OP1 0:A2757 2.8 49.8 1.0 O B:GLY337 3.0 54.4 1.0 O B:HOH9031 3.2 59.8 1.0 O B:ASN335 3.2 49.8 1.0 OP2 0:C2720 3.2 44.5 1.0 O 0:HOH4561 3.3 50.4 1.0 C B:ASN335 3.9 49.3 1.0 O 0:HOH7242 3.9 0.9 1.0 P 0:A2757 4.0 52.4 1.0 P 0:C2720 4.1 44.5 1.0 OP2 0:A2719 4.1 43.6 1.0 N B:GLY337 4.1 51.4 1.0 OP1 0:C2720 4.1 44.7 1.0 C B:GLY337 4.2 54.2 1.0 O B:HOH9141 4.3 33.9 1.0 OP2 0:A2757 4.4 52.8 1.0 CA B:ASN335 4.5 49.2 1.0 N B:GLN336 4.6 49.6 1.0 O3' 0:A2719 4.7 43.3 1.0 CA B:GLY337 4.8 52.9 1.0 CA B:GLN336 4.8 50.4 1.0 C B:GLN336 4.9 50.7 1.0 O3' 0:U2756 5.0 50.6 1.0 O5' 0:A2719 5.0 43.1 1.0

Magnesium binding site 5 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg8042 b:0.3 occ:1.00 O B:HOH9141 2.7 33.9 1.0 O 0:HOH9682 2.8 65.3 1.0 O 0:HOH7268 2.9 42.7 1.0 OXT B:GLY337 3.2 54.0 1.0 O 0:HOH4648 3.2 0.2 1.0 O B:HOH9025 3.7 50.0 1.0 O B:HOH9142 3.7 85.8 1.0 O B:HOH9026 4.0 81.5 1.0 C B:GLY337 4.1 54.2 1.0 O B:HOH9038 4.4 84.8 1.0 CB U:SER33 4.5 37.3 1.0 O U:CYS32 4.6 40.4 1.0 O B:GLY337 4.6 54.4 1.0 OE2 B:GLU333 4.9 61.3 1.0 CA B:GLY337 4.9 52.9 1.0 O U:HOH3194 4.9 56.6 1.0

Magnesium binding site 6 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg8012 b:17.1 occ:1.00 O C:HOH8661 2.3 30.1 1.0 O C:HOH8561 2.5 49.8 1.0 OP2 0:G456 2.5 32.9 1.0 O 0:HOH9565 2.5 35.3 1.0 O C:HOH8565 2.5 36.3 1.0 O 0:HOH3330 2.6 43.8 1.0 O C:GLY86 3.2 34.2 1.0 O 0:HOH6269 3.7 58.8 1.0 CA C:LYS85 3.8 31.2 1.0 C C:LYS85 3.9 30.7 1.0 OP2 0:G458 3.9 30.1 1.0 P 0:G456 3.9 36.4 1.0 OP1 0:A455 4.1 34.2 1.0 O C:LYS85 4.2 31.1 1.0 N C:GLY86 4.2 31.9 1.0 C C:GLY86 4.3 33.6 1.0 N C:LYS85 4.5 31.6 1.0 OP2 0:A455 4.5 32.7 1.0 O5' 0:G456 4.5 33.8 1.0 OP1 0:G456 4.6 33.7 1.0 O 0:HOH3372 4.7 33.6 1.0 P 0:A455 4.7 34.7 1.0 CE C:LYS85 4.9 24.9 1.0 CA C:GLY86 4.9 32.9 1.0 OP2 0:U457 5.0 29.8 1.0

Magnesium binding site 7 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg8054 b:15.4 occ:1.00 O 0:HOH6903 2.6 21.0 1.0 OD1 K:ASN42 2.6 33.6 1.0 O 0:HOH9686 2.6 27.2 1.0 O 0:HOH5127 2.7 33.9 1.0 O 0:HOH4325 2.7 44.5 1.0 O K:HOH2121 2.7 21.7 1.0 O 0:HOH5569 2.9 49.2 1.0 O 0:HOH6407 3.0 81.2 1.0 CG K:ASN42 3.8 35.0 1.0 OP1 0:A2583 4.3 30.8 1.0 OP1 0:U1749 4.4 30.0 1.0 ND2 K:ASN42 4.5 33.8 1.0 O 0:HOH9566 4.6 79.3 1.0 OP1 0:U2546 4.8 32.0 1.0 CB K:ASN42 4.8 34.5 1.0 CA K:ASN42 4.9 34.7 1.0 OP1 0:U2545 4.9 36.9 1.0 O 0:HOH5141 4.9 51.5 1.0 OP2 0:G2584 5.0 26.6 1.0

Magnesium binding site 8 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg8057 b:31.4 occ:1.00 O T:LEU112 2.5 75.7 1.0 O T:SER114 2.6 94.3 1.0 O T:HOH2868 2.8 36.2 1.0 O T:ASP117 3.0 1.0 1.0 OE1 T:GLN37 3.0 57.3 1.0 C T:SER114 3.5 94.5 1.0 C T:LEU112 3.5 76.4 1.0 O T:ARG111 3.5 70.1 1.0 O T:TYR35 3.7 65.9 1.0 CD T:GLN37 3.7 56.9 1.0 OG T:SER114 3.8 95.1 1.0 CG T:GLN37 3.9 57.1 1.0 N T:SER114 3.9 87.8 1.0 C T:ASP117 4.0 0.7 1.0 CA T:LEU112 4.2 74.7 1.0 CA T:SER114 4.2 91.8 1.0 N T:GLU115 4.3 98.0 1.0 CA T:SER118 4.3 0.2 1.0 C T:GLU113 4.3 84.6 1.0 CA T:GLU115 4.4 0.8 1.0 N T:GLU113 4.5 79.4 1.0 N T:SER118 4.6 0.7 1.0 C T:ARG111 4.6 70.7 1.0 CB T:SER114 4.7 92.6 1.0 CA T:GLU113 4.7 82.5 1.0 C T:TYR35 4.9 64.9 1.0 N T:LEU112 4.9 72.3 1.0 N T:ALA119 4.9 0.3 1.0 O T:GLU113 4.9 85.1 1.0 NE2 T:GLN37 4.9 56.5 1.0 C T:SER118 5.0 0.5 1.0

Magnesium binding site 9 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg8086 b:48.1 occ:1.00 O Y:HIS133 2.6 34.9 1.0 O Y:LYS136 2.6 34.8 1.0 O Y:VAL139 2.6 29.2 1.0 O Y:HOH8885 2.8 43.8 1.0 O Y:HOH8861 2.8 26.4 1.0 O Y:HOH8925 2.9 36.5 1.0 CA Y:LYS137 3.3 34.5 1.0 C Y:LYS136 3.4 34.8 1.0 O Y:LYS137 3.6 35.6 1.0 C Y:LYS137 3.7 35.2 1.0 N Y:LYS137 3.7 34.1 1.0 C Y:VAL139 3.8 29.6 1.0 C Y:HIS133 3.8 34.9 1.0 N Y:VAL139 4.3 30.0 1.0 CB Y:LYS137 4.4 35.6 1.0 CA Y:VAL139 4.6 29.5 1.0 N Y:ARG138 4.7 34.1 1.0 CA Y:HIS133 4.7 34.3 1.0 CA Y:LYS136 4.7 34.3 1.0 CG Y:LYS137 4.7 36.9 1.0 N Y:LYS136 4.7 34.1 1.0 N Y:HIS134 4.7 34.7 1.0 N Y:SER140 4.8 31.0 1.0 CA Y:HIS134 4.8 34.8 1.0 CD2 Y:HIS133 4.8 36.8 1.0 O Y:HOH8836 4.8 31.7 1.0 CA Y:SER140 4.8 32.0 1.0 CB Y:VAL139 4.9 27.6 1.0 CB Y:HIS133 4.9 36.2 1.0

Magnesium binding site 10 out of 93 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg8060 b:45.4 occ:1.00 O 0:HOH9638 2.7 21.9 1.0 O 0:HOH7689 2.8 74.3 1.0 O 0:HOH9688 3.0 41.6 1.0 O 2:HOH7875 3.6 69.6 1.0 O 0:HOH9637 3.6 48.5 1.0 O S:HOH8546 4.2 37.3 1.0 O 0:HOH5028 4.2 32.5 1.0 OD1 2:ASP15 4.7 59.6 1.0 OD2 2:ASP15 4.9 59.1 1.0 N7 0:G1443 4.9 41.7 1.0

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908