Magnesium in PDB 6cao: Structure of the Ribosomal Decoding Complex at Ambient Temperature

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature, PDB code: 6cao was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.22 / 3.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.300, 402.300, 176.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.2

The structure of Structure of the Ribosomal Decoding Complex at Ambient Temperature also contains other interesting chemical elements:

Potassium	(K)	37 atoms
Zinc	(Zn)	2 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 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 303;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Ribosomal Decoding Complex at Ambient Temperature (pdb code 6cao). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 303 binding sites of Magnesium where determined in the Structure of the Ribosomal Decoding Complex at Ambient Temperature, PDB code: 6cao:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range:

Magnesium binding site 2 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1643 b:51.0 occ:1.00 O A:HOH2193 2.1 45.9 1.0 O A:HOH2084 2.1 55.6 1.0 O A:HOH2093 2.1 54.1 1.0 N7 A:G376 3.9 68.4 1.0 O6 A:G376 4.4 58.4 1.0 O6 A:G377 4.6 81.8 1.0 C5 A:G376 4.6 64.9 1.0 MG A:MG1831 4.7 44.1 1.0 C8 A:G376 4.7 67.2 1.0 C6 A:G376 4.8 67.4 1.0 C5 A:U375 4.8 88.8 1.0 N7 A:G377 4.9 75.0 1.0

Magnesium binding site 3 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1644 b:59.5 occ:1.00 O A:HOH2173 2.1 54.2 1.0 O A:HOH2107 2.1 62.8 1.0 O A:HOH2138 2.1 61.1 1.0 O6 A:G650 3.3 61.3 1.0 N7 A:G650 3.9 64.0 1.0 O6 A:G649 4.0 55.4 1.0 N7 A:G649 4.0 74.4 1.0 C6 A:G650 4.2 62.9 1.0 C5 A:G650 4.4 61.0 1.0 OP2 A:A753 4.5 71.1 1.0 C5 A:G649 4.5 77.1 1.0 C6 A:G649 4.5 73.4 1.0 C8 A:G649 5.0 73.6 1.0

Magnesium binding site 4 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1645 b:90.4 occ:1.00 O A:HOH2090 2.1 89.6 1.0 O A:HOH2060 2.1 91.7 1.0 OP2 A:C749 2.9 93.9 1.0 OP2 A:G750 3.0 95.7 1.0 OP1 A:C749 3.2 93.3 1.0 P A:C749 3.5 88.3 1.0 O2' A:C748 4.0 85.8 1.0 O3' A:C748 4.0 92.2 1.0 P A:G750 4.2 91.8 1.0 OP1 A:G750 4.6 96.6 1.0 O5' A:C749 5.0 72.1 1.0 C2' A:C748 5.0 83.4 1.0

Magnesium binding site 5 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1646 b:27.5 occ:1.00 O2 A:U871 3.8 66.9 1.0 OP2 A:G855 4.3 58.0 1.0 N3 A:G818 4.7 61.4 1.0 C2 A:U871 4.7 60.6 1.0 C4 A:G818 4.9 64.4 1.0 C2 A:G818 4.9 62.8 1.0 O4' A:G818 5.0 60.6 1.0

Magnesium binding site 6 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1647 b:68.4 occ:1.00 O A:HOH2007 2.1 85.7 1.0 O A:HOH2004 2.1 63.9 1.0 O A:HOH2046 2.1 65.6 1.0 O A:HOH2006 2.1 68.1 1.0 OP2 A:G117 2.8 55.5 1.0 OP2 A:G289 3.0 52.7 1.0 OP1 A:A116 3.4 55.9 1.0 P A:G117 3.7 54.3 1.0 O4 A:U118 3.8 75.8 1.0 C3' A:A288 3.8 46.2 1.0 OP1 A:G117 3.8 46.5 1.0 O5' A:A288 3.9 57.6 1.0 P A:G289 4.0 52.0 1.0 O3' A:A288 4.1 51.0 1.0 C8 A:A288 4.2 63.2 1.0 C5 A:U118 4.4 64.2 1.0 P A:A116 4.4 56.0 1.0 OP2 A:A116 4.4 62.3 1.0 C4 A:U118 4.4 68.1 1.0 OP2 A:A288 4.5 76.3 1.0 OP1 A:G289 4.5 51.7 1.0 N7 A:G117 4.5 70.3 1.0 C2' A:A288 4.6 45.5 1.0 O5' A:G117 4.6 57.9 1.0 N7 A:A288 4.7 64.2 1.0 P A:A288 4.7 68.0 1.0 C4' A:A288 4.8 48.2 1.0 N9 A:A288 4.8 59.1 1.0 C5' A:A288 4.9 51.3 1.0 C8 A:G117 4.9 67.4 1.0 O3' A:A116 4.9 57.3 1.0 C5' A:A116 5.0 51.2 1.0

Magnesium binding site 7 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1648 b:58.8 occ:1.00 OP2 A:C48 2.7 73.1 1.0 OP1 A:A51 3.3 57.0 1.0 OP2 A:U49 3.7 73.7 1.0 OP1 A:G115 3.9 51.6 1.0 P A:C48 4.1 64.7 1.0 O23 A:PAR1603 4.1 0.8 1.0 P A:A51 4.6 51.7 1.0 OP1 A:C48 4.6 99.7 1.0 C23 A:PAR1603 4.7 92.7 1.0 O3' A:C47 4.8 58.0 1.0 C5' A:A51 4.8 61.9 1.0 O2' A:C47 4.9 51.4 1.0 C5' A:G115 5.0 53.7 1.0

Magnesium binding site 8 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1649 b:0.7 occ:1.00 O A:HOH2068 2.1 0.5 1.0 O A:HOH2187 2.1 0.0 1.0 O A:HOH2087 2.1 0.5 1.0 O A:HOH2137 2.1 0.9 1.0 N7 A:G752 3.9 62.7 1.0 OP2 A:U751 4.2 70.5 1.0 OP2 A:U652 4.2 79.3 1.0 OP1 A:C651 4.2 88.1 1.0 OP1 A:U751 4.6 67.1 1.0 C8 A:G752 4.6 63.4 1.0 P A:U751 4.8 66.0 1.0 OP2 A:G752 4.9 74.2 1.0

Magnesium binding site 9 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1650 b:49.6 occ:1.00 O A:HOH2156 2.1 43.7 1.0 O A:HOH2196 2.1 45.8 1.0 O A:HOH2089 2.1 46.1 1.0 O6 A:G800 3.4 54.5 1.0 O A:HOH2066 3.8 64.5 1.0 N7 A:G799 3.9 56.5 1.0 C6 A:G800 4.1 54.7 1.0 O6 A:G799 4.2 66.1 1.0 OP2 A:A781 4.4 53.2 1.0 N1 A:G800 4.5 54.3 1.0 C5 A:G799 4.8 56.5 1.0 N7 A:G798 4.8 57.9 1.0 OP2 A:A780 4.8 64.7 1.0 C6 A:G799 4.8 59.0 1.0 C8 A:G799 4.9 57.1 1.0 O6 A:G798 5.0 56.6 1.0 OP1 A:A781 5.0 64.3 1.0

Magnesium binding site 10 out of 303 in the Structure of the Ribosomal Decoding Complex at Ambient Temperature


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Ribosomal Decoding Complex at Ambient Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1651 b:30.8 occ:1.00 N7 A:G1508 3.7 49.5 1.0 N7 A:A1507 3.8 54.6 1.0 C8 A:A1507 4.1 55.8 1.0 O6 A:G1508 4.3 48.9 1.0 O A:HOH2183 4.5 0.9 1.0 OP2 A:G1508 4.5 72.7 1.0 O A:HOH2111 4.5 0.2 1.0 C5 A:A1507 4.6 54.0 1.0 C8 A:G1508 4.6 49.7 1.0 C5 A:G1508 4.6 49.2 1.0 C6 A:G1508 4.8 49.0 1.0 N9 A:A1507 4.9 50.1 1.0

E.H.Dao, F.Poitevin, R.G.Sierra, C.Gati, Y.Rao, H.I.Ciftci, F.Aksit, A.Mcgurk, T.Obrinski, P.Mgbam, B.Hayes, C.De Lichtenberg, F.Pardo-Avila, N.Corsepius, L.Zhang, M.H.Seaberg, M.S.Hunter, M.Liang, J.E.Koglin, S.Wakatsuki, H.Demirci. Structure of the 30S Ribosomal Decoding Complex at Ambient Temperature. Rna V. 24 1667 2018.
ISSN: ESSN 1469-9001
PubMed: 30139800
DOI: 10.1261/RNA.067660.118