Magnesium in PDB 7y41: Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth

The structure of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth also contains other interesting chemical elements:

Zinc

(Zn)

4 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 - 310; Page 32, Binding sites: 311 - 320; Page 33, Binding sites: 321 - 330; Page 34, Binding sites: 331 - 340; Page 35, Binding sites: 341 - 350; Page 36, Binding sites: 351 - 360; Page 37, Binding sites: 361 - 370; Page 38, Binding sites: 371 - 380; Page 39, Binding sites: 381 - 390; Page 40, Binding sites: 391 - 400; Page 41, Binding sites: 401 - 407;

Binding sites:

The binding sites of Magnesium atom in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth (pdb code 7y41). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 407 binding sites of Magnesium where determined in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth, PDB code: 7y41:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:111.6 occ:1.00 O6 A:G2671 2.0 107.0 1.0 O6 A:G2285 2.8 110.6 1.0 C6 A:G2671 2.9 107.0 1.0 O4' A:C2725 3.0 109.1 1.0 N7 A:G2671 3.2 107.0 1.0 O4 A:U2728 3.3 111.1 1.0 O2 A:C2725 3.3 109.1 1.0 C5 A:G2671 3.3 107.0 1.0 C1' A:C2725 3.6 109.1 1.0 C6 A:G2285 3.6 110.6 1.0 C2 A:C2725 3.6 109.1 1.0 N7 A:G2285 3.7 110.6 1.0 N1 A:C2725 3.8 109.1 1.0 C5 A:U2728 3.9 111.1 1.0 C4 A:U2728 3.9 111.1 1.0 C5 A:G2285 4.0 110.6 1.0 C4' A:C2725 4.1 109.1 1.0 N6 A:A2675 4.1 108.2 1.0 N1 A:G2671 4.2 107.0 1.0 N3 A:C2725 4.4 109.1 1.0 C8 A:G2671 4.4 107.0 1.0 C5' A:C2725 4.5 109.1 1.0 C6 A:C2725 4.7 109.1 1.0 C4 A:G2671 4.7 107.0 1.0 N1 A:G2285 4.8 110.6 1.0 O5' A:C2725 4.9 109.1 1.0 N4 A:C2676 4.9 107.6 1.0 C8 A:G2285 4.9 110.6 1.0 C2' A:U2724 4.9 107.1 1.0

Magnesium binding site 2 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:96.6 occ:1.00 N7 A:G848 2.0 100.8 1.0 N7 A:A876 2.1 105.6 1.0 C8 A:G848 2.9 100.8 1.0 C5 A:G848 3.1 100.8 1.0 C8 A:A876 3.1 105.6 1.0 C5 A:A876 3.1 105.6 1.0 N6 A:A876 3.3 105.6 1.0 O6 A:G848 3.5 100.8 1.0 C6 A:G848 3.6 100.8 1.0 C6 A:A876 3.6 105.6 1.0 OP2 A:G848 3.8 100.8 1.0 N9 A:G848 4.1 100.8 1.0 C4 A:G848 4.1 100.8 1.0 OP2 A:C847 4.2 101.9 1.0 N9 A:A876 4.2 105.6 1.0 C4 A:A876 4.3 105.6 1.0 OP2 A:A876 4.4 105.6 1.0 OP2 A:G875 4.6 106.1 1.0 C5 A:C847 4.7 101.9 1.0 O5' A:G848 4.7 100.8 1.0 C6 A:C847 4.8 101.9 1.0 O5' A:C847 4.8 101.9 1.0 P A:G848 4.9 100.8 1.0 N1 A:G848 4.9 100.8 1.0 N1 A:A876 4.9 105.6 1.0

Magnesium binding site 3 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4003 b:104.7 occ:1.00 OP1 A:A2229 2.1 107.1 1.0 OP2 A:G1384 2.1 110.2 1.0 P A:G1384 3.3 110.2 1.0 P A:A2229 3.5 107.1 1.0 OP1 A:G1384 3.9 110.2 1.0 O3' A:A1383 3.9 112.7 1.0 OP1 A:A1383 4.1 112.7 1.0 O5' A:A2229 4.2 107.1 1.0 O5' A:A1383 4.2 112.7 1.0 C5' A:A2229 4.2 107.1 1.0 C3' A:A1383 4.2 112.7 1.0 N7 A:G1384 4.3 110.2 1.0 C8 A:G1384 4.4 110.2 1.0 OP2 A:A2229 4.4 107.1 1.0 P A:A1383 4.4 112.7 1.0 OP2 A:A1383 4.5 112.7 1.0 O3' A:G2228 4.5 106.6 1.0 OP2 A:C2230 4.5 108.4 1.0 O5' A:G1384 4.6 110.2 1.0 C5' A:A1383 4.7 112.7 1.0

Magnesium binding site 4 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4004 b:106.7 occ:1.00 N7 A:G2277 2.0 101.2 1.0 C6 A:G2276 2.1 102.8 1.0 C5 A:G2276 2.2 102.8 1.0 O6 A:G2276 2.4 102.8 1.0 C5 A:G2277 2.6 101.2 1.0 N7 A:G2276 2.7 102.8 1.0 O6 A:G2277 2.8 101.2 1.0 N1 A:G2276 2.9 102.8 1.0 C6 A:G2277 2.9 101.2 1.0 C8 A:G2277 3.0 101.2 1.0 C4 A:G2276 3.1 102.8 1.0 C8 A:G2276 3.5 102.8 1.0 C2 A:G2276 3.6 102.8 1.0 C4 A:G2277 3.7 101.2 1.0 N3 A:G2276 3.8 102.8 1.0 N9 A:G2276 3.8 102.8 1.0 N9 A:G2277 3.9 101.2 1.0 N3 A:A2275 4.0 102.6 1.0 N1 A:G2277 4.2 101.2 1.0 C2 A:A2275 4.4 102.6 1.0 N4 A:C2841 4.5 101.6 1.0 N1 A:A2838 4.5 105.0 1.0 O2' A:A2275 4.6 102.6 1.0 C2 A:A2838 4.7 105.0 1.0 N2 A:G2276 4.7 102.8 1.0 N6 A:A2801 4.8 106.3 1.0 N3 A:G2277 4.8 101.2 1.0 N3 A:C2841 4.9 101.6 1.0 C2 A:G2277 4.9 101.2 1.0

Magnesium binding site 5 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4005 b:93.5 occ:1.00 OP1 A:C793 2.0 105.5 1.0 O6 A:G891 2.0 107.2 1.0 OP1 A:C2295 2.6 107.5 1.0 C6 A:G891 3.0 107.2 1.0 P A:C793 3.4 105.5 1.0 N1 A:G891 3.7 107.2 1.0 P A:C2295 3.9 107.5 1.0 OP2 A:C793 4.1 105.5 1.0 C5 A:G891 4.1 107.2 1.0 O5' A:C793 4.1 105.5 1.0 O3' A:A2294 4.1 108.1 1.0 O2' A:A908 4.2 105.5 1.0 O3' A:G792 4.5 108.1 1.0 N7 A:G891 4.5 107.2 1.0 C5' A:C793 4.6 105.5 1.0 C2' A:A908 4.6 105.5 1.0 OP2 A:C2295 4.8 107.5 1.0 O5' A:C2295 4.9 107.5 1.0 C2 A:G891 5.0 107.2 1.0

Magnesium binding site 6 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4006 b:111.5 occ:1.00 OP1 A:A1832 2.1 109.3 1.0 OP1 A:G866 2.1 115.6 1.0 P A:G866 3.4 115.6 1.0 P A:A1832 3.5 109.3 1.0 O3' A:A865 3.7 114.9 1.0 O3' A:A1831 4.1 111.0 1.0 N7 A:A1832 4.1 109.3 1.0 N3 A:C1835 4.2 114.4 1.0 O5' A:G866 4.2 115.6 1.0 OP2 A:A1832 4.3 109.3 1.0 O2' A:A1831 4.3 111.0 1.0 C2' A:A1831 4.4 111.0 1.0 C8 A:A1832 4.4 109.3 1.0 N4 A:C1835 4.4 114.4 1.0 O5' A:A1832 4.6 109.3 1.0 OP2 A:G866 4.6 115.6 1.0 N7 A:G866 4.6 115.6 1.0 N4 A:C1833 4.6 112.3 1.0 C3' A:A1831 4.7 111.0 1.0 C8 A:G866 4.8 115.6 1.0 C4 A:C1835 4.8 114.4 1.0 N6 A:A904 4.9 118.0 1.0 C5 A:C1833 5.0 112.3 1.0 C3' A:A865 5.0 114.9 1.0

Magnesium binding site 7 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4007 b:103.0 occ:1.00 OP1 A:A2801 2.0 106.3 1.0 OP1 A:G2800 2.1 111.9 1.0 P A:A2801 2.9 106.3 1.0 OP2 A:A2801 3.0 106.3 1.0 MG A:MG4211 3.3 105.7 1.0 P A:G2800 3.4 111.9 1.0 O3' A:C2799 3.7 107.4 1.0 O5' A:A2801 4.0 106.3 1.0 O3' A:G2800 4.1 111.9 1.0 N2 A:G2800 4.3 111.9 1.0 O5' A:G2800 4.3 111.9 1.0 OP2 A:G2277 4.4 101.2 1.0 OP1 A:G2277 4.4 101.2 1.0 OP2 A:G2276 4.4 102.8 1.0 C5' A:G2800 4.4 111.9 1.0 C3' A:G2800 4.4 111.9 1.0 OP2 A:G2800 4.5 111.9 1.0 P A:G2277 4.9 101.2 1.0 C8 A:A2801 4.9 106.3 1.0 N3 A:G2800 5.0 111.9 1.0 N7 A:A2801 5.0 106.3 1.0

Magnesium binding site 8 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4008 b:130.0 occ:1.00 O4 A:U1060 2.5 103.6 1.0 C4 A:U1060 3.7 103.6 1.0 OP2 A:C949 4.1 110.3 1.0 O6 A:G1059 4.4 103.5 1.0 N3 A:U1060 4.4 103.6 1.0 O6 A:G951 4.5 105.3 1.0 C5 A:U1060 4.8 103.6 1.0 OP2 A:G948 4.9 110.7 1.0 N7 A:G1061 4.9 105.0 1.0 C5 A:C949 4.9 110.3 1.0

Magnesium binding site 9 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4009 b:103.0 occ:1.00 O6 A:G662 1.9 103.0 1.0 OP1 A:A2672 2.0 106.2 1.0 OP1 A:C2723 2.2 104.8 1.0 C6 A:G662 3.1 103.0 1.0 P A:A2672 3.2 106.2 1.0 OP2 A:A2672 3.6 106.2 1.0 P A:C2723 3.6 104.8 1.0 N1 A:G662 3.8 103.0 1.0 O5' A:A2672 4.0 106.2 1.0 C2 A:A2254 4.1 104.2 1.0 N1 A:A2254 4.1 104.2 1.0 C5 A:G662 4.2 103.0 1.0 OP2 A:C2723 4.3 104.8 1.0 O2' A:U660 4.4 103.6 1.0 O3' A:C2722 4.4 105.3 1.0 OP2 A:U2724 4.4 107.1 1.0 O3' A:G2671 4.5 107.0 1.0 O4 A:U661 4.5 103.2 1.0 O5' A:C2723 4.6 104.8 1.0 N7 A:G662 4.7 103.0 1.0 C3' A:G2671 4.8 107.0 1.0 C5' A:C2723 5.0 104.8 1.0

Magnesium binding site 10 out of 407 in the Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mycobacterium Smegmatis 50S Ribosomal Subunit From Log Phase of Growth within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4010 b:95.1 occ:1.00 OP2 A:A2281 2.0 107.7 1.0 OP2 A:G2280 2.4 106.4 1.0 P A:A2281 3.4 107.7 1.0 P A:G2280 3.6 106.4 1.0 O5' A:A2281 4.0 107.7 1.0 OP1 A:G2280 4.0 106.4 1.0 O5' A:G2280 4.2 106.4 1.0 OP1 A:A2281 4.2 107.7 1.0 N7 A:A2282 4.3 107.8 1.0 N6 A:A2282 4.4 107.8 1.0 O3' A:G2280 4.4 106.4 1.0 C3' A:G2280 4.5 106.4 1.0 N7 A:A2281 4.5 107.7 1.0 C8 A:A2281 4.6 107.7 1.0 O3' A:C2279 4.9 101.9 1.0 C5' A:G2280 4.9 106.4 1.0

J.Sengupta, P.Baid. Cryo-Em Structures Reveal A Unique Conformational Dynamics of the Mycobacterium 23S Rrna Helices To Be Published.