Magnesium in PDB 7a18: 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV, PDB code: 7a18 was solved by E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.59, 410.128, 690.477, 90, 90, 90
R / Rfree (%)	28.4 / 31.8

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 - 277;

Binding sites:

The binding sites of Magnesium atom in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV (pdb code 7a18). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 277 binding sites of Magnesium where determined in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV, PDB code: 7a18:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2902 b:82.2 occ:1.00 OP1 X:U2057 2.6 85.5 1.0 OP2 X:G2218 2.8 91.8 1.0 OP2 X:U2219 3.8 91.2 1.0 O A:PRO228 3.9 83.6 1.0 P X:U2057 3.9 84.9 1.0 OP1 X:U2219 4.1 89.3 1.0 C5' X:G2218 4.2 93.6 1.0 P X:G2218 4.2 93.7 1.0 CA A:PRO232 4.3 85.6 1.0 CG A:PRO232 4.3 87.9 1.0 P X:U2219 4.3 91.0 1.0 OP2 X:U2057 4.4 85.6 1.0 N A:PRO232 4.5 85.2 1.0 O3' X:G2218 4.6 92.1 1.0 CD A:PRO232 4.7 86.6 1.0 CB A:PRO232 4.7 87.5 1.0 O5' X:G2218 4.7 94.6 1.0 O A:HIS231 4.8 84.2 1.0 C A:HIS231 4.8 85.3 1.0 O3' X:G2217 4.9 93.2 1.0 O5' X:U2057 4.9 85.2 1.0 O3' X:C2056 5.0 83.8 1.0

Magnesium binding site 2 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:60.5 occ:1.00 OP1 X:U800 2.2 70.7 1.0 OP2 X:C803 2.3 68.0 1.0 P X:U800 3.1 71.2 1.0 OP2 X:U800 3.2 71.1 1.0 P X:C803 3.5 67.2 1.0 OP1 X:C803 4.0 66.8 1.0 C3' X:A802 4.0 63.6 1.0 O3' X:A802 4.1 63.1 1.0 O3' X:C799 4.1 71.0 1.0 OP2 X:C804 4.2 69.8 1.0 C4' X:A802 4.3 63.7 1.0 N7 X:A1771 4.3 68.0 1.0 C5' X:A802 4.4 64.5 1.0 O5' X:U800 4.5 72.2 1.0 N6 X:A1771 4.5 69.2 1.0 OP1 X:A802 4.9 65.2 1.0 C5 X:A1771 4.9 68.1 1.0 O5' X:C803 4.9 66.9 1.0

Magnesium binding site 3 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:49.0 occ:1.00 OP1 X:U2000 3.3 50.9 1.0 OP2 X:A587 4.1 54.2 1.0 OP2 X:G586 4.2 54.5 1.0 P X:U2000 4.6 50.7 1.0 OP1 X:G586 4.6 53.2 1.0 P X:G586 4.8 54.2 1.0 O5' X:U2000 5.0 51.6 1.0 OP1 X:A2041 5.0 55.3 1.0 OP2 X:G2001 5.0 52.7 1.0

Magnesium binding site 4 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:62.6 occ:1.00 OP1 X:U823 1.9 64.2 1.0 N7 X:G1266 2.7 61.1 1.0 P X:U823 2.9 64.1 1.0 OP2 X:U823 2.9 64.4 1.0 C8 X:G1266 3.1 60.4 1.0 O2' X:C574 3.8 60.7 1.0 O3' X:G822 4.0 63.3 1.0 C5 X:G1266 4.0 60.8 1.0 O5' X:U823 4.1 64.7 1.0 OP1 X:U824 4.2 66.2 1.0 N9 X:G1266 4.4 59.6 1.0 O3' X:C574 4.5 62.7 1.0 C4 X:G1266 4.9 59.9 1.0 C5' X:U823 4.9 64.5 1.0 C6 X:G1266 4.9 61.3 1.0 C4' X:C574 4.9 61.4 1.0 O6 X:G1266 5.0 62.1 1.0

Magnesium binding site 5 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2906 b:75.5 occ:1.00 OP2 X:A774 2.0 75.4 0.5 OP2 X:A743 2.1 81.9 1.0 OP1 X:A774 2.3 75.2 0.5 OP2 X:C744 2.4 79.8 1.0 P X:A774 3.3 74.7 0.5 P X:A743 3.4 82.3 1.0 P X:C744 3.8 79.5 1.0 P X:A774 3.8 74.3 0.5 OP1 X:G776 3.8 83.8 1.0 OP1 X:A774 3.9 74.9 0.5 O3' X:G742 3.9 84.1 1.0 O5' X:A774 4.1 74.8 0.5 C3' X:A743 4.1 82.8 1.0 C5' X:A743 4.2 83.7 1.0 C5' X:A774 4.2 75.1 0.5 O3' X:A743 4.2 81.8 1.0 O5' X:A743 4.3 83.0 1.0 O3' X:G773 4.4 74.0 1.0 O5' X:A774 4.4 74.5 0.5 OP1 X:A743 4.5 81.6 1.0 OP1 X:C744 4.5 78.6 1.0 OP1 X:U775 4.5 79.8 1.0 C4' X:A743 4.7 83.5 1.0 C5' X:U775 4.8 80.7 1.0 O5' X:C744 4.9 79.4 1.0 OP2 X:A774 4.9 73.7 0.5 C5' X:A774 4.9 75.0 0.5

Magnesium binding site 6 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2907 b:46.5 occ:1.00 OP2 X:A2040 2.4 54.5 1.0 OP2 X:G2039 2.6 52.5 1.0 N6 X:A2041 3.6 53.5 1.0 P X:A2040 3.7 54.6 1.0 P X:G2039 3.8 53.5 1.0 O5' X:A2040 4.2 53.5 1.0 OP1 X:G2039 4.3 54.3 1.0 O5' X:G2039 4.3 53.4 1.0 OP1 X:A2040 4.4 55.3 1.0 N7 X:A2041 4.5 53.2 1.0 C6 X:A2041 4.5 53.0 1.0 OP1 X:G2484 4.6 53.6 1.0 C3' X:A2482 4.7 54.8 1.0 O2' X:A2482 4.7 53.7 1.0 N6 X:A2042 4.8 56.2 1.0 C5 X:A2041 4.9 52.9 1.0 O3' X:G2039 4.9 52.4 1.0 C2' X:A2482 4.9 54.4 1.0

Magnesium binding site 7 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2908 b:39.4 occ:1.00 O6 X:G2699 2.9 44.0 1.0 C6 X:G2699 3.9 43.8 1.0 O6 X:G2698 4.0 43.5 1.0 O4 X:U2693 4.2 41.1 1.0 N7 X:G2698 4.5 44.3 1.0 N1 X:G2699 4.6 43.5 1.0 C4 X:U2693 4.6 41.1 1.0 O6 X:G2697 4.7 44.3 1.0 N3 X:U2693 4.8 41.3 1.0 N7 X:G2697 4.9 44.7 1.0 C6 X:G2698 4.9 43.9 1.0 C5 X:G2699 4.9 44.0 1.0

Magnesium binding site 8 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2909 b:44.6 occ:1.00 OP2 X:C1340 2.0 48.0 1.0 P X:C1340 2.9 47.5 1.0 OP1 X:C1340 2.9 48.1 1.0 O5' X:C1340 3.8 47.8 1.0 O3' X:U1339 4.2 46.4 1.0 OP2 X:U1339 4.3 46.8 1.0 OP1 X:U1339 4.3 46.6 1.0 N7 X:G1341 4.3 51.2 1.0 N7 X:G1337 4.4 56.5 1.0 C8 X:G1337 4.6 55.6 1.0 O6 X:G1341 4.7 50.8 1.0 P X:U1339 4.7 46.3 1.0 OP2 X:G1341 4.7 51.6 1.0

Magnesium binding site 9 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2910 b:41.3 occ:1.00 OP2 X:G2698 4.1 45.5 1.0 OP1 X:G2698 4.2 45.9 1.0 P X:G2698 4.6 45.8 1.0 OP1 X:G2665 4.6 42.6 1.0

Magnesium binding site 10 out of 277 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2911 b:39.8 occ:1.00 OP1 X:G2557 3.6 43.6 1.0 N7 X:A2593 3.7 45.0 1.0 OP2 X:G2557 4.0 42.6 1.0 N7 X:A2034 4.0 45.0 1.0 P X:G2557 4.2 43.3 1.0 OP2 X:A2034 4.3 43.8 1.0 C8 X:A2593 4.3 44.9 1.0 C8 X:A2034 4.4 45.3 1.0 OP2 X:A2593 4.6 42.8 1.0 OP1 X:U2592 4.7 46.7 1.0 C5 X:A2593 4.9 45.9 1.0

E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin IV To Be Published.