Magnesium in PDB 5jvg: The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin

The structure of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin, PDB code: 5jvg was solved by M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, 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)	49.55 / 3.43
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.034, 412.632, 698.142, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.3

The structure of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin also contains other interesting chemical elements:

Chlorine

(Cl)

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 - 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 - 410; Page 42, Binding sites: 411 - 420; Page 43, Binding sites: 421 - 430; Page 44, Binding sites: 431 - 440; Page 45, Binding sites: 441 - 446;

Binding sites:

The binding sites of Magnesium atom in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin (pdb code 5jvg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 446 binding sites of Magnesium where determined in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin, PDB code: 5jvg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2902 b:27.8 occ:1.00 OP1 X:U2057 2.3 71.6 1.0 OP2 X:G2218 3.2 84.0 1.0 P X:U2057 3.6 71.0 1.0 OP2 X:U2219 3.8 78.5 1.0 OP2 X:U2057 4.1 71.4 1.0 O A:PRO228 4.1 80.5 1.0 CA A:PRO232 4.3 94.1 1.0 O5' X:U2057 4.5 71.5 1.0 OP1 X:U2219 4.6 77.1 1.0 P X:G2218 4.6 85.8 1.0 P X:U2219 4.6 78.4 1.0 N A:PRO232 4.7 92.6 1.0 O3' X:C2056 4.7 75.8 1.0 CG A:PRO232 4.8 93.2 1.0 CB A:PRO232 4.8 94.0 1.0 O2' X:G2217 4.9 84.6 1.0 OP2 X:U2058 4.9 75.5 1.0 O3' X:G2217 4.9 86.7 1.0 O A:HIS231 4.9 98.4 1.0 C A:HIS231 5.0 97.6 1.0

Magnesium binding site 2 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2903 b:12.0 occ:1.00 OP2 X:G2661 1.9 58.5 1.0 OP1 X:A2701 2.3 47.2 1.0 P X:G2661 3.4 59.5 1.0 P X:A2701 3.4 46.7 1.0 OP2 X:A2701 3.8 46.5 1.0 O3' X:C2660 3.9 53.9 1.0 O5' X:G2661 4.1 60.2 1.0 O5' X:A2701 4.1 46.3 1.0 OP2 X:G2702 4.2 49.3 1.0 OP2 X:C2662 4.3 46.5 1.0 C5' X:A2701 4.4 46.5 1.0 OP1 X:G2661 4.5 60.4 1.0 O3' X:U2700 4.7 48.0 1.0 C5' X:G2661 4.7 61.1 1.0 O2' X:C2660 4.9 52.1 1.0

Magnesium binding site 3 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2904 b:64.8 occ:1.00 OP2 X:U2706 4.1 60.9 1.0 O3' X:A2705 4.8 60.5 1.0 P X:U2706 4.8 60.8 1.0 C5' X:A2705 4.9 59.3 1.0

Magnesium binding site 4 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2905 b:13.1 occ:1.00 OP1 X:A2690 2.3 43.2 1.0 OP1 X:A2692 2.3 48.0 1.0 P X:A2692 3.5 47.9 1.0 P X:A2690 3.7 43.4 1.0 OP1 X:C1310 3.8 43.3 1.0 OP2 X:A2692 3.9 48.0 1.0 O3' X:C2689 4.0 50.9 1.0 O3' X:C2691 4.0 54.1 1.0 OP2 X:A2690 4.7 43.1 1.0 C5' X:C1310 4.7 43.1 1.0 C5' X:A2690 4.7 44.0 1.0 O5' X:A2690 4.7 43.6 1.0 O5' X:A2692 4.8 47.5 1.0

Magnesium binding site 5 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2906 b:35.9 occ:1.00 OP2 X:C803 1.9 0.0 1.0 OP1 X:U800 2.2 56.1 1.0 P X:U800 3.3 57.1 1.0 P X:C803 3.3 0.3 1.0 OP2 X:U800 3.5 57.3 1.0 O5' X:C803 3.6 0.9 1.0 C5' X:A802 4.1 71.2 1.0 C4' X:A802 4.3 70.2 1.0 OP1 X:C803 4.3 0.7 1.0 O3' X:C799 4.3 56.5 1.0 O3' X:A802 4.3 69.8 1.0 C3' X:A802 4.4 70.2 1.0 OP2 X:C804 4.4 57.6 1.0 O5' X:U800 4.4 58.7 1.0 C5' X:A801 4.7 52.9 1.0

Magnesium binding site 6 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2907 b:19.0 occ:1.00 OP1 X:U2000 2.3 62.6 1.0 P X:U2000 3.7 62.0 1.0 OP2 X:A587 3.9 52.5 1.0 OP2 X:U2000 4.4 62.0 1.0 O5' X:U2000 4.4 62.1 1.0 OP1 X:A2041 4.5 49.5 1.0 OP2 X:G2001 4.6 58.0 1.0 C5' X:U2000 4.8 62.1 1.0 O3' X:U1999 4.9 53.6 1.0 OP2 X:G586 4.9 57.6 1.0

Magnesium binding site 7 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2908 b:15.6 occ:1.00 OP1 X:U823 2.4 59.0 1.0 OP2 X:U823 3.0 59.4 1.0 N7 X:G1266 3.0 67.3 1.0 P X:U823 3.1 59.1 1.0 C8 X:G1266 3.6 66.6 1.0 O3' X:C574 3.8 57.8 1.0 O2' X:C574 4.0 56.1 1.0 OP1 X:U824 4.1 62.1 1.0 O5' X:U823 4.2 60.1 1.0 C5 X:G1266 4.2 66.5 1.0 OP1 X:U575 4.4 71.0 1.0 O3' X:G822 4.4 58.1 1.0 C3' X:C574 4.7 57.0 1.0 C4' X:C574 4.7 57.2 1.0 O6 X:G1266 4.8 67.8 1.0 P X:U575 4.8 69.8 1.0 N9 X:G1266 4.9 65.4 1.0 C6 X:G1266 4.9 66.8 1.0 NE2 O:GLN79 4.9 85.9 1.0 C2' X:C574 5.0 55.9 1.0

Magnesium binding site 8 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2909 b:24.5 occ:1.00 OP1 X:C1665 1.8 42.1 1.0 OP2 X:G1284 2.2 49.3 1.0 OP1 X:A1285 2.3 47.7 1.0 OP1 X:G1664 2.5 54.8 1.0 O5' X:G1664 3.2 55.5 1.0 P X:C1665 3.2 42.3 1.0 P X:G1284 3.3 49.2 1.0 P X:G1664 3.4 55.7 1.0 O5' X:G1284 3.5 49.3 1.0 P X:A1285 3.7 47.8 1.0 O3' X:C1283 3.8 45.0 1.0 MG X:MG3183 3.8 41.0 1.0 OP2 X:C1665 3.8 42.1 1.0 O5' X:C1665 4.2 42.2 1.0 C3' X:G1664 4.2 55.4 1.0 O3' X:G1664 4.2 55.0 1.0 C5' X:C1665 4.3 42.2 1.0 OP2 X:G1664 4.3 56.2 1.0 C5' X:G1664 4.3 56.1 1.0 C4' X:G1664 4.4 55.6 1.0 OP2 X:A1285 4.4 48.2 1.0 O3' X:G1284 4.6 49.5 1.0 O5' X:A1285 4.6 47.6 1.0 C3' X:G1284 4.6 49.6 1.0 OP1 X:G1284 4.7 49.0 1.0 O3' X:C1663 4.7 54.4 1.0 C5' X:G1284 4.8 49.2 1.0

Magnesium binding site 9 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2910 b:25.6 occ:1.00 OP2 X:A743 2.3 63.3 1.0 OP2 X:C744 2.8 78.3 1.0 OP1 X:A774 2.8 52.2 1.0 OP1 X:G776 3.0 68.7 1.0 OP1 X:U775 3.4 85.8 1.0 P X:A743 3.6 64.2 1.0 O3' X:G742 3.9 66.7 1.0 P X:C744 4.1 78.5 1.0 P X:A774 4.2 51.1 1.0 C5' X:A743 4.2 65.9 1.0 P X:G776 4.3 69.6 1.0 C3' X:A743 4.3 64.4 1.0 O5' X:G776 4.3 69.0 1.0 O5' X:A743 4.4 65.5 1.0 O3' X:A743 4.5 63.5 1.0 O5' X:A774 4.6 50.6 1.0 C5' X:U775 4.7 87.3 1.0 OP1 X:A743 4.7 63.8 1.0 P X:U775 4.8 85.5 1.0 C4' X:A743 4.9 65.8 1.0 C3' X:U775 4.9 89.7 1.0 OP1 X:C744 4.9 77.9 1.0 C5' X:A774 4.9 50.7 1.0 OP2 X:A774 5.0 50.6 1.0 C8 X:A743 5.0 66.0 1.0

Magnesium binding site 10 out of 446 in the The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Large Ribosomal Subunit From Deinococcus Radiodurans in Complex with Avilamycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2911 b:11.8 occ:1.00 OP2 X:A2040 2.8 64.3 1.0 OP2 X:G2039 2.8 58.4 1.0 N6 X:A2041 3.6 49.1 1.0 P X:G2039 3.9 59.1 1.0 N7 X:A2041 4.0 48.8 1.0 N6 X:A2042 4.1 61.7 1.0 P X:A2040 4.2 64.3 1.0 O2' X:A2482 4.2 51.3 1.0 N7 X:A2040 4.2 61.6 1.0 O5' X:G2039 4.3 58.5 1.0 OP1 X:G2039 4.4 60.1 1.0 C6 X:A2041 4.5 48.9 1.0 C8 X:A2040 4.6 61.8 1.0 O5' X:A2040 4.6 63.5 1.0 C5 X:A2041 4.6 48.8 1.0 OP2 X:A2482 4.8 51.7 1.0 OP1 X:A2040 4.9 65.2 1.0 OP1 X:G2484 4.9 61.2 1.0 C2' X:A2482 4.9 51.8 1.0

M.Krupkin, I.Wekselman, D.Matzov, Z.Eyal, Y.Diskin Posner, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. Avilamycin and Evernimicin Induce Structural Changes in Rproteins UL16 and Ctc That Enhance the Inhibition of A-Site Trna Binding. Proc.Natl.Acad.Sci.Usa V. 113 E6796 2016.
ISSN: ESSN 1091-6490
PubMed: 27791159
DOI: 10.1073/PNAS.1614297113