Magnesium in PDB 1n8r: Structure of Large Ribosomal Subunit in Complex with Virginiamycin M

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r was solved by J.L.Hansen, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M also contains other interesting chemical elements:

Potassium	(K)	1 atom
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M (pdb code 1n8r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8001 b:29.9 occ:1.00 O A:HOH9577 1.7 40.0 1.0 O A:HOH8262 1.9 15.7 1.0 O A:HOH4011 2.1 15.4 1.0 OP2 A:C2533 2.1 19.3 1.0 OP2 A:A2483 2.3 21.4 1.0 OP2 A:C2534 2.4 23.4 1.0 O3' A:G2482 3.3 22.0 1.0 P A:A2483 3.4 20.9 1.0 P A:C2533 3.5 22.0 1.0 P A:C2534 3.8 25.2 1.0 O A:HOH3033 3.8 21.8 1.0 OP2 A:U2484 3.9 26.7 1.0 O3' A:A2532 3.9 23.1 1.0 O2' A:A2532 3.9 26.3 1.0 O A:HOH4714 4.3 22.9 1.0 OP1 A:A2483 4.3 21.2 1.0 O2' A:G2482 4.5 28.5 1.0 O5' A:C2533 4.5 20.7 1.0 O A:HOH6758 4.5 64.5 1.0 O A:HOH7856 4.5 28.0 1.0 O5' A:A2483 4.5 17.7 1.0 O3' A:C2533 4.5 21.0 1.0 OP1 A:C2533 4.5 22.7 1.0 OP1 A:C2534 4.6 23.9 1.0 C5' A:A2483 4.6 18.8 1.0 C3' A:C2533 4.7 19.7 1.0 C3' A:G2482 4.7 24.7 1.0 O5' A:C2534 4.7 23.2 1.0 C3' A:A2532 4.9 23.9 1.0 C2' A:A2532 4.9 25.0 1.0 C2' A:G2482 5.0 25.7 1.0

Magnesium binding site 2 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8002 b:34.7 occ:1.00 O6 A:G627 1.9 25.5 1.0 O A:HOH8240 2.0 9.9 1.0 OP1 A:A2483 2.0 21.2 1.0 OP1 A:C2534 2.1 23.9 1.0 O A:HOH8241 2.2 30.8 1.0 O A:HOH4714 2.2 22.9 1.0 C6 A:G627 3.1 23.5 1.0 P A:A2483 3.2 20.9 1.0 P A:C2534 3.4 25.2 1.0 OP2 A:A2483 3.7 21.4 1.0 N1 A:G627 3.8 23.6 1.0 O4 A:U626 3.9 20.1 1.0 OP2 A:C2534 3.9 23.4 1.0 O2' A:U625 4.1 16.1 1.0 O A:HOH9658 4.1 3.1 1.0 O A:HOH7482 4.2 50.3 1.0 O3' A:C2533 4.2 21.0 1.0 O5' A:A2483 4.2 17.7 1.0 O A:HOH6259 4.2 26.3 1.0 C5 A:G627 4.2 22.3 1.0 OP2 A:U2535 4.3 26.8 1.0 O3' A:G2482 4.4 22.0 1.0 C4 A:U626 4.4 18.9 1.0 C5 A:U626 4.4 18.8 1.0 O A:HOH3922 4.5 44.3 1.0 O5' A:C2534 4.5 23.2 1.0 N7 A:G627 4.7 22.1 1.0 C3' A:G2482 4.8 24.7 1.0 C5' A:C2534 4.9 21.6 1.0

Magnesium binding site 3 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8003 b:9.2 occ:1.00 OP1 A:A2624 1.7 22.6 1.0 OP2 A:A876 2.1 20.2 1.0 OP2 A:G877 2.1 21.6 1.0 O A:HOH4061 2.4 46.6 1.0 O A:HOH9424 2.4 2.9 1.0 O C:HOH8537 2.6 15.5 1.0 P A:A2624 3.2 25.2 1.0 P A:G877 3.3 21.7 1.0 P A:A876 3.4 22.2 1.0 O3' A:G2623 3.7 23.8 1.0 OP1 A:G877 3.7 21.1 1.0 O5' A:A876 3.9 21.0 1.0 O3' A:A876 4.0 20.5 1.0 O3' A:A875 4.0 19.7 1.0 OP2 A:A2624 4.1 24.0 1.0 C5' A:A876 4.1 19.1 1.0 O A:HOH7544 4.2 57.3 1.0 O5' A:A2624 4.2 25.5 1.0 O C:HOH8615 4.3 47.3 1.0 O A:HOH9423 4.3 8.9 1.0 O C:HOH8572 4.4 33.9 1.0 C5' A:A2624 4.4 25.0 1.0 O C:ALA193 4.4 25.1 1.0 O C:HOH8633 4.4 27.3 1.0 C3' A:A876 4.5 19.9 1.0 OD1 C:ASN195 4.5 28.9 1.0 O5' A:G877 4.5 21.5 1.0 OP1 A:A876 4.6 21.2 1.0 C4' A:A876 4.9 19.9 1.0

Magnesium binding site 4 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8004 b:34.7 occ:1.00 O6 A:G456 1.7 26.7 1.0 OP1 A:A459 1.8 18.8 1.0 O A:HOH9451 1.8 4.7 1.0 O A:HOH3171 1.9 3.2 1.0 O A:HOH8247 1.9 23.4 1.0 O A:HOH4178 2.0 18.2 1.0 C6 A:G456 2.9 27.8 1.0 P A:A459 3.2 21.6 1.0 C5 A:G456 3.8 27.4 1.0 O5' A:A459 3.9 21.2 1.0 N7 A:G456 3.9 26.9 1.0 OP2 A:A459 3.9 22.4 1.0 N1 A:G456 4.0 27.6 1.0 O A:HOH9730 4.0 31.8 1.0 C5' A:A459 4.1 22.9 1.0 O3' A:G458 4.3 20.6 1.0 O A:HOH4098 4.3 29.1 1.0 CE E:LYS85 4.3 14.2 1.0 O A:HOH6344 4.4 34.3 1.0 NZ E:LYS85 4.4 13.8 1.0 O A:HOH3908 4.4 24.5 1.0 OP1 A:A460 4.6 26.0 1.0 OP2 A:A455 4.6 17.1 1.0 N7 A:A455 4.6 30.3 1.0 O A:HOH5787 4.8 19.2 1.0 CD E:LYS85 4.9 15.4 1.0 OP1 A:A477 4.9 19.1 1.0 N6 A:A455 5.0 31.4 1.0

Magnesium binding site 5 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8005 b:27.2 occ:1.00 OP2 A:A1839 1.8 19.7 1.0 O A:HOH8264 1.8 11.9 1.0 O A:HOH8263 2.1 14.3 1.0 OP1 A:A1836 2.1 18.3 1.0 OP1 A:U1838 2.1 20.3 1.0 O A:HOH4007 2.1 5.2 1.0 P A:A1839 3.3 21.4 1.0 P A:U1838 3.4 20.4 1.0 O A:HOH5940 3.6 50.1 1.0 P A:A1836 3.6 19.0 1.0 O A:HOH5883 3.6 42.3 1.0 O A:HOH9410 3.9 12.3 1.0 O5' A:A1839 4.0 18.8 1.0 OP2 A:U1838 4.0 19.7 1.0 O A:HOH3030 4.1 20.5 1.0 OP1 A:A1839 4.2 21.7 1.0 O3' A:U1838 4.2 20.2 1.0 O5' A:U1838 4.2 16.6 1.0 O5' A:A1836 4.3 17.9 1.0 O3' A:U1835 4.4 16.7 1.0 C2' A:U1835 4.4 17.5 1.0 C3' A:U1835 4.5 17.9 1.0 C3' A:U1838 4.5 18.8 1.0 N7 A:A1839 4.5 17.1 1.0 OP2 A:A1836 4.5 19.4 1.0 C3' A:G1837 4.5 21.8 1.0 O A:HOH8410 4.5 43.0 1.0 O3' A:G1837 4.5 19.6 1.0 C8 A:A1839 4.6 17.2 1.0 C5' A:U1838 4.6 16.9 1.0 OP2 A:G1837 4.7 19.4 1.0 O A:HOH9903 4.7 25.9 1.0 O2' A:U1835 4.8 20.3 1.0

Magnesium binding site 6 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8006 b:44.0 occ:1.00 OP2 A:C822 1.7 28.5 1.0 OP2 A:U821 1.8 27.4 1.0 O A:HOH4149 2.0 31.6 1.0 OP1 A:G854 2.1 27.7 1.0 O A:HOH4013 2.1 15.2 1.0 O A:HOH3202 2.2 35.5 1.0 P A:C822 2.9 29.3 1.0 P A:U821 3.2 28.8 1.0 O3' A:U821 3.4 30.0 1.0 P A:G854 3.5 29.6 1.0 O5' A:U821 3.6 28.1 1.0 OP1 A:C822 3.6 29.3 1.0 C3' A:U821 3.7 30.0 1.0 NA A:NA8327 3.7 22.4 1.0 O A:HOH3594 3.8 27.8 1.0 OP1 A:G856 3.8 34.4 1.0 O3' A:G820 4.1 27.7 1.0 OP2 A:G854 4.1 28.9 1.0 O5' A:G854 4.1 27.1 1.0 O5' A:C822 4.2 26.4 1.0 OP1 A:U821 4.3 28.4 1.0 O A:HOH5385 4.4 22.1 1.0 C5' A:G854 4.4 25.7 1.0 O3' A:C853 4.6 27.4 1.0 C5' A:U821 4.7 31.5 1.0 C4' A:U821 4.7 30.9 1.0 C2' A:U821 4.9 29.8 1.0 OP1 A:U855 4.9 24.6 1.0 O A:HOH3123 5.0 46.6 1.0 C5 A:C822 5.0 27.2 1.0

Magnesium binding site 7 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8007 b:9.3 occ:1.00 OP2 A:U832 1.9 23.4 1.0 O A:HOH9410 2.0 12.3 1.0 O A:HOH8252 2.1 11.8 1.0 OP2 A:A1840 2.2 22.3 1.0 O A:HOH3748 2.2 17.3 1.0 OP1 A:A1839 2.3 21.7 1.0 O A:HOH9503 3.1 9.7 1.0 P A:U832 3.3 23.9 1.0 P A:A1840 3.5 23.6 1.0 O A:HOH3030 3.6 20.5 1.0 P A:A1839 3.7 21.4 1.0 OP1 A:A1840 3.9 22.2 1.0 OP1 A:U832 4.0 23.4 1.0 O A:HOH6736 4.1 39.2 1.0 O5' A:U832 4.2 23.7 1.0 O3' A:U831 4.3 23.4 1.0 OP2 A:A1839 4.3 19.7 1.0 O3' A:A1839 4.4 19.2 1.0 O3' A:U1838 4.6 20.2 1.0 C3' A:U831 4.6 24.0 1.0 O5' A:A1840 4.6 21.9 1.0 O5' A:A1839 4.6 18.8 1.0 O A:HOH8410 4.7 43.0 1.0 C5' A:U832 4.7 23.1 1.0 C3' A:A1839 4.7 18.2 1.0 OP2 A:G833 4.9 22.9 1.0 C5' A:A1839 4.9 19.0 1.0

Magnesium binding site 8 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8008 b:17.1 occ:1.00 OP1 A:U919 1.9 20.4 1.0 OP1 A:A2465 2.0 29.4 1.0 O A:HOH8411 2.1 24.5 1.0 OP1 A:C2464 2.2 25.6 1.0 O A:HOH8256 2.3 18.6 1.0 O A:HOH4025 2.3 3.9 1.0 P A:U919 3.3 22.2 1.0 P A:A2465 3.3 30.2 1.0 P A:C2464 3.6 28.1 1.0 O A:HOH3740 3.6 28.1 1.0 O5' A:A2465 3.7 28.7 1.0 C5' A:C2464 3.8 27.9 1.0 OP1 A:G2466 3.8 34.0 1.0 O A:HOH9845 3.9 47.2 1.0 O5' A:U919 3.9 20.0 1.0 O5' A:C2464 3.9 26.9 1.0 OP2 A:U919 4.0 22.2 1.0 C3' A:A2465 4.1 32.5 1.0 OP2 A:A2465 4.2 30.7 1.0 C5' A:U919 4.2 23.5 1.0 O A:HOH9937 4.4 31.1 1.0 C5' A:A2465 4.4 30.8 1.0 O3' A:G918 4.4 20.4 1.0 O A:HOH6271 4.4 35.8 1.0 O3' A:C2464 4.5 29.0 1.0 O3' A:A2463 4.5 29.0 1.0 O A:HOH3313 4.5 62.1 1.0 C2' A:A2465 4.5 32.7 1.0 C5' A:G2466 4.6 32.4 1.0 OP2 A:C2464 4.6 29.6 1.0 C4' A:C2464 4.7 27.4 1.0 C4' A:A2465 4.9 31.4 1.0 C3' A:C2464 4.9 27.1 1.0 P A:G2466 4.9 35.5 1.0

Magnesium binding site 9 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8009 b:16.4 occ:1.00 O A:HOH8258 1.7 35.4 1.0 OP1 A:A2612 1.8 17.1 1.0 O A:HOH8257 1.8 15.2 1.0 O A:HOH7808 2.2 15.1 1.0 OP1 A:G2611 2.2 19.7 1.0 O A:HOH4136 2.3 11.9 1.0 P A:A2612 3.2 18.2 1.0 P A:G2611 3.3 20.3 1.0 O A:HOH9731 3.4 15.9 1.0 O3' A:U2610 3.4 20.2 1.0 OP2 A:G2093 3.7 18.9 1.0 NA A:NA8358 3.7 79.2 1.0 OP2 A:A2612 3.8 19.6 1.0 C5' A:G2611 3.9 16.3 1.0 O3' A:G2611 4.1 17.9 1.0 O5' A:G2611 4.1 17.7 1.0 O5' A:A2612 4.1 19.0 1.0 O A:HOH9864 4.1 16.5 1.0 C3' A:G2611 4.3 14.5 1.0 OP2 A:G2094 4.4 18.3 1.0 OP1 A:G2094 4.4 16.6 1.0 OP2 A:G2611 4.6 19.1 1.0 O A:HOH9701 4.6 27.9 1.0 C4' A:G2611 4.7 15.1 1.0 C3' A:U2610 4.8 21.7 1.0 P A:G2094 4.8 19.1 1.0

Magnesium binding site 10 out of 117 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8010 b:19.2 occ:1.00 OP1 A:G836 1.6 19.5 1.0 O D:HOH8526 1.7 32.4 1.0 O A:HOH4236 1.8 29.6 1.0 O A:HOH9757 2.1 20.3 1.0 OE1 D:GLN230 2.3 21.9 1.0 OP1 A:U2615 2.6 19.8 1.0 P A:G836 3.0 21.0 1.0 CD D:GLN230 3.5 21.7 1.0 O A:HOH5429 3.8 46.2 1.0 OP2 A:G836 3.8 21.3 1.0 C5' A:G836 3.8 18.8 1.0 O5' A:G836 3.8 18.5 1.0 O A:HOH4388 3.9 22.0 1.0 O3' A:U835 4.0 18.0 1.0 C3' A:U835 4.0 17.3 1.0 P A:U2615 4.1 21.6 1.0 CG D:GLN230 4.2 23.2 1.0 CB D:GLN230 4.4 22.5 1.0 O A:HOH9603 4.4 33.1 1.0 NE2 D:GLN230 4.5 20.3 1.0 O A:HOH7205 4.6 34.3 1.0 C5' A:U835 4.6 19.9 1.0 OP2 A:U2615 4.8 22.4 1.0 CA D:GLN230 4.8 24.8 1.0 O A:HOH9939 4.8 35.6 1.0 O D:GLN230 4.9 26.0 1.0 OP2 A:G2616 4.9 18.6 1.0 O3' A:C2614 4.9 21.1 1.0 C4' A:U835 4.9 18.5 1.0

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5