Magnesium in PDB 1yit: Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit was solved by D.Tu, G.Blaha, 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)	29.99 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.583, 299.758, 573.560, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.1

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	1 atom
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	85 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 - 118;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yit). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 118 binding sites of Magnesium where determined in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:33.8 occ:1.00 OP2 0:C2533 1.8 31.0 1.0 OP2 0:C2534 2.0 35.8 1.0 OP2 0:A2483 2.3 34.0 1.0 P 0:C2533 3.3 32.1 1.0 P 0:A2483 3.4 31.6 1.0 O3' 0:G2482 3.4 34.9 1.0 P 0:C2534 3.5 35.8 1.0 O3' 0:A2532 3.8 32.9 1.0 O2' 0:A2532 4.0 32.2 1.0 O5' 0:C2533 4.0 30.8 1.0 OP2 0:U2484 4.1 31.4 1.0 O3' 0:C2533 4.2 33.5 1.0 OP1 0:A2483 4.3 33.3 1.0 OP1 0:C2534 4.3 35.5 1.0 OP1 0:C2533 4.3 33.9 1.0 C3' 0:C2533 4.4 31.1 1.0 O2' 0:G2482 4.4 36.2 1.0 O5' 0:C2534 4.4 35.6 1.0 O5' 0:A2483 4.6 32.6 1.0 C3' 0:G2482 4.7 34.9 1.0 C5' 0:A2483 4.8 30.5 1.0 C3' 0:A2532 4.8 33.7 1.0 C5' 0:C2533 4.9 29.0 1.0 C2' 0:A2532 4.9 33.4 1.0

Magnesium binding site 2 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:28.9 occ:1.00 O6 0:G627 2.0 30.2 1.0 OP1 0:A2483 2.0 33.3 1.0 OP1 0:C2534 2.2 35.5 1.0 C6 0:G627 3.2 29.5 1.0 P 0:A2483 3.3 31.6 1.0 P 0:C2534 3.5 35.8 1.0 OP2 0:A2483 3.8 34.0 1.0 N1 0:G627 4.0 28.9 1.0 O4 0:U626 4.0 36.4 1.0 OP2 0:C2534 4.1 35.8 1.0 O2' 0:U625 4.1 30.6 1.0 C5 0:U626 4.3 33.4 1.0 O5' 0:A2483 4.3 32.6 1.0 O3' 0:C2533 4.3 33.5 1.0 O3' 0:G2482 4.3 34.9 1.0 C5 0:G627 4.4 29.2 1.0 OP2 0:U2535 4.4 33.8 1.0 C4 0:U626 4.4 34.1 1.0 O5' 0:C2534 4.7 35.6 1.0 N7 0:G627 4.8 27.4 1.0 C3' 0:G2482 4.8 34.9 1.0

Magnesium binding site 3 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:31.7 occ:1.00 OP1 0:A2624 1.9 29.4 1.0 OP2 0:G877 2.1 26.8 1.0 OP2 0:A876 2.2 28.6 1.0 P 0:A2624 3.3 31.0 1.0 P 0:G877 3.4 29.3 1.0 P 0:A876 3.5 30.2 1.0 O3' 0:G2623 3.9 31.4 1.0 OP1 0:G877 3.9 29.8 1.0 O5' 0:A876 4.1 29.4 1.0 O3' 0:A875 4.1 28.2 1.0 O3' 0:A876 4.2 28.5 1.0 OP2 0:A2624 4.3 33.3 1.0 O A:ALA193 4.3 30.6 1.0 O5' 0:A2624 4.3 34.9 1.0 OD1 A:ASN195 4.4 29.6 1.0 C5' 0:A876 4.4 29.2 1.0 C5' 0:A2624 4.5 33.5 1.0 O5' 0:G877 4.5 28.3 1.0 C3' 0:A876 4.7 30.1 1.0 OP1 0:A876 4.8 28.9 1.0

Magnesium binding site 4 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:39.6 occ:1.00 OP1 0:A459 1.9 29.5 1.0 O6 0:G456 2.0 37.8 1.0 C6 0:G456 3.1 37.3 1.0 P 0:A459 3.2 30.9 1.0 C5 0:G456 3.8 36.1 1.0 N7 0:G456 3.8 34.5 1.0 OP2 0:A459 3.9 33.6 1.0 O5' 0:A459 3.9 30.8 1.0 CE C:LYS85 4.1 25.4 1.0 C5' 0:A459 4.2 30.9 1.0 N1 0:G456 4.3 38.3 1.0 OP2 0:A455 4.3 27.0 1.0 O3' 0:G458 4.3 29.8 1.0 NZ C:LYS85 4.3 25.4 1.0 N7 0:A455 4.5 37.8 1.0 OP1 0:A460 4.6 32.5 1.0 CD C:LYS85 4.6 26.7 1.0 OP1 0:A477 4.6 30.3 1.0

Magnesium binding site 5 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:31.7 occ:1.00 OP2 0:A1839 1.9 29.9 1.0 OP1 0:U1838 2.1 26.9 1.0 OP1 0:A1836 2.2 29.5 1.0 P 0:A1839 3.4 31.0 1.0 P 0:U1838 3.5 29.5 1.0 P 0:A1836 3.7 28.6 1.0 O5' 0:A1839 4.0 30.4 1.0 O3' 0:U1838 4.2 29.3 1.0 O5' 0:U1838 4.2 25.4 1.0 OP1 0:A1839 4.3 29.7 1.0 OP2 0:U1838 4.4 28.3 1.0 C3' 0:U1838 4.4 27.7 1.0 O5' 0:A1836 4.4 28.4 1.0 C2' 0:U1835 4.4 29.5 1.0 N7 0:A1839 4.4 29.2 1.0 C5' 0:U1838 4.5 24.8 1.0 C8 0:A1839 4.5 29.9 1.0 OP2 0:A1836 4.5 30.4 1.0 O3' 0:U1835 4.5 26.6 1.0 C3' 0:G1837 4.5 30.1 1.0 O3' 0:G1837 4.6 29.1 1.0 C3' 0:U1835 4.6 28.1 1.0 OP2 0:G1837 4.8 30.4 1.0 O2' 0:U1835 4.9 28.8 1.0

Magnesium binding site 6 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:32.6 occ:1.00 OP2 0:C822 1.8 39.6 1.0 OP1 0:G854 2.0 32.0 1.0 OP2 0:U821 2.0 38.4 1.0 P 0:C822 3.1 41.4 1.0 P 0:G854 3.3 32.4 1.0 P 0:U821 3.4 38.2 1.0 O5' 0:U821 3.7 39.5 1.0 O3' 0:U821 3.8 42.0 1.0 OP1 0:G856 3.8 40.5 1.0 NA 0:NA8527 3.9 51.7 1.0 OP1 0:C822 3.9 41.1 1.0 C3' 0:U821 3.9 39.1 1.0 O5' 0:G854 4.0 31.0 1.0 OP2 0:G854 4.0 30.4 1.0 O3' 0:G820 4.2 39.4 1.0 O5' 0:C822 4.3 38.9 1.0 OP1 0:U855 4.3 36.1 1.0 C5' 0:G854 4.3 32.1 1.0 O3' 0:C853 4.4 30.2 1.0 OP1 0:U821 4.5 37.6 1.0 C5' 0:U821 4.9 40.0 1.0 C4' 0:U821 4.9 39.7 1.0 C5 0:C822 4.9 35.5 1.0

Magnesium binding site 7 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:18.6 occ:1.00 OP2 0:U832 2.0 36.9 1.0 OP2 0:A1840 2.1 28.2 1.0 OP1 0:A1839 2.1 29.7 1.0 P 0:A1840 3.1 27.8 1.0 OP1 0:A1840 3.3 27.0 1.0 P 0:U832 3.3 34.4 1.0 P 0:A1839 3.5 31.0 1.0 O3' 0:A1839 4.0 25.8 1.0 OP1 0:U832 4.0 33.9 1.0 O5' 0:U832 4.0 35.9 1.0 OP2 0:G833 4.3 33.8 1.0 OP2 0:A1839 4.3 29.9 1.0 O5' 0:A1840 4.3 26.6 1.0 O5' 0:A1839 4.4 30.4 1.0 O3' 0:U1838 4.4 29.3 1.0 O3' 0:U831 4.5 31.6 1.0 C5' 0:U832 4.5 35.4 1.0 C3' 0:A1839 4.5 27.3 1.0 C5' 0:A1839 4.6 28.7 1.0 C3' 0:U831 5.0 31.1 1.0

Magnesium binding site 8 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:35.7 occ:1.00 OP1 0:U919 1.8 30.2 1.0 OP1 0:A2465 2.0 38.5 1.0 OP1 0:C2464 2.3 32.6 1.0 P 0:U919 3.1 30.0 1.0 P 0:A2465 3.3 36.9 1.0 O5' 0:A2465 3.6 35.2 1.0 OP2 0:U919 3.7 29.2 1.0 P 0:C2464 3.7 34.2 1.0 O5' 0:U919 3.7 27.5 1.0 O5' 0:C2464 4.1 34.5 1.0 C5' 0:C2464 4.1 36.8 1.0 OP2 0:A2465 4.1 37.7 1.0 OP1 0:G2466 4.2 34.9 1.0 C5' 0:U919 4.2 29.8 1.0 C3' 0:A2465 4.3 34.6 1.0 O3' 0:G918 4.3 29.8 1.0 C5' 0:A2465 4.4 32.9 1.0 O3' 0:C2464 4.4 36.8 1.0 OP2 0:C2464 4.5 35.0 1.0 C2' 0:A2465 4.6 34.9 1.0 O3' 0:A2463 4.7 35.3 1.0 C3' 0:C2464 4.9 36.1 1.0 C5' 0:G2466 5.0 37.2 1.0 C4' 0:A2465 5.0 32.7 1.0 C4' 0:C2464 5.0 37.5 1.0

Magnesium binding site 9 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:28.5 occ:1.00 OP1 0:A2612 1.9 25.0 1.0 OP1 0:G2611 2.0 31.5 1.0 P 0:G2611 3.2 31.5 1.0 O3' 0:U2610 3.3 31.2 1.0 P 0:A2612 3.4 28.3 1.0 OP2 0:G2093 3.9 27.5 1.0 C5' 0:G2611 4.0 28.7 1.0 O5' 0:G2611 4.0 30.4 1.0 OP2 0:A2612 4.1 31.6 1.0 OP1 0:G2094 4.2 23.7 1.0 OP2 0:G2094 4.2 25.1 1.0 O3' 0:G2611 4.2 28.6 1.0 O5' 0:A2612 4.3 30.9 1.0 OP2 0:G2611 4.4 31.8 1.0 C3' 0:G2611 4.5 27.0 1.0 C3' 0:U2610 4.6 31.1 1.0 P 0:G2094 4.6 27.2 1.0 C4' 0:G2611 4.8 26.0 1.0 C4' 0:U2610 4.9 30.6 1.0 O2' 0:U2610 4.9 30.2 1.0

Magnesium binding site 10 out of 118 in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:34.2 occ:1.00 OP1 0:G836 1.9 27.9 1.0 OE1 B:GLN230 2.0 31.3 1.0 OP1 0:U2615 2.2 31.5 1.0 CD B:GLN230 3.2 29.7 1.0 P 0:G836 3.3 31.1 1.0 P 0:U2615 3.7 31.9 1.0 CG B:GLN230 3.9 30.2 1.0 C5' 0:G836 4.0 27.3 1.0 CB B:GLN230 4.0 30.6 1.0 O5' 0:G836 4.1 29.6 1.0 OP2 0:G836 4.2 31.0 1.0 NE2 B:GLN230 4.2 29.4 1.0 O3' 0:U835 4.3 29.5 1.0 C3' 0:U835 4.3 29.0 1.0 OP2 0:U2615 4.4 29.7 1.0 O3' 0:C2614 4.4 30.5 1.0 CA B:GLN230 4.4 30.1 1.0 O B:GLN230 4.6 30.6 1.0 OP2 0:G2616 4.6 26.7 1.0 O5' 0:U2615 4.7 29.8 1.0 C5' 0:U835 4.7 30.4 1.0 N2 0:G2616 4.9 31.4 1.0 C5' 0:U2615 5.0 26.6 1.0

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005