Magnesium in PDB 1yjn: Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yjn 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)	29.97 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.512, 300.125, 573.849, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.8

The structure of Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	23 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 - 116;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yjn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 116 binding sites of Magnesium where determined in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yjn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:35.1 occ:1.00 O 0:HOH9177 1.9 34.8 1.0 OP2 0:C2533 2.0 33.2 1.0 OP2 0:C2534 2.0 39.4 1.0 O 0:HOH7761 2.0 22.6 1.0 O 0:HOH3626 2.2 22.2 1.0 OP2 0:A2483 2.2 37.5 1.0 O3' 0:G2482 3.2 38.8 1.0 P 0:A2483 3.2 37.1 1.0 P 0:C2533 3.4 36.1 1.0 P 0:C2534 3.4 39.5 1.0 O 0:HOH4345 3.9 21.3 1.0 O3' 0:A2532 4.0 36.3 1.0 OP1 0:A2483 4.1 38.1 1.0 O2' 0:A2532 4.1 37.9 1.0 OP2 0:U2484 4.1 37.6 1.0 O3' 0:C2533 4.2 36.8 1.0 O2' 0:G2482 4.2 39.3 1.0 O 0:HOH9644 4.2 52.1 1.0 OP1 0:C2534 4.3 37.6 1.0 O5' 0:C2533 4.3 34.7 1.0 O5' 0:C2534 4.3 38.0 1.0 C3' 0:C2533 4.4 34.2 1.0 OP1 0:C2533 4.4 38.8 1.0 O5' 0:A2483 4.5 37.2 1.0 C3' 0:G2482 4.5 38.4 1.0 O 0:HOH7469 4.6 34.2 1.0 C5' 0:A2483 4.8 36.9 1.0 C2' 0:G2482 4.8 38.1 1.0 C5 0:C2534 4.8 45.6 1.0

Magnesium binding site 2 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:41.9 occ:1.00 O 0:HOH7739 1.8 41.5 1.0 O 0:HOH7740 1.9 33.3 1.0 OP1 0:A2483 2.0 38.1 1.0 O6 0:G627 2.0 35.3 1.0 OP1 0:C2534 2.3 37.6 1.0 O 0:HOH4345 2.4 21.3 1.0 C6 0:G627 3.2 33.7 1.0 P 0:A2483 3.3 37.1 1.0 P 0:C2534 3.6 39.5 1.0 O 0:HOH9264 3.6 22.9 1.0 O4 0:U626 3.9 39.4 1.0 OP2 0:A2483 3.9 37.5 1.0 N1 0:G627 3.9 34.0 1.0 O2' 0:U625 4.0 30.3 1.0 O 0:HOH5888 4.1 46.6 1.0 OP2 0:C2534 4.1 39.4 1.0 O5' 0:A2483 4.2 37.2 1.0 OP2 0:U2535 4.3 38.5 1.0 C5 0:G627 4.3 33.0 1.0 O3' 0:G2482 4.4 38.8 1.0 O3' 0:C2533 4.4 36.8 1.0 C5 0:U626 4.5 36.7 1.0 O 0:HOH3537 4.5 52.6 1.0 C4 0:U626 4.5 37.8 1.0 O 0:HOH7099 4.6 53.1 1.0 C3' 0:G2482 4.7 38.4 1.0 O5' 0:C2534 4.7 38.0 1.0 N7 0:G627 4.7 33.7 1.0 O 0:HOH3132 4.8 18.1 1.0 O2 0:C2071 5.0 35.9 1.0

Magnesium binding site 3 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:33.7 occ:1.00 O 0:HOH9020 2.0 32.3 1.0 OP2 0:G877 2.0 29.0 1.0 O 0:HOH3679 2.0 35.8 1.0 OP1 0:A2624 2.0 33.1 1.0 OP2 0:A876 2.2 35.5 1.0 O 0:HOH9832 2.4 21.0 1.0 P 0:G877 3.2 31.2 1.0 P 0:A2624 3.4 33.9 1.0 P 0:A876 3.5 36.6 1.0 OP1 0:G877 3.8 29.3 1.0 O3' 0:G2623 3.8 33.8 1.0 O3' 0:A875 4.0 33.7 1.0 O3' 0:A876 4.1 31.6 1.0 O5' 0:A876 4.1 36.3 1.0 O A:HOH8900 4.3 35.2 1.0 OD1 A:ASN195 4.3 32.5 1.0 OP2 0:A2624 4.3 35.4 1.0 C5' 0:A876 4.3 34.8 1.0 O A:ALA193 4.4 31.5 1.0 O5' 0:G877 4.4 28.3 1.0 O5' 0:A2624 4.4 35.5 1.0 O A:HOH8918 4.4 46.3 1.0 C3' 0:A876 4.5 33.1 1.0 C5' 0:A2624 4.6 37.1 1.0 O 0:HOH9019 4.6 45.2 1.0 OP1 0:A876 4.7 36.1 1.0 O 0:HOH4499 4.8 45.8 1.0 O A:HOH8838 4.9 58.0 1.0 CG A:ASN195 5.0 31.6 1.0

Magnesium binding site 4 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:43.4 occ:1.00 OP1 0:A459 1.7 32.3 1.0 O6 0:G456 1.8 35.9 1.0 O 0:HOH9048 1.8 24.2 1.0 O 0:HOH9785 2.1 17.7 1.0 O 0:HOH7746 2.2 33.4 1.0 O 0:HOH3798 2.5 34.1 1.0 C6 0:G456 2.9 38.0 1.0 P 0:A459 3.1 35.3 1.0 C5 0:G456 3.7 37.5 1.0 OP2 0:A459 3.8 37.1 1.0 O5' 0:A459 3.8 34.4 1.0 N7 0:G456 3.8 36.2 1.0 C5' 0:A459 4.0 36.1 1.0 N1 0:G456 4.1 38.6 1.0 O 0:HOH9337 4.2 27.6 1.0 O3' 0:G458 4.2 32.8 1.0 CE C:LYS85 4.4 22.6 1.0 O 0:HOH3716 4.4 32.5 1.0 O 0:HOH3522 4.4 53.3 1.0 OP2 0:A455 4.5 32.4 1.0 O 0:HOH5973 4.5 68.0 1.0 OP1 0:A460 4.6 37.2 1.0 O 0:HOH5414 4.6 39.4 1.0 N7 0:A455 4.6 40.7 1.0 NZ C:LYS85 4.7 19.8 1.0 OP1 0:A477 4.8 30.6 1.0 CD C:LYS85 4.8 24.6 1.0 OP2 0:A460 4.9 38.2 1.0

Magnesium binding site 5 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:35.8 occ:1.00 O 0:HOH7763 1.8 33.3 1.0 OP1 0:U1838 1.9 33.8 1.0 OP2 0:A1839 2.0 35.7 1.0 O 0:HOH7762 2.0 25.5 1.0 OP1 0:A1836 2.2 32.3 1.0 O 0:HOH3622 2.4 23.1 1.0 P 0:U1838 3.4 33.4 1.0 P 0:A1839 3.4 36.6 1.0 P 0:A1836 3.6 32.3 1.0 O 0:HOH9006 4.0 31.3 1.0 O 0:HOH5513 4.0 35.1 1.0 O 0:HOH5571 4.0 66.5 1.0 O5' 0:U1838 4.1 32.1 1.0 O3' 0:U1838 4.2 34.9 1.0 C3' 0:G1837 4.2 35.1 1.0 OP1 0:A1839 4.3 36.5 1.0 OP2 0:U1838 4.3 34.4 1.0 O5' 0:A1836 4.3 31.6 1.0 OP2 0:A1836 4.3 34.5 1.0 O 0:HOH7839 4.3 36.4 1.0 O3' 0:G1837 4.3 34.2 1.0 C5' 0:U1838 4.3 30.9 1.0 O5' 0:A1839 4.4 34.8 1.0 OP2 0:G1837 4.4 35.1 1.0 C3' 0:U1838 4.4 32.0 1.0 O3' 0:U1835 4.6 33.0 1.0 O 0:HOH9516 4.6 35.4 1.0 C2' 0:U1835 4.7 35.7 1.0 N7 0:A1839 4.7 34.9 1.0 C3' 0:U1835 4.8 34.4 1.0 C8 0:A1839 4.9 35.8 1.0 C4' 0:U1838 5.0 30.9 1.0

Magnesium binding site 6 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:37.1 occ:1.00 O 0:HOH3628 2.0 31.3 1.0 OP2 0:C822 2.0 45.1 1.0 OP1 0:G854 2.1 38.2 1.0 O 0:HOH3768 2.1 30.5 1.0 OP2 0:U821 2.2 44.0 1.0 O 0:HOH9816 2.4 43.0 1.0 P 0:G854 3.3 39.2 1.0 P 0:C822 3.4 46.2 1.0 P 0:U821 3.5 43.4 1.0 OP1 0:G856 3.7 46.2 1.0 O5' 0:G854 3.8 36.5 1.0 O5' 0:U821 3.9 45.1 1.0 O 0:HOH3211 4.0 41.0 1.0 NA 0:NA8527 4.0 41.8 1.0 OP1 0:U855 4.0 37.9 1.0 C5' 0:G854 4.0 35.0 1.0 OP2 0:G854 4.1 38.6 1.0 O 0:HOH5014 4.1 47.8 1.0 O3' 0:U821 4.2 49.0 1.0 C3' 0:U821 4.2 48.2 1.0 OP1 0:C822 4.2 46.5 1.0 O3' 0:G820 4.3 41.4 1.0 O5' 0:C822 4.5 44.6 1.0 O3' 0:C853 4.5 36.9 1.0 OP1 0:U821 4.6 41.9 1.0 C5 0:C822 4.8 40.6 1.0 O 0:HOH9311 4.9 72.6 1.0

Magnesium binding site 7 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:34.3 occ:1.00 OP2 0:U832 2.0 40.2 1.0 O 0:HOH9006 2.0 31.3 1.0 O 0:HOH3366 2.0 27.6 1.0 OP1 0:A1839 2.0 36.5 1.0 O 0:HOH7751 2.1 17.7 1.0 OP2 0:A1840 2.2 35.3 1.0 P 0:U832 3.4 38.9 1.0 O 0:HOH9101 3.4 45.7 1.0 P 0:A1840 3.4 35.5 1.0 P 0:A1839 3.5 36.6 1.0 O 0:HOH6355 3.8 52.1 1.0 OP1 0:A1840 3.8 36.7 1.0 O 0:HOH9640 4.0 55.1 1.0 OP1 0:U832 4.1 38.7 1.0 O5' 0:U832 4.1 39.1 1.0 OP2 0:A1839 4.2 35.7 1.0 O3' 0:A1839 4.3 34.3 1.0 O3' 0:U1838 4.3 34.9 1.0 O3' 0:U831 4.4 36.0 1.0 O5' 0:A1839 4.4 34.8 1.0 O 0:HOH7839 4.5 36.4 1.0 O5' 0:A1840 4.6 33.2 1.0 OP2 0:G833 4.6 37.3 1.0 C3' 0:A1839 4.6 34.4 1.0 C5' 0:A1839 4.7 34.5 1.0 C5' 0:U832 4.8 40.1 1.0 C3' 0:U831 4.9 35.4 1.0 O 0:HOH7762 5.0 25.5 1.0

Magnesium binding site 8 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:41.0 occ:1.00 O 0:HOH7840 1.8 31.2 1.0 OP1 0:U919 1.9 35.0 1.0 OP1 0:A2465 1.9 45.8 1.0 O 0:HOH7755 2.1 27.9 1.0 O 0:HOH3641 2.2 20.4 1.0 OP1 0:C2464 2.3 40.5 1.0 P 0:U919 3.1 35.8 1.0 P 0:A2465 3.1 45.8 1.0 O5' 0:A2465 3.5 42.6 1.0 P 0:C2464 3.6 40.9 1.0 OP2 0:U919 3.7 35.7 1.0 O5' 0:U919 3.7 33.9 1.0 O 0:HOH3356 3.9 38.8 1.0 OP2 0:A2465 4.0 46.8 1.0 C5' 0:C2464 4.0 41.9 1.0 O5' 0:C2464 4.0 40.7 1.0 O 0:HOH9550 4.1 27.1 1.0 O 0:HOH9454 4.2 35.7 1.0 C5' 0:U919 4.2 36.1 1.0 OP1 0:G2466 4.3 43.9 1.0 C3' 0:A2465 4.3 42.3 1.0 O3' 0:G918 4.3 35.4 1.0 O3' 0:C2464 4.4 44.1 1.0 O 0:HOH5898 4.4 44.8 1.0 C5' 0:A2465 4.4 41.4 1.0 OP2 0:C2464 4.5 41.5 1.0 C2' 0:A2465 4.6 42.7 1.0 O3' 0:A2463 4.7 41.5 1.0 C3' 0:C2464 4.8 43.1 1.0 O 0:HOH9932 4.9 47.4 1.0 C4' 0:C2464 4.9 43.1 1.0 C5' 0:G2466 5.0 43.9 1.0 C4' 0:A2465 5.0 41.5 1.0

Magnesium binding site 9 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:38.0 occ:1.00 O 0:HOH7757 1.9 27.8 1.0 O 0:HOH3752 1.9 20.6 1.0 OP1 0:A2612 1.9 30.5 1.0 O 0:HOH7423 2.0 21.4 1.0 OP1 0:G2611 2.1 35.1 1.0 O 0:HOH7756 2.1 18.0 1.0 P 0:G2611 3.2 35.9 1.0 O3' 0:U2610 3.3 34.8 1.0 P 0:A2612 3.4 33.0 1.0 OP2 0:G2093 3.7 33.9 1.0 O 0:HOH9338 3.8 32.3 1.0 C5' 0:G2611 3.9 33.3 1.0 O5' 0:G2611 4.0 33.7 1.0 O B:HOH8826 4.1 22.0 1.0 OP2 0:G2094 4.1 32.4 1.0 OP2 0:A2612 4.2 34.2 1.0 O3' 0:G2611 4.2 31.2 1.0 NA 0:NA8558 4.2 70.8 1.0 O5' 0:A2612 4.3 33.8 1.0 OP1 0:G2094 4.3 30.3 1.0 OP2 0:G2611 4.5 35.3 1.0 C3' 0:G2611 4.5 31.0 1.0 C3' 0:U2610 4.6 36.0 1.0 P 0:G2094 4.6 35.1 1.0 C4' 0:G2611 4.7 32.2 1.0 O2' 0:U2610 4.8 34.6 1.0 C4' 0:U2610 4.9 37.2 1.0 O 0:HOH7773 5.0 40.5 1.0

Magnesium binding site 10 out of 116 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:41.7 occ:1.00 O B:HOH8825 1.8 41.5 1.0 O 0:HOH3857 1.8 36.8 1.0 OP1 0:G836 2.0 29.6 1.0 OP1 0:U2615 2.0 33.4 1.0 OE1 B:GLN230 2.2 36.2 1.0 O 0:HOH9367 2.3 52.9 1.0 CD B:GLN230 3.3 35.1 1.0 O 0:HOH5059 3.4 41.1 1.0 P 0:G836 3.4 31.1 1.0 P 0:U2615 3.5 34.1 1.0 O B:HOH8941 3.7 72.6 1.0 CG B:GLN230 3.9 35.1 1.0 CB B:GLN230 4.1 35.2 1.0 C5' 0:G836 4.2 29.8 1.0 OP2 0:U2615 4.2 34.8 1.0 OP2 0:G836 4.2 31.5 1.0 O5' 0:G836 4.3 30.1 1.0 O3' 0:C2614 4.3 33.3 1.0 C3' 0:U835 4.3 30.9 1.0 O 0:HOH9206 4.3 23.4 1.0 O3' 0:U835 4.4 30.1 1.0 O5' 0:U2615 4.4 33.7 1.0 NE2 B:GLN230 4.4 32.6 1.0 OP2 0:G2616 4.5 34.4 1.0 O 0:HOH4006 4.5 28.8 1.0 CA B:GLN230 4.6 37.0 1.0 N2 0:G2616 4.7 37.0 1.0 C5' 0:U835 4.8 34.2 1.0 C5' 0:U2615 4.8 31.6 1.0 O B:GLN230 4.8 39.7 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