Magnesium in PDB 3cc4: Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4 was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.85 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.780, 299.084, 573.837, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.4

The structure of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 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 - 93;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit (pdb code 3cc4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 93 binding sites of Magnesium where determined in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit, PDB code: 3cc4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8051 b:82.0 occ:1.00 OP2 0:G1873 2.6 34.0 1.0 O A:HOH9026 2.7 84.8 1.0 NH2 A:ARG120 2.7 38.9 1.0 N A:LEU27 2.8 61.5 1.0 OP1 0:G1873 3.0 38.7 1.0 OD2 A:ASP26 3.0 69.4 1.0 P 0:G1873 3.1 36.8 1.0 O A:LEU27 3.1 65.2 1.0 C A:ASP26 3.2 61.8 1.0 C A:LEU27 3.3 63.8 1.0 CA A:LEU27 3.4 62.2 1.0 CA A:ASP26 3.5 61.6 1.0 CG A:ASP26 3.5 68.0 1.0 CZ A:ARG120 3.5 38.5 1.0 NH1 A:ARG120 3.6 38.0 1.0 O3' 0:C1872 3.8 34.9 1.0 CB A:LEU27 3.9 59.2 1.0 O A:ASP26 3.9 62.9 1.0 O 0:HOH5243 4.1 65.7 1.0 CB A:ASP26 4.1 64.5 1.0 OD1 A:ASP26 4.2 69.3 1.0 N A:GLU28 4.2 66.0 1.0 SR A:SR8930 4.3 0.8 1.0 CG A:GLU28 4.4 70.6 1.0 O 0:HOH7973 4.4 62.1 1.0 O A:HOH9002 4.5 54.9 1.0 CG A:LEU27 4.5 56.8 1.0 O5' 0:G1873 4.6 37.0 1.0 NE A:ARG120 4.8 36.7 1.0 N A:ASP26 4.8 59.7 1.0 O A:ALA25 4.9 56.9 1.0 CA A:GLU28 5.0 68.0 1.0

Magnesium binding site 2 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg8042 b:50.3 occ:1.00 O 0:HOH3800 2.5 44.6 1.0 O B:HOH9125 2.5 59.1 1.0 O 0:HOH3838 2.5 47.5 1.0 O 0:HOH7791 2.7 66.6 1.0 O 0:HOH6491 2.7 41.6 1.0 O B:HOH9127 3.5 65.3 1.0 OXT B:GLY337 3.7 54.3 1.0 C B:GLY337 4.1 51.9 1.0 O B:GLY337 4.2 51.6 1.0 OP1 0:C2720 4.3 42.8 1.0 OP2 0:U2721 4.4 41.3 1.0 OE2 B:GLU333 4.6 52.3 1.0 O 0:HOH3742 4.6 59.2 1.0 OE1 B:GLU333 4.7 51.4 1.0 OP1 0:U2721 4.8 41.1 1.0 CG2 U:THR17 4.8 48.8 1.0 O B:HOH9009 4.9 46.9 1.0 O B:HOH9028 4.9 42.4 1.0 CD B:GLU333 4.9 50.6 1.0

Magnesium binding site 3 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg8054 b:39.6 occ:1.00 O 0:HOH7960 2.4 67.8 1.0 O 0:HOH4296 2.5 53.4 1.0 O 0:HOH6116 2.6 40.7 1.0 O K:HOH2121 2.6 22.3 1.0 OD1 K:ASN42 2.7 35.1 1.0 O 0:HOH3460 2.7 38.3 1.0 O 0:HOH4744 3.3 43.9 1.0 CG K:ASN42 3.9 34.8 1.0 O 0:HOH5602 4.2 55.0 1.0 O 0:HOH7836 4.3 24.9 1.0 OP1 0:A2583 4.3 34.0 1.0 OP1 0:U2546 4.6 31.2 1.0 OP1 0:U1749 4.7 33.6 1.0 CE K:LYS41 4.7 43.8 1.0 ND2 K:ASN42 4.7 31.9 1.0 O 0:HOH7847 4.8 61.5 1.0 CA K:ASN42 4.8 33.9 1.0 CB K:ASN42 4.9 34.0 1.0 N K:ASN42 5.0 34.3 1.0

Magnesium binding site 4 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg8057 b:58.0 occ:1.00 O T:SER114 2.6 93.3 1.0 O T:ASP117 2.8 0.5 1.0 O T:LEU112 2.9 74.6 1.0 O T:HOH2868 2.9 57.0 1.0 OE1 T:GLN37 2.9 60.6 1.0 O T:ARG111 3.2 69.0 1.0 C T:LEU112 3.5 75.2 1.0 C T:SER114 3.8 93.3 1.0 O T:TYR35 3.8 58.3 1.0 CD T:GLN37 3.8 60.2 1.0 C T:ASP117 3.9 0.1 1.0 CA T:LEU112 3.9 73.0 1.0 CG T:GLN37 3.9 59.5 1.0 N T:SER114 4.1 86.6 1.0 CA T:SER118 4.1 0.7 1.0 C T:ARG111 4.2 68.8 1.0 N T:GLU113 4.3 78.5 1.0 N T:SER118 4.4 0.5 1.0 OG T:SER114 4.5 92.7 1.0 CA T:SER114 4.5 90.7 1.0 N T:LEU112 4.5 70.4 1.0 C T:GLU113 4.5 83.8 1.0 N T:GLU115 4.8 97.3 1.0 CA T:GLU113 4.8 82.0 1.0 CB T:SER118 4.9 0.8 1.0 CA T:GLU115 4.9 0.5 1.0

Magnesium binding site 5 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg8086 b:39.2 occ:1.00 O Y:HIS133 2.5 32.5 1.0 O Y:HOH8877 2.6 33.8 1.0 O Y:VAL139 2.6 31.6 1.0 O Y:HOH8912 2.7 55.1 1.0 O Y:LYS136 2.7 33.2 1.0 O Y:HOH8856 2.9 47.0 1.0 CA Y:LYS137 3.4 30.6 1.0 O Y:LYS137 3.4 31.1 1.0 C Y:LYS136 3.6 30.6 1.0 C Y:LYS137 3.6 30.4 1.0 C Y:HIS133 3.6 31.5 1.0 C Y:VAL139 3.7 32.2 1.0 N Y:LYS137 3.9 29.5 1.0 N Y:VAL139 4.3 29.8 1.0 CA Y:HIS133 4.4 31.4 1.0 CA Y:VAL139 4.5 31.6 1.0 O Y:HOH8833 4.6 24.4 1.0 N Y:ARG138 4.6 31.2 1.0 N Y:SER140 4.6 32.4 1.0 CB Y:LYS137 4.6 32.6 1.0 N Y:HIS134 4.7 30.8 1.0 CB Y:HIS133 4.7 31.9 1.0 CA Y:SER140 4.7 33.5 1.0 CA Y:LYS136 4.9 30.0 1.0 CG Y:LYS137 4.9 35.1 1.0 N Y:LYS136 4.9 30.8 1.0 CB Y:VAL139 4.9 32.3 1.0 CA Y:HIS134 4.9 31.6 1.0

Magnesium binding site 6 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:25.8 occ:1.00 OP2 0:C2534 2.2 34.1 1.0 O 0:HOH9191 2.4 24.3 1.0 O 0:HOH7849 2.4 57.2 1.0 O 0:HOH3658 2.5 23.2 1.0 OP2 0:A2483 2.6 30.5 1.0 OP2 0:C2533 2.7 30.4 1.0 O3' 0:G2482 2.8 32.2 1.0 P 0:A2483 3.2 30.3 1.0 O 0:HOH9666 3.4 34.3 1.0 O2' 0:G2482 3.4 31.7 1.0 P 0:C2534 3.6 36.7 1.0 C3' 0:G2482 4.0 31.8 1.0 OP1 0:A2483 4.1 30.9 1.0 C2' 0:G2482 4.1 30.8 1.0 P 0:C2533 4.1 35.8 1.0 O2' 0:A2532 4.3 34.0 1.0 OP1 0:C2534 4.3 35.6 1.0 O5' 0:C2534 4.3 34.3 1.0 C1' 0:G2482 4.4 32.0 1.0 O 0:HOH6442 4.5 70.1 1.0 O5' 0:A2483 4.5 30.0 1.0 OP2 0:U2484 4.5 31.5 1.0 O3' 0:A2532 4.6 33.7 1.0 O 0:HOH4380 4.6 34.1 1.0 O3' 0:C2533 4.7 33.1 1.0 C5' 0:A2483 4.7 27.7 1.0 C5 0:C2534 4.7 40.1 1.0 N3 0:G2482 4.8 31.6 1.0 C3' 0:C2533 4.9 30.2 1.0 OP2 0:U2535 5.0 34.7 1.0 C6 0:C2534 5.0 39.8 1.0 O5' 0:C2533 5.0 32.6 1.0

Magnesium binding site 7 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:22.8 occ:1.00 OP1 0:A2483 2.2 30.9 1.0 O6 0:G627 2.2 33.1 1.0 OP1 0:C2534 2.3 35.6 1.0 O 0:HOH7827 2.4 42.8 1.0 O 0:HOH7828 2.5 25.2 1.0 O 0:HOH4380 2.5 34.1 1.0 P 0:A2483 3.2 30.3 1.0 C6 0:G627 3.4 31.7 1.0 O 0:HOH7182 3.4 43.2 1.0 O 0:HOH9277 3.5 31.4 1.0 OP2 0:A2483 3.5 30.5 1.0 P 0:C2534 3.6 36.7 1.0 O4 0:U626 3.8 36.9 1.0 N1 0:G627 4.0 31.7 1.0 O5' 0:A2483 4.1 30.0 1.0 OP2 0:C2534 4.2 34.1 1.0 C5 0:U626 4.2 34.1 1.0 O2' 0:U625 4.2 27.0 1.0 C4 0:U626 4.3 35.4 1.0 O3' 0:C2533 4.4 33.1 1.0 O 0:HOH3570 4.4 44.3 1.0 O 0:HOH5939 4.4 42.4 1.0 O3' 0:G2482 4.4 32.2 1.0 C5 0:G627 4.5 30.7 1.0 OP2 0:U2535 4.7 34.7 1.0 O5' 0:C2534 4.8 34.3 1.0 C3' 0:G2482 4.9 31.8 1.0 N7 0:G627 4.9 30.1 1.0

Magnesium binding site 8 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:30.9 occ:1.00 OP2 0:G877 2.3 25.7 1.0 OP1 0:A2624 2.3 26.2 1.0 O A:HOH8980 2.4 24.3 1.0 O 0:HOH3707 2.4 38.0 1.0 OP2 0:A876 2.4 26.0 1.0 O A:HOH8998 2.6 41.0 1.0 P 0:G877 3.5 28.4 1.0 P 0:A2624 3.7 27.1 1.0 OD1 A:ASN195 3.8 23.8 1.0 P 0:A876 3.8 28.9 1.0 OP1 0:G877 3.8 29.3 1.0 O A:ALA193 4.1 29.0 1.0 O A:HOH9009 4.2 23.5 1.0 O3' 0:A875 4.2 24.2 1.0 O3' 0:G2623 4.3 26.6 1.0 O 0:HOH6348 4.3 33.4 1.0 O5' 0:A876 4.4 25.5 1.0 OP2 0:A2624 4.4 30.8 1.0 O3' 0:A876 4.5 26.9 1.0 O A:HOH9077 4.5 45.0 1.0 O5' 0:G877 4.6 25.2 1.0 O 0:HOH7242 4.7 57.1 1.0 CG A:ASN195 4.7 20.6 1.0 O 0:HOH9026 4.7 42.9 1.0 O5' 0:A2624 4.7 28.9 1.0 C5' 0:A876 4.8 26.9 1.0 O A:HOH9030 4.8 31.8 1.0 MG 0:MG8009 4.9 21.2 1.0 C5' 0:A2624 5.0 28.0 1.0 C3' 0:A876 5.0 29.2 1.0 OP1 0:A876 5.0 25.4 1.0

Magnesium binding site 9 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:25.8 occ:1.00 O 0:HOH3827 2.3 29.3 1.0 O 0:HOH9053 2.3 30.7 1.0 O 0:HOH9807 2.3 36.7 1.0 O 0:HOH7834 2.3 33.2 1.0 OP1 0:A459 2.3 24.4 1.0 O6 0:G456 2.4 32.3 1.0 C6 0:G456 3.4 33.7 1.0 O 0:HOH6026 3.7 68.7 1.0 P 0:A459 3.7 30.1 1.0 N7 0:G456 4.0 30.7 1.0 C5 0:G456 4.0 32.5 1.0 O 0:HOH3744 4.1 36.2 1.0 O 0:HOH3556 4.2 39.5 1.0 OP2 0:A455 4.2 27.8 1.0 N7 0:A455 4.3 31.3 1.0 CE C:LYS85 4.3 26.9 1.0 OP2 0:A459 4.4 30.0 1.0 O5' 0:A459 4.4 26.1 1.0 O 0:HOH9354 4.5 30.6 1.0 N1 0:G456 4.5 35.6 1.0 C5' 0:A459 4.5 27.2 1.0 OP1 0:A460 4.5 31.5 1.0 NZ C:LYS85 4.5 28.8 1.0 C5' 0:U454 4.6 27.4 1.0 CD C:LYS85 4.7 26.1 1.0 O3' 0:G458 4.8 28.2 1.0 OP1 0:A477 4.8 28.2 1.0 N6 0:A455 5.0 28.3 1.0

Magnesium binding site 10 out of 93 in the Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Crystal Structure of Anisomycin Bound to the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:27.0 occ:1.00 OP2 0:A1839 2.1 30.6 1.0 O 0:HOH7851 2.3 47.8 1.0 OP1 0:A1836 2.4 26.8 1.0 O 0:HOH7850 2.5 54.6 1.0 O 0:HOH3653 2.5 16.3 1.0 OP1 0:U1838 2.5 22.8 1.0 P 0:A1839 3.4 29.5 1.0 O 0:HOH9014 3.7 22.6 1.0 P 0:A1836 3.8 28.3 1.0 OP1 0:A1839 4.0 31.7 1.0 P 0:U1838 4.0 24.9 1.0 O 0:HOH9663 4.1 44.5 1.0 O5' 0:A1836 4.2 28.6 1.0 O 0:HOH5618 4.3 52.6 1.0 O 0:HOH7923 4.3 19.9 1.0 OP2 0:G1837 4.3 25.0 1.0 O5' 0:A1839 4.4 28.9 1.0 O3' 0:U1838 4.4 30.6 1.0 O 0:HOH5559 4.5 40.1 1.0 C3' 0:G1837 4.6 24.5 1.0 C2' 0:U1835 4.6 27.7 1.0 C3' 0:U1835 4.7 26.7 1.0 OP2 0:A1836 4.7 29.2 1.0 O3' 0:U1835 4.7 26.0 1.0 O5' 0:U1838 4.7 24.7 1.0 C5' 0:U1838 4.8 23.3 1.0 O3' 0:G1837 4.8 22.4 1.0 C8 0:A1839 4.9 25.9 1.0 C3' 0:U1838 4.9 26.7 1.0 N7 0:A1839 4.9 25.6 1.0 OP2 0:U1838 4.9 22.6 1.0 O 0:HOH9540 5.0 33.4 1.0

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075