Magnesium in PDB 5dm7: Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A

The structure of Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A, PDB code: 5dm7 was solved by T.Kaminishi, A.Schedlbauer, B.Ochoa-Lizarralde, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.02 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.820, 411.540, 695.650, 90.00, 90.00, 90.00
R / Rfree (%)	28.4 / 32.6

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 - 186;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A (pdb code 5dm7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 186 binding sites of Magnesium where determined in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A, PDB code: 5dm7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:0.8 occ:1.00 OP1 X:A2577 2.1 0.3 1.0 O A:ALA242 2.9 0.1 1.0 O A:GLY234 3.2 0.0 1.0 O A:HIS233 3.3 0.1 1.0 P X:A2577 3.3 0.5 1.0 O3' X:G2576 3.4 0.0 1.0 C A:HIS233 3.9 0.1 1.0 C A:ALA242 4.0 0.7 1.0 O5' X:A2577 4.3 0.5 1.0 C A:GLY234 4.3 0.6 1.0 C5' X:A2577 4.3 0.5 1.0 CA A:HIS233 4.3 0.5 1.0 OP2 X:A2577 4.4 0.8 1.0 O A:PRO232 4.5 0.3 1.0 C3' X:G2576 4.6 0.1 1.0 N A:GLY234 4.6 0.7 1.0 CA A:ALA242 4.7 0.8 1.0 C4' X:G2576 4.8 0.8 1.0 C5' X:G2576 4.9 0.3 1.0

Magnesium binding site 2 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:0.8 occ:1.00 O H:ALA66 3.1 96.0 1.0 OP2 X:U1934 4.0 0.0 1.0 OP1 X:G1933 4.2 0.3 1.0 C H:ALA66 4.4 90.9 1.0 CB H:ALA66 4.8 84.2 1.0

Magnesium binding site 3 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:71.6 occ:1.00 ND2 M:ASN58 3.5 86.5 1.0 OP1 X:G2699 3.6 85.8 1.0 OP1 X:U2700 4.2 99.1 1.0 CG M:ASN58 4.5 89.2 1.0 O5' X:G2699 4.6 95.1 1.0 OP2 X:G2665 4.6 80.3 1.0 P X:G2699 4.6 85.7 1.0 C5' X:G2699 4.7 90.7 1.0 OP2 X:G2664 4.7 77.5 1.0 OH M:TYR105 4.9 64.9 1.0

Magnesium binding site 4 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:74.3 occ:1.00 OP1 X:G1266 2.4 92.5 1.0 NH2 N:ARG33 3.5 0.3 1.0 P X:G1266 3.7 97.4 1.0 O6 X:G1269 3.7 1.0 1.0 O3' X:G1265 4.1 89.5 1.0 N7 X:G1269 4.1 0.5 1.0 OP2 X:G1266 4.3 99.2 1.0 N4 X:C1270 4.4 94.3 1.0 CZ N:ARG33 4.4 0.6 1.0 C6 X:G1269 4.5 0.5 1.0 OP2 X:A1267 4.6 93.7 1.0 C5 X:G1269 4.7 0.7 1.0 NH1 N:ARG33 4.9 0.3 1.0 O6 X:G592 4.9 0.3 1.0 O5' X:G1266 5.0 96.5 1.0 C4' X:G1266 5.0 0.5 1.0

Magnesium binding site 5 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6001 b:67.1 occ:1.00 OP2 X:A1681 2.5 56.4 1.0 N7 X:G1975 3.2 63.2 1.0 OP1 X:G1975 3.7 60.0 1.0 O6 X:G1684 3.8 84.1 1.0 C8 X:G1975 3.8 66.0 1.0 N6 X:A1681 3.9 80.0 1.0 N7 X:A1681 3.9 74.2 1.0 P X:A1681 4.0 82.0 1.0 N6 X:A1682 4.1 83.6 1.0 C5 X:G1975 4.3 63.5 1.0 C2' X:U1680 4.4 69.3 1.0 OP2 X:G1975 4.4 86.8 1.0 O6 X:G1683 4.5 78.3 1.0 P X:G1975 4.6 79.1 1.0 C3' X:U1680 4.6 76.0 1.0 C5 X:A1681 4.6 76.4 1.0 C6 X:A1681 4.7 84.7 1.0 N7 X:A1682 4.7 75.8 1.0 C6 X:G1684 4.8 94.5 1.0 O5' X:A1681 4.8 69.8 1.0 C8 X:A1681 4.8 74.9 1.0 OP1 X:A1681 4.8 75.0 1.0 O3' X:U1680 4.9 78.2 1.0 O6 X:G1975 4.9 68.8 1.0 C6 X:G1975 4.9 63.6 1.0 N1 X:U1680 5.0 59.6 1.0

Magnesium binding site 6 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6002 b:91.6 occ:1.00 OP1 X:A1285 1.9 0.2 1.0 OP2 X:G1284 2.0 98.4 1.0 OP1 X:C1665 2.2 0.5 1.0 OP1 X:G1664 2.7 0.6 1.0 O5' X:G1664 3.0 89.5 1.0 P X:A1285 3.3 98.3 1.0 P X:G1284 3.4 0.1 1.0 P X:G1664 3.4 96.3 1.0 P X:C1665 3.4 94.1 1.0 OP2 X:C1665 3.8 89.3 1.0 O3' X:C1283 3.9 93.5 1.0 O5' X:G1284 3.9 0.4 1.0 O5' X:A1285 3.9 95.3 1.0 OP2 X:A1285 4.1 97.8 1.0 C5' X:G1664 4.2 95.6 1.0 OP2 X:G1664 4.3 89.0 1.0 O3' X:G1284 4.4 83.3 1.0 O3' X:G1664 4.4 96.5 1.0 C3' X:G1664 4.5 98.4 1.0 O5' X:C1665 4.5 78.6 1.0 C4' X:G1664 4.5 97.4 1.0 C3' X:G1284 4.6 97.5 1.0 C5' X:C1665 4.6 81.5 1.0 OP1 X:G1284 4.6 97.7 1.0 O3' X:C1663 4.7 87.4 1.0 C5' X:G1284 4.8 94.5 1.0 C3' X:C1663 4.9 96.8 1.0

Magnesium binding site 7 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6003 b:72.2 occ:1.00 OP2 X:C1340 1.8 89.7 1.0 P X:C1340 3.2 86.5 1.0 N7 X:G1337 3.8 97.6 1.0 O5' X:C1340 4.0 81.8 1.0 OP1 X:C1340 4.0 78.7 1.0 OP1 X:U1339 4.0 88.6 1.0 C8 X:G1337 4.3 93.3 1.0 O3' X:U1339 4.3 84.5 1.0 OP2 X:U1339 4.3 80.5 1.0 N7 X:G1341 4.5 97.4 1.0 P X:U1339 4.6 88.0 1.0 C3' X:U1339 4.8 86.1 1.0 C5 X:G1337 4.9 94.5 1.0

Magnesium binding site 8 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6004 b:93.8 occ:1.00 OP1 X:A764 1.9 98.0 1.0 OP1 X:A1630 2.0 99.7 1.0 P X:A1630 3.3 0.7 1.0 P X:A764 3.3 96.2 1.0 O3' X:A763 3.8 93.1 1.0 OP2 X:A1630 3.8 99.1 1.0 N7 X:A1630 3.9 0.4 1.0 O3' X:G1629 4.0 0.6 1.0 O2' X:G1629 4.2 0.4 1.0 C8 X:A1630 4.2 1.0 1.0 O5' X:A764 4.3 0.3 1.0 OP2 X:A764 4.3 89.6 1.0 N4 X:C1633 4.4 0.7 1.0 C2' X:G1629 4.5 1.0 1.0 O5' X:A1630 4.5 0.9 1.0 N3 X:C1633 4.5 0.6 1.0 N1 X:A802 4.6 97.6 1.0 O P:ARG111 4.6 0.1 1.0 N7 X:A764 4.6 0.1 1.0 C3' X:G1629 4.8 0.9 1.0 C8 X:A764 5.0 97.6 1.0

Magnesium binding site 9 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6005 b:58.7 occ:1.00 N7 X:A1667 3.7 90.7 1.0 N6 X:A1667 3.8 90.8 1.0 O6 X:G1668 4.1 93.0 1.0 OD1 K:ASN11 4.1 82.6 1.0 N7 X:G1668 4.1 79.8 1.0 C5 X:A1667 4.4 87.2 1.0 C6 X:A1667 4.4 87.4 1.0 C8 X:A1667 4.7 84.0 1.0 CG K:ASN11 4.8 81.7 1.0 OP2 X:G1987 4.8 77.7 1.0 C6 X:G1668 4.9 88.7 1.0 C5 X:G1668 4.9 83.5 1.0

Magnesium binding site 10 out of 186 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A


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 the 50S Ribosomal Subunit From Deinococcus Radiodurans in Complex with Hygromycin A within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6006 b:70.9 occ:1.00 OP2 X:A1980 2.4 77.6 1.0 P X:A1980 3.4 84.3 1.0 O5' X:A1980 3.5 81.0 1.0 O3' X:C1979 4.0 84.7 1.0 O B:GLY125 4.1 71.9 1.0 OP2 X:U1978 4.2 82.9 1.0 OP1 X:C1977 4.3 74.6 1.0 O B:ALA123 4.4 73.6 1.0 N B:GLY125 4.6 58.7 1.0 OP1 X:A1980 4.8 78.1 1.0 C5' X:A1980 4.8 78.9 1.0 C8 X:A1980 4.9 69.5 1.0 C B:GLY125 5.0 71.6 1.0

T.Kaminishi, A.Schedlbauer, A.Fabbretti, L.Brandi, B.Ochoa-Lizarralde, C.G.He, P.Milon, S.R.Connell, C.O.Gualerzi, P.Fucini. Crystallographic Characterization of the Ribosomal Binding Site and Molecular Mechanism of Action of Hygromycin A. Nucleic Acids Res. V. 43 10015 2015.
ISSN: ESSN 1362-4962
PubMed: 26464437
DOI: 10.1093/NAR/GKV975