Magnesium in PDB 5dm6: Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans

The structure of Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans, PDB code: 5dm6 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)	58.96 / 2.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.900, 410.760, 696.120, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27

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 - 190; Page 20, Binding sites: 191 - 198;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans (pdb code 5dm6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 198 binding sites of Magnesium where determined in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans, PDB code: 5dm6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:69.6 occ:1.00 OD1 M:ASN58 3.4 69.0 1.0 OP1 X:G2719 4.0 75.4 1.0 OP2 X:G2686 4.4 66.7 1.0 OP2 X:G2685 4.5 83.8 1.0 OP1 X:U2720 4.6 72.8 1.0 CG M:ASN58 4.6 67.6 1.0 C5' X:G2685 4.8 75.9 1.0 O5' X:G2719 4.9 78.8 1.0

Magnesium binding site 2 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6001 b:69.6 occ:1.00 OP2 X:A1664 2.1 61.5 1.0 P X:A1664 3.5 79.7 1.0 N7 X:G1992 3.8 54.3 1.0 O6 X:G1667 3.8 73.8 1.0 N6 X:A1665 4.1 77.5 1.0 OP1 X:A1664 4.1 65.7 1.0 OP1 X:G1992 4.2 68.2 1.0 OP2 X:G1992 4.2 68.6 1.0 O6 X:G1666 4.3 68.9 1.0 C3' X:U1663 4.4 65.9 1.0 N7 X:A1664 4.4 69.5 1.0 N7 X:A1665 4.4 64.8 1.0 C2' X:U1663 4.4 62.5 1.0 O5' X:A1664 4.5 66.3 1.0 O3' X:U1663 4.5 77.1 1.0 C8 X:G1992 4.5 53.5 1.0 C6 X:G1667 4.6 76.5 1.0 C5 X:G1992 4.6 57.1 1.0 P X:G1992 4.7 70.0 1.0 O6 X:G1992 4.7 55.6 1.0 N7 X:G1666 4.9 73.0 1.0 C8 X:A1664 4.9 68.4 1.0 N1 X:G1667 4.9 72.7 1.0 C6 X:A1665 5.0 79.5 1.0

Magnesium binding site 3 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6002 b:78.8 occ:1.00 OP2 X:G1271 1.9 76.7 1.0 OP1 X:G1647 2.0 81.0 1.0 OP1 X:C1648 2.3 77.0 1.0 OP1 X:A1272 2.6 76.5 1.0 P X:A1272 3.3 75.8 1.0 OP2 X:A1272 3.3 73.3 1.0 P X:G1647 3.4 72.7 1.0 P X:G1271 3.4 85.3 1.0 P X:C1648 3.5 78.8 1.0 O5' X:G1647 3.7 76.4 1.0 OP2 X:C1648 3.9 62.6 1.0 OP2 X:G1647 4.0 78.2 1.0 O3' X:C1270 4.1 80.1 1.0 OP1 X:G1271 4.1 85.8 1.0 O5' X:G1271 4.2 83.2 1.0 O3' X:G1271 4.4 71.6 1.0 O5' X:A1272 4.4 88.3 1.0 C3' X:G1271 4.4 76.1 1.0 O5' X:C1648 4.5 66.5 1.0 C3' X:G1647 4.5 79.7 1.0 C5' X:G1271 4.5 77.1 1.0 O3' X:G1647 4.5 73.1 1.0 C5' X:C1648 4.6 67.1 1.0 O3' X:C1646 4.6 78.7 1.0 C4' X:G1647 4.8 85.2 1.0 C5' X:G1647 4.8 79.2 1.0 C3' X:C1646 4.9 77.5 1.0

Magnesium binding site 4 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6003 b:70.0 occ:1.00 OP2 X:C1327 2.1 66.7 1.0 P X:C1327 3.4 71.4 1.0 OP1 X:U1326 3.8 74.5 1.0 O5' X:C1327 4.0 80.2 1.0 N7 X:G1324 4.0 84.5 1.0 OP1 X:C1327 4.2 73.7 1.0 OP2 X:U1326 4.2 61.0 1.0 N7 X:G1328 4.3 80.0 1.0 P X:U1326 4.4 74.7 1.0 C8 X:G1324 4.4 80.7 1.0 O3' X:U1326 4.6 68.5 1.0 O5' X:U1326 4.7 63.5 1.0 O6 X:G1328 4.8 75.3 1.0 C5 X:C1327 4.8 68.5 1.0 C3' X:U1326 4.9 75.0 1.0 C6 X:C1327 4.9 73.3 1.0 C5 X:G1324 4.9 80.2 1.0

Magnesium binding site 5 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6004 b:76.4 occ:1.00 OP1 X:A751 1.9 83.9 1.0 OP1 X:A1614 2.1 85.2 1.0 P X:A751 3.3 81.8 1.0 P X:A1614 3.4 83.5 1.0 O3' X:A750 3.6 80.0 1.0 O2' X:G1613 3.7 87.2 1.0 OP2 X:A1614 3.9 77.5 1.0 C2' X:G1613 4.0 85.0 1.0 O5' X:A751 4.1 87.4 1.0 O3' X:G1613 4.2 75.0 1.0 N1 X:A789 4.3 93.2 1.0 N3 X:C1617 4.4 86.4 1.0 OP2 X:A751 4.4 78.7 1.0 O5' X:A1614 4.6 84.5 1.0 N7 X:A1614 4.6 76.9 1.0 C3' X:G1613 4.6 78.3 1.0 N4 X:C1617 4.6 86.4 1.0 N7 X:A751 4.7 84.5 1.0 C8 X:A1614 4.8 75.0 1.0 C8 X:A751 4.9 84.3 1.0 C2 X:A789 4.9 88.0 1.0 C3' X:A750 5.0 85.0 1.0

Magnesium binding site 6 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6005 b:69.6 occ:1.00 N7 X:A1650 4.0 67.1 1.0 OD1 K:ASN11 4.1 61.7 1.0 N6 X:A1650 4.1 69.6 1.0 OP1 X:G2004 4.4 80.6 1.0 O6 X:G1651 4.6 72.6 1.0 N7 X:G1651 4.6 59.5 1.0 OP2 X:G2004 4.6 70.4 1.0 C5 X:A1650 4.7 65.5 1.0 CG K:ASN11 4.7 68.1 1.0 C6 X:A1650 4.8 71.4 1.0 C8 X:A1650 5.0 64.1 1.0

Magnesium binding site 7 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6006 b:69.6 occ:1.00 OP2 X:A1997 1.9 67.3 1.0 P X:A1997 3.2 66.5 1.0 O3' X:C1996 3.6 70.0 1.0 O5' X:A1997 3.7 69.5 1.0 OP2 X:U1995 3.7 72.3 1.0 OP1 X:C1994 4.2 64.8 1.0 O2' X:C1996 4.4 72.9 1.0 C8 X:A1997 4.4 53.2 1.0 OP1 X:A1997 4.5 67.0 1.0 O B:GLY125 4.6 65.3 1.0 O B:ALA123 4.6 71.8 1.0 C3' X:C1996 4.7 65.5 1.0 N7 X:A1997 4.8 49.2 1.0 P X:U1995 4.8 73.9 1.0

Magnesium binding site 8 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6007 b:70.6 occ:1.00 OP2 X:A2712A 1.9 68.7 1.0 OP2 X:G2714 2.0 76.1 1.0 OP2 X:A2711 2.2 72.8 1.0 P X:A2711 3.3 75.3 1.0 P X:G2714 3.3 67.8 1.0 P X:A2712A 3.3 68.6 1.0 OP1 X:A2711 3.4 69.1 1.0 O2' X:C2712 3.4 78.1 1.0 O5' X:G2714 3.7 67.0 1.0 C5' X:G2714 3.9 71.3 1.0 OP2 X:U2713 3.9 51.7 1.0 C5' X:A2712A 3.9 52.6 1.0 OP1 X:A2712A 4.0 72.9 1.0 O5' X:A2712A 4.1 59.8 1.0 O3' X:U2713 4.2 60.2 1.0 O3' X:C2712 4.4 76.3 1.0 OP1 X:G2714 4.4 73.6 1.0 C2' X:C2712 4.4 68.2 1.0 O3' X:C2710 4.4 76.9 1.0 O5' X:A2711 4.4 77.8 1.0 C3' X:C2712 4.4 66.2 1.0 OG K:SER15 4.5 57.6 1.0 OP1 X:C2710 4.7 68.5 1.0 C3' X:U2713 4.7 63.2 1.0 MG X:MG6044 5.0 73.1 1.0

Magnesium binding site 9 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6008 b:81.2 occ:1.00 OP2 X:G2502 2.2 81.9 1.0 OP2 X:G2061 2.2 79.9 1.0 P X:G2502 3.3 83.4 1.0 O5' X:G2502 3.5 77.3 1.0 P X:G2061 3.6 86.7 1.0 O3' X:C2501 3.6 80.0 1.0 OP1 X:G2061 4.2 87.7 1.0 O2' X:C2501 4.2 87.1 1.0 O2' X:A2060 4.2 83.2 1.0 C5' X:G2061 4.3 86.0 1.0 C2' X:A2060 4.4 88.0 1.0 C3' X:G2061 4.4 82.6 1.0 O5' X:G2061 4.4 83.4 1.0 O6 X:G2446 4.5 90.8 1.0 N7 X:G2446 4.5 84.6 1.0 C3' X:C2501 4.5 79.8 1.0 N7 X:G2445 4.6 82.2 1.0 C2' X:C2501 4.6 82.5 1.0 OP1 X:G2502 4.7 78.8 1.0 C2' X:G2061 4.7 71.2 1.0 O3' X:A2060 4.8 82.0 1.0 OP1 X:A2062 4.9 82.5 1.0 C5' X:G2502 4.9 82.1 1.0 C4' X:G2061 4.9 89.4 1.0

Magnesium binding site 10 out of 198 in the Crystal Structure of the 50S Ribosomal Subunit From Deinococcus Radiodurans


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 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg6009 b:69.6 occ:1.00 OP2 X:A1665 2.3 63.3 1.0 OP1 X:A1664 2.8 65.7 1.0 P X:A1665 3.6 73.3 1.0 P X:A1664 3.8 79.7 1.0 O5' X:A1664 4.0 66.3 1.0 OP1 X:A1665 4.1 73.3 1.0 O5' X:A1665 4.3 75.1 1.0 OP2 X:A1664 4.5 61.5 1.0 C5' X:A1664 4.6 64.9 1.0 OP2 X:G1666 4.7 79.2 1.0 O3' X:A1664 4.7 57.3 1.0 C3' X:A1664 4.9 70.2 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