Magnesium in PDB 8a5i: Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit.

The structure of Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	2 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 - 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 - 165;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. (pdb code 8a5i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 165 binding sites of Magnesium where determined in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit., PDB code: 8a5i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3002 b:48.5 occ:1.00 OP2 A:G847 2.0 46.5 1.0 O A:HOH3893 2.0 38.4 1.0 O A:HOH3458 2.0 62.1 1.0 O A:HOH3819 2.1 51.9 1.0 O A:HOH3489 2.2 42.7 1.0 O A:HOH4247 2.3 48.2 1.0 P A:G847 3.3 39.4 1.0 O3' A:A846 3.5 40.6 1.0 O I:HOH310 4.2 53.4 1.0 OP1 A:G847 4.2 45.6 1.0 OP2 A:G845 4.3 36.0 1.0 O5' A:G847 4.4 40.1 1.0 O I:GLY59 4.4 42.5 1.0 C5' A:G847 4.5 40.8 1.0 OP1 A:G844 4.5 46.0 1.0 O2' A:A846 4.6 36.3 1.0 O A:HOH3810 4.6 43.2 1.0 O I:SER55 4.6 52.0 1.0 C3' A:A846 4.7 36.4 1.0 CA I:GLY61 4.7 37.1 1.0 O I:GLY60 4.9 41.2 1.0 N I:GLY61 5.0 37.6 1.0 CA I:SER55 5.0 43.8 1.0

Magnesium binding site 2 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3003 b:73.9 occ:1.00 O A:HOH3480 1.9 57.1 1.0 O A:HOH4407 1.9 53.2 1.0 O A:HOH4253 2.0 57.9 1.0 O A:HOH4206 2.3 64.9 1.0 O A:HOH3829 2.6 35.3 1.0 N7 A:A2486 3.9 39.2 1.0 O A:HOH3849 4.0 85.5 1.0 O6 A:G2487 4.1 38.1 1.0 N7 A:G2487 4.3 37.2 1.0 O6 A:G2488 4.4 39.6 1.0 N1 A:A2530 4.5 41.7 1.0 C8 A:A2486 4.6 35.9 1.0 N4 A:C2529 4.6 39.8 1.0 OP2 A:A2486 4.7 45.4 1.0 OP2 A:C2485 4.7 52.7 1.0 C2 A:A2530 4.7 41.9 1.0 C5 A:A2486 4.9 38.8 1.0 N6 A:A2486 4.9 35.0 1.0 C6 A:G2487 4.9 33.1 1.0 C5 A:G2487 5.0 34.6 1.0

Magnesium binding site 3 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3004 b:61.9 occ:1.00 OP2 A:C2649 2.0 49.2 1.0 OP2 A:U2648 2.0 48.6 1.0 O A:HOH4394 2.7 88.3 1.0 P A:U2648 3.3 34.9 1.0 P A:C2649 3.3 38.1 1.0 O5' A:U2648 3.6 39.4 1.0 O3' A:U2648 3.9 41.0 1.0 O3' A:A2647 4.0 37.7 1.0 OP1 A:C2649 4.1 44.9 1.0 C3' A:U2648 4.1 38.4 1.0 O A:HOH3846 4.1 48.3 1.0 C5' A:U2648 4.1 37.1 1.0 O A:HOH3909 4.4 29.4 1.0 O5' A:C2649 4.5 40.9 1.0 OP1 A:U2648 4.6 44.0 1.0 O2' A:A2647 4.6 34.0 1.0 C4' A:U2648 4.7 39.1 1.0 O A:HOH4290 5.0 47.1 1.0

Magnesium binding site 4 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3005 b:65.3 occ:1.00 OP1 A:U614 2.0 47.0 1.0 O A:HOH4110 2.4 43.3 1.0 P A:U614 3.4 37.2 1.0 OP2 A:U614 4.0 40.6 1.0 O3' A:G613 4.2 39.1 1.0 O A:HOH3467 4.2 44.1 1.0 O5' A:U614 4.5 40.1 1.0 O A:HOH4135 4.5 40.4 1.0 O U:HOH203 4.6 48.9 1.0 CE U:LYS80 4.8 39.0 1.0 C5' A:U614 4.8 38.1 1.0 NZ U:LYS80 4.9 38.5 1.0

Magnesium binding site 5 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3006 b:64.7 occ:1.00 O A:HOH4364 2.8 35.0 1.0 O4 A:U2613 3.7 37.2 1.0 O6 A:G2542 3.7 36.1 1.0 N4 A:C2612 4.0 31.8 1.0 C5 A:G2609 4.1 35.2 1.0 N7 A:G2609 4.1 35.7 1.0 O A:HOH3483 4.2 45.3 1.0 O6 A:G2541 4.2 40.7 1.0 C4 A:G2609 4.2 35.4 1.0 C8 A:G2609 4.2 32.7 1.0 N9 A:G2609 4.3 34.2 1.0 O4' A:G2609 4.5 32.6 1.0 O A:HOH3746 4.5 39.4 1.0 C6 A:G2609 4.5 38.6 1.0 O5' A:G2609 4.6 29.7 1.0 C6 A:G2542 4.8 36.7 1.0 C4 A:U2613 4.8 34.9 1.0 O A:HOH3395 4.8 51.0 1.0 N3 A:G2609 4.8 38.8 1.0 O6 A:G2609 5.0 40.9 1.0

Magnesium binding site 6 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3007 b:83.5 occ:1.00 O A:HOH4183 2.6 73.4 1.0 N3 A:A1477 3.9 41.0 1.0 C5 A:C1478 4.0 46.5 1.0 OP1 A:A1621 4.1 53.2 1.0 OP2 A:A1622 4.4 43.4 1.0 C6 A:C1478 4.4 43.5 1.0 C2 A:A1477 4.5 40.4 1.0 NE2 G:GLN61 4.5 62.4 1.0 C1' A:A1477 4.7 47.9 1.0 CD1 G:LEU34 4.8 54.5 1.0 C4 A:A1477 4.8 40.5 1.0 O3' A:A1477 4.9 59.0 1.0 OP1 A:A1622 5.0 48.3 1.0

Magnesium binding site 7 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3008 b:102.4 occ:1.00 OP2 A:C1033 3.3 52.0 1.0 NE 3:ARG15 3.7 54.9 1.0 CZ 3:ARG15 3.7 60.5 1.0 OP1 A:C1033 3.8 57.0 1.0 O 3:GLY14 3.9 48.8 1.0 P A:C1033 4.0 48.1 1.0 NH1 3:ARG15 4.1 57.0 1.0 NH2 3:ARG15 4.1 61.0 1.0 C 3:GLY14 4.2 43.4 1.0 CD 3:ARG15 4.2 51.4 1.0 O 3:ILE13 4.2 45.5 1.0 CA 3:GLY14 4.4 42.2 1.0 N 3:ARG15 4.9 46.0 1.0 CG 3:ARG15 5.0 49.8 1.0

Magnesium binding site 8 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3009 b:82.0 occ:1.00 O A:HOH3230 2.6 47.8 1.0 O6 A:G804 4.0 35.3 1.0 N1 A:A785 4.1 39.1 1.0 O6 A:G803 4.2 42.0 1.0 O A:HOH3834 4.3 50.5 1.0 C2 A:A785 4.4 40.0 1.0 N7 A:G803 4.4 37.5 1.0 N4 A:C802 4.5 34.2 1.0 C6 A:G804 4.7 32.2 1.0 N7 A:G804 4.8 33.8 1.0 C5 A:C802 4.9 36.8 1.0 C5 A:G804 5.0 31.1 1.0

Magnesium binding site 9 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3010 b:91.0 occ:1.00 OP2 A:G1421 2.0 56.3 1.0 P A:G1421 3.3 43.7 1.0 O5' A:G1421 3.8 46.4 1.0 OP1 A:G1421 4.1 57.6 1.0 OP1 A:A1393 4.1 75.0 1.0 C8 A:G1421 4.4 35.6 1.0 N7 A:G1421 4.5 39.4 1.0 OP2 A:A1422 4.5 52.2 1.0 O3' A:C1420 4.5 45.2 1.0 C3' A:C1420 4.7 43.3 1.0 O4 A:U1396 4.9 39.1 1.0

Magnesium binding site 10 out of 165 in the Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 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 Cryo-Em Structure of Lincomycin Bound to the Listeria Monocytogenes 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3011 b:72.1 occ:1.00 OP1 A:U2587 2.0 68.0 1.0 O A:HOH4356 2.6 37.0 1.0 O A:HOH3307 3.0 36.6 1.0 MG A:MG3155 3.1 49.8 1.0 O A:HOH3562 3.2 50.5 1.0 P A:U2587 3.4 51.6 1.0 O4 A:U2585 3.5 49.2 1.0 C5 A:U2585 3.5 49.4 1.0 C5' A:C1721 3.8 37.8 1.0 C4 A:U2585 3.8 46.7 1.0 O3' A:C1721 3.8 39.8 1.0 OP2 A:G1722 3.9 42.4 1.0 OP1 A:G1722 3.9 43.4 1.0 P A:G1722 4.0 38.3 1.0 O5' A:U2587 4.0 55.4 1.0 OP2 A:U2587 4.1 58.0 1.0 C4' A:C1721 4.3 37.8 1.0 OP2 A:C1721 4.4 44.5 1.0 O A:HOH4287 4.4 29.9 1.0 O3' A:G2586 4.5 52.1 1.0 C6 A:U2585 4.6 49.2 1.0 C3' A:C1721 4.6 39.3 1.0 O5' A:C1721 4.8 39.9 1.0 O A:HOH3845 4.9 43.1 1.0 N3 A:U2585 5.0 46.3 1.0

T.O.Koller, K.J.Turnbull, K.Vaitkevicius, C.Crowe-Mcauliffe, M.Roghanian, O.Bulvas, J.A.Nakamoto, T.Kurata, C.Julius, G.C.Atkinson, J.Johansson, V.Hauryliuk, D.N.Wilson. Structural Basis For Hflxr-Mediated Antibiotic Resistance in Listeria Monocytogenes. Nucleic Acids Res. V. 50 11285 2022.
ISSN: ESSN 1362-4962
PubMed: 36300626
DOI: 10.1093/NAR/GKAC934