Magnesium in PDB 3cxc: The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui

The structure of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui, PDB code: 3cxc was solved by J.A.Ippolito, D.Wang, Z.F.Kanyo, E.M.Duffy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.660, 300.710, 575.370, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 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 - 117;

Binding sites:

The binding sites of Magnesium atom in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui (pdb code 3cxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui, PDB code: 3cxc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:46.1 occ:1.00 OP2 0:C2533 2.1 45.1 1.0 OP2 0:C2534 2.1 52.4 1.0 O 0:HOH3165 2.1 66.9 1.0 O 0:HOH4566 2.1 60.8 1.0 O 0:HOH8673 2.1 43.1 1.0 OP2 0:A2483 2.4 45.7 1.0 O3' 0:G2482 3.4 46.1 1.0 P 0:C2533 3.4 46.4 1.0 P 0:A2483 3.5 46.8 1.0 P 0:C2534 3.5 51.1 1.0 O 0:HOH3620 3.8 61.0 1.0 O2' 0:A2532 3.8 45.7 1.0 O3' 0:A2532 3.9 45.9 1.0 O2' 0:G2482 4.1 47.3 1.0 O5' 0:C2533 4.1 46.1 1.0 O 0:HOH7277 4.2 0.8 1.0 OP2 0:U2484 4.3 51.8 1.0 OP1 0:C2534 4.3 51.5 1.0 O5' 0:C2534 4.4 48.5 1.0 O3' 0:C2533 4.4 47.8 1.0 OP1 0:A2483 4.4 47.0 1.0 O 0:HOH5265 4.5 61.7 1.0 OP1 0:C2533 4.5 47.9 1.0 C3' 0:C2533 4.6 46.4 1.0 O5' 0:A2483 4.6 44.7 1.0 C3' 0:G2482 4.7 45.5 1.0 C5' 0:A2483 4.8 46.7 1.0 C2' 0:G2482 4.8 44.7 1.0 C2' 0:A2532 4.9 45.0 1.0 O 0:HOH8981 4.9 66.5 1.0 C3' 0:A2532 4.9 44.9 1.0 C1' 0:G2482 5.0 45.7 1.0

Magnesium binding site 2 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:51.6 occ:1.00 O6 0:G627 1.9 45.9 1.0 OP1 0:A2483 2.0 47.0 1.0 O 0:HOH8651 2.1 42.7 1.0 O 0:HOH8652 2.1 42.6 1.0 O 0:HOH5265 2.1 61.7 1.0 OP1 0:C2534 2.2 51.5 1.0 C6 0:G627 3.1 44.6 1.0 P 0:A2483 3.2 46.8 1.0 P 0:C2534 3.5 51.1 1.0 O 0:HOH3247 3.6 34.1 1.0 OP2 0:A2483 3.6 45.7 1.0 N1 0:G627 3.8 43.4 1.0 O4 0:U626 3.9 44.9 1.0 O5' 0:A2483 4.1 44.7 1.0 O 0:HOH6784 4.1 53.0 1.0 OP2 0:C2534 4.1 52.4 1.0 O2' 0:U625 4.1 43.9 1.0 O 0:HOH7996 4.2 68.8 1.0 C5 0:G627 4.3 44.7 1.0 O3' 0:C2533 4.3 47.8 1.0 O3' 0:G2482 4.4 46.1 1.0 OP2 0:U2535 4.5 47.1 1.0 C4 0:U626 4.5 44.2 1.0 O 0:HOH4481 4.5 64.3 1.0 C5 0:U626 4.5 44.5 1.0 O5' 0:C2534 4.6 48.5 1.0 N7 0:G627 4.8 45.5 1.0 C3' 0:G2482 4.8 45.5 1.0 O 0:HOH4091 5.0 62.5 1.0

Magnesium binding site 3 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:51.7 occ:1.00 O A:HOH8512 2.0 53.5 1.0 OP1 0:A2624 2.1 49.8 1.0 O 0:HOH4614 2.2 45.8 1.0 OP2 0:G877 2.2 49.1 1.0 OP2 0:A876 2.2 48.4 1.0 O 0:HOH3804 2.3 56.9 1.0 P 0:G877 3.5 49.8 1.0 P 0:A2624 3.5 51.2 1.0 P 0:A876 3.5 49.1 1.0 O A:ALA193 3.9 50.2 1.0 O 0:HOH7179 4.0 57.9 1.0 OP1 0:G877 4.0 50.8 1.0 O3' 0:A875 4.0 44.5 1.0 O3' 0:G2623 4.1 50.0 1.0 O 0:HOH8859 4.2 74.5 1.0 O5' 0:A876 4.2 48.5 1.0 OD1 A:ASN195 4.2 47.8 1.0 O A:HOH8634 4.3 66.7 1.0 O3' 0:A876 4.3 48.5 1.0 OP2 0:A2624 4.4 50.8 1.0 O 0:HOH3018 4.5 42.1 1.0 C5' 0:A876 4.5 47.3 1.0 O5' 0:A2624 4.5 49.8 1.0 O 0:HOH5410 4.6 70.4 1.0 O5' 0:G877 4.6 48.3 1.0 OP1 0:A876 4.7 48.2 1.0 C5' 0:A2624 4.7 50.5 1.0 C3' 0:A876 4.8 48.3 1.0 O A:HOH8548 4.8 64.4 1.0

Magnesium binding site 4 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:51.0 occ:1.00 O 0:HOH3045 2.0 46.9 1.0 O 0:HOH4732 2.0 46.1 1.0 O 0:HOH8658 2.0 53.8 1.0 O 0:HOH3753 2.1 47.8 1.0 O6 0:G456 2.1 52.2 1.0 OP1 0:A459 2.1 48.4 1.0 C6 0:G456 3.2 51.7 1.0 P 0:A459 3.5 48.7 1.0 O 0:HOH4651 3.8 52.5 1.0 C5 0:G456 4.0 51.0 1.0 O 0:HOH6870 4.0 87.7 1.0 N7 0:G456 4.0 50.3 1.0 O5' 0:A459 4.1 47.4 1.0 O 0:HOH4467 4.1 71.5 1.0 OP2 0:A459 4.2 50.8 1.0 N1 0:G456 4.2 51.9 1.0 C5' 0:A459 4.3 47.1 1.0 OP2 0:A455 4.3 48.2 1.0 O 0:HOH3321 4.4 59.5 1.0 N7 0:A455 4.5 52.7 1.0 O3' 0:G458 4.5 49.4 1.0 CE C:LYS85 4.5 42.8 1.0 OP1 0:A460 4.6 50.1 1.0 OP1 0:A477 4.7 50.3 1.0 NZ C:LYS85 4.8 41.9 1.0 CD C:LYS85 4.8 45.2 1.0 C5' 0:U454 4.8 46.8 1.0 N6 0:A455 5.0 55.3 1.0 O 0:HOH6318 5.0 48.6 1.0

Magnesium binding site 5 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:58.9 occ:1.00 OP1 0:A1836 2.0 45.0 1.0 OP2 0:A1839 2.0 44.5 1.0 O 0:HOH8675 2.0 54.9 1.0 O 0:HOH8674 2.2 55.1 1.0 O 0:HOH4562 2.2 35.1 1.0 OP1 0:U1838 2.2 46.7 1.0 P 0:A1836 3.4 46.2 1.0 P 0:A1839 3.4 46.2 1.0 P 0:U1838 3.6 45.1 1.0 O 0:HOH3006 3.9 54.2 1.0 O5' 0:A1836 4.0 46.5 1.0 O 0:HOH6473 4.0 83.5 1.0 O 0:HOH6416 4.2 54.4 1.0 OP1 0:A1839 4.2 44.4 1.0 O5' 0:A1839 4.2 45.0 1.0 C2' 0:U1835 4.3 47.2 1.0 O3' 0:U1835 4.3 43.8 1.0 OP2 0:A1836 4.3 50.9 1.0 OP2 0:G1837 4.4 53.2 1.0 O5' 0:U1838 4.4 40.8 1.0 O3' 0:U1838 4.4 43.1 1.0 C3' 0:U1835 4.4 46.6 1.0 OP2 0:U1838 4.4 45.2 1.0 C3' 0:G1837 4.5 50.7 1.0 O3' 0:G1837 4.5 48.1 1.0 O 0:HOH3616 4.6 59.8 1.0 O 0:HOH8748 4.6 50.5 1.0 N7 0:A1839 4.6 43.0 1.0 O2' 0:U1835 4.7 47.8 1.0 C5' 0:U1838 4.7 40.9 1.0 C8 0:A1839 4.7 43.5 1.0 C3' 0:U1838 4.7 41.3 1.0 O 0:HOH3494 4.8 49.7 1.0

Magnesium binding site 6 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:60.5 occ:1.00 O 0:HOH4568 2.1 52.1 1.0 O 0:HOH3787 2.1 61.3 1.0 O 0:HOH4703 2.2 72.7 1.0 OP2 0:C822 2.2 57.9 1.0 OP2 0:U821 2.2 55.7 1.0 OP1 0:G854 2.4 51.0 1.0 OP1 0:G856 3.3 53.6 1.0 P 0:G854 3.6 52.4 1.0 P 0:U821 3.6 57.2 1.0 P 0:C822 3.6 58.8 1.0 O 0:HOH5928 3.9 47.5 1.0 O5' 0:G854 3.9 49.9 1.0 O5' 0:U821 3.9 57.6 1.0 O 0:HOH4169 4.0 78.1 1.0 OP1 0:U855 4.1 53.8 1.0 C3' 0:U821 4.2 57.6 1.0 O3' 0:G820 4.3 55.1 1.0 O3' 0:U821 4.3 59.3 1.0 OP2 0:G854 4.3 52.9 1.0 C5' 0:G854 4.3 48.7 1.0 NA 0:NA8327 4.4 46.0 1.0 OP1 0:C822 4.4 59.5 1.0 O5' 0:C822 4.6 56.0 1.0 P 0:G856 4.7 55.5 1.0 OP1 0:U821 4.8 56.6 1.0 O3' 0:C853 4.8 50.9 1.0 C5 0:C822 4.9 49.1 1.0 C5' 0:U855 5.0 55.0 1.0 O5' 0:G856 5.0 55.8 1.0

Magnesium binding site 7 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:47.8 occ:1.00 OP1 0:A1839 1.9 44.4 1.0 OP2 0:U832 2.0 47.7 1.0 O 0:HOH4320 2.1 58.9 1.0 O 0:HOH3006 2.1 54.2 1.0 O 0:HOH8663 2.2 38.2 1.0 OP2 0:A1840 2.3 46.1 1.0 P 0:A1839 3.3 46.2 1.0 O 0:HOH3098 3.3 62.5 1.0 P 0:U832 3.4 47.9 1.0 P 0:A1840 3.5 46.9 1.0 OP1 0:A1840 3.9 46.9 1.0 OP2 0:A1839 4.0 44.5 1.0 O 0:HOH7255 4.0 77.6 1.0 OP1 0:U832 4.1 45.9 1.0 O 0:HOH3616 4.2 59.8 1.0 O3' 0:U1838 4.2 43.1 1.0 O5' 0:A1839 4.3 45.0 1.0 O3' 0:A1839 4.3 43.8 1.0 O5' 0:U832 4.3 46.5 1.0 O3' 0:U831 4.4 46.2 1.0 O 0:HOH8748 4.6 50.5 1.0 C5' 0:A1839 4.6 44.0 1.0 O5' 0:A1840 4.7 46.5 1.0 C3' 0:A1839 4.7 43.1 1.0 OP2 0:G833 4.8 47.5 1.0 C3' 0:U831 4.8 46.4 1.0 O 0:HOH8674 4.9 55.1 1.0 O 0:HOH8675 4.9 54.9 1.0 C5' 0:U832 4.9 46.2 1.0

Magnesium binding site 8 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:52.8 occ:1.00 OP1 0:U919 1.9 44.4 1.0 OP1 0:C2464 2.0 47.4 1.0 O 0:HOH8749 2.0 69.5 1.0 OP1 0:A2465 2.1 54.6 1.0 O 0:HOH8667 2.2 46.4 1.0 O 0:HOH4578 2.3 65.0 1.0 P 0:U919 3.0 43.3 1.0 OP2 0:U919 3.3 42.8 1.0 P 0:C2464 3.3 49.9 1.0 P 0:A2465 3.4 53.5 1.0 O5' 0:U919 3.7 39.6 1.0 O 0:HOH6796 3.8 85.6 1.0 OP2 0:A2465 3.9 52.9 1.0 O5' 0:C2464 4.0 50.2 1.0 O 0:HOH3436 4.0 71.1 1.0 O 0:HOH4311 4.0 47.5 1.0 OP2 0:C2464 4.0 50.8 1.0 O5' 0:A2465 4.0 51.3 1.0 O 0:HOH3527 4.1 54.0 1.0 C5' 0:C2464 4.2 51.9 1.0 O3' 0:G918 4.3 41.6 1.0 C5' 0:U919 4.4 43.2 1.0 O3' 0:A2463 4.5 49.9 1.0 O3' 0:C2464 4.6 51.9 1.0 O 0:HOH3896 4.6 89.7 1.0 OP1 0:G2466 4.8 49.2 1.0 C3' 0:A2465 4.9 50.0 1.0 OP1 0:G2293 4.9 56.9 1.0 C3' 0:C2464 4.9 51.7 1.0 C5' 0:A2465 5.0 49.4 1.0

Magnesium binding site 9 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:44.7 occ:1.00 OP1 0:A2612 2.1 38.9 1.0 O 0:HOH8939 2.1 61.6 1.0 O 0:HOH4688 2.1 47.2 1.0 O 0:HOH8668 2.1 36.9 1.0 O 0:HOH8669 2.3 53.1 1.0 OP1 0:G2611 2.4 43.2 1.0 NA 0:NA8358 3.0 0.5 1.0 P 0:A2612 3.5 41.2 1.0 P 0:G2611 3.5 41.3 1.0 O3' 0:U2610 3.5 39.3 1.0 OP2 0:G2094 3.7 38.9 1.0 O 0:HOH3322 3.8 41.7 1.0 OP2 0:G2093 3.8 43.0 1.0 OP1 0:G2094 4.0 39.3 1.0 O B:HOH8529 4.1 47.7 1.0 OP2 0:A2612 4.2 41.7 1.0 P 0:G2094 4.3 40.7 1.0 O5' 0:A2612 4.4 41.1 1.0 O3' 0:G2611 4.4 40.4 1.0 O5' 0:G2611 4.4 40.3 1.0 C5' 0:G2611 4.4 40.4 1.0 OP2 0:G2611 4.6 40.2 1.0 O 0:HOH3293 4.6 46.6 1.0 C3' 0:G2611 4.8 39.5 1.0 O 0:HOH8684 4.8 53.0 1.0 C3' 0:U2610 4.8 41.3 1.0 O 0:HOH3119 4.9 58.3 1.0 O3' 0:G2093 4.9 37.1 1.0

Magnesium binding site 10 out of 117 in the The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of An Enhanced Oxazolidinone Inhibitor Bound to the 50S Ribosomal Subunit of H. Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:47.8 occ:1.00 OP1 0:U2615 2.0 38.4 1.0 OP1 0:G836 2.0 41.8 1.0 O 0:HOH3259 2.0 49.5 1.0 O 0:HOH4788 2.1 51.1 1.0 OE1 B:GLN230 2.2 48.8 1.0 O 0:HOH3349 2.3 52.1 1.0 CD B:GLN230 3.3 46.7 1.0 P 0:U2615 3.4 43.8 1.0 P 0:G836 3.4 42.3 1.0 O 0:HOH5970 3.8 75.4 1.0 CG B:GLN230 4.0 47.8 1.0 O 0:HOH3193 4.0 57.1 1.0 OP2 0:U2615 4.1 44.1 1.0 CB B:GLN230 4.1 48.2 1.0 OP2 0:G836 4.2 43.5 1.0 O5' 0:G836 4.2 41.5 1.0 C5' 0:G836 4.2 43.4 1.0 O 0:HOH7721 4.2 72.1 1.0 O3' 0:C2614 4.3 42.4 1.0 O5' 0:U2615 4.4 43.3 1.0 NE2 B:GLN230 4.4 44.9 1.0 O 0:HOH4937 4.4 65.5 1.0 O3' 0:U835 4.4 41.8 1.0 C3' 0:U835 4.5 43.5 1.0 O 0:HOH3529 4.6 64.3 1.0 CA B:GLN230 4.6 50.4 1.0 O B:GLN230 4.7 51.8 1.0 OP2 0:G2616 4.8 45.0 1.0 C5' 0:U2615 4.9 41.6 1.0 N2 0:G2616 4.9 46.7 1.0

J.Zhou, A.Bhattacharjee, S.Chen, Y.Chen, E.Duffy, J.Farmer, J.Goldberg, R.Hanselmann, J.A.Ippolito, R.Lou, A.Orbin, A.Oyelere, J.Salvino, D.Springer, J.Tran, D.Wang, Y.Wu, G.Johnson. Design at the Atomic Level: Design of Biaryloxazolidinones As Potent Orally Active Antibiotics. Bioorg.Med.Chem.Lett. V. 18 6175 2008.
ISSN: ISSN 0960-894X
PubMed: 18947996
DOI: 10.1016/J.BMCL.2008.10.011