Sodium 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
Magnesium	(Mg)	117 atoms
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 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 - 86;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 86 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 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 Sodium with other atoms in the Na 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:Na8301 b:59.0 occ:1.00 OP2 0:C1069 2.2 41.7 1.0 O 0:HOH5904 2.5 87.1 1.0 N7 0:G1072 2.7 45.9 1.0 O 0:HOH4135 2.9 53.7 1.0 O 0:HOH4165 3.2 77.0 1.0 O6 0:G1087 3.2 50.3 1.0 O6 0:G1072 3.2 47.6 1.0 C5 0:G1072 3.4 45.4 1.0 P 0:C1069 3.6 42.6 1.0 C6 0:G1072 3.6 46.8 1.0 C8 0:G1072 3.7 45.8 1.0 O 0:HOH3066 3.7 33.7 1.0 C6 0:G1087 4.2 49.9 1.0 O3' 0:C1068 4.2 42.2 1.0 C5' 0:C1068 4.2 48.6 1.0 C3' 0:C1068 4.2 44.3 1.0 O 0:HOH4487 4.3 46.4 1.0 OP1 0:C1069 4.4 40.0 1.0 C4 0:G1072 4.6 44.6 1.0 O 0:HOH5212 4.6 86.2 1.0 O5' 0:C1069 4.6 37.1 1.0 N9 0:G1072 4.7 44.6 1.0 N1 0:G1087 4.8 48.2 1.0 C4' 0:C1068 4.8 44.9 1.0 OP2 0:C1068 4.9 53.0 1.0 N1 0:G1072 5.0 46.1 1.0

Sodium binding site 2 out of 86 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 Sodium with other atoms in the Na 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:Na8302 b:55.4 occ:1.00 O2' 0:G1119 2.7 49.5 1.0 O 0:HOH6602 2.8 89.6 1.0 OP2 0:U1120 2.8 49.7 1.0 O3' 0:G1119 2.9 48.4 1.0 O 0:HOH5113 3.0 67.0 1.0 O6 0:G1121 3.0 51.2 1.0 O 0:HOH8688 3.1 72.5 1.0 N7 0:G1121 3.2 49.3 1.0 O 0:HOH5477 3.3 56.7 1.0 P 0:U1120 3.4 51.0 1.0 MG 0:MG8025 3.6 59.1 1.0 C6 0:G1121 3.7 50.5 1.0 C2' 0:G1119 3.7 49.0 1.0 O4 0:U1122 3.8 54.1 1.0 C5 0:G1121 3.8 49.6 1.0 C3' 0:G1119 3.8 48.9 1.0 OP1 0:U1120 4.2 52.4 1.0 C1' 0:G1119 4.3 48.4 1.0 O 0:HOH7830 4.3 84.5 1.0 C8 0:G1121 4.4 50.0 1.0 C4 0:U1122 4.5 53.7 1.0 O5' 0:U1120 4.7 49.6 1.0 C5 0:U1122 4.8 54.4 1.0 C5' 0:U1120 4.9 52.5 1.0 OP2 0:G1121 4.9 54.8 1.0

Sodium binding site 3 out of 86 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 Sodium with other atoms in the Na 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:Na8303 b:55.7 occ:1.00 O4 0:U904 3.0 46.1 1.0 OP2 0:A643 3.0 45.1 1.0 OP1 0:G644 3.1 42.8 1.0 OP1 0:G1354 3.1 46.4 1.0 NH2 K:ARG8 3.3 46.9 1.0 O5' 0:A643 3.5 45.5 1.0 P 0:A643 3.5 47.3 1.0 O 0:HOH4225 3.7 64.0 1.0 OP1 0:C1353 3.8 65.3 1.0 OP1 0:A643 3.8 49.0 1.0 C4 0:U904 3.9 44.3 1.0 O 0:HOH5532 4.0 0.3 1.0 O 0:HOH3417 4.1 49.8 1.0 N3 0:U904 4.1 44.1 1.0 P 0:G1354 4.1 47.5 1.0 CZ K:ARG8 4.3 45.9 1.0 P 0:G644 4.3 44.4 1.0 C5' 0:A643 4.4 44.2 1.0 OP2 0:G1354 4.4 46.9 1.0 C3' 0:A643 4.6 41.5 1.0 O3' 0:C1353 4.7 49.3 1.0 O3' 0:A643 4.8 43.2 1.0 P 0:C1353 4.9 66.1 1.0 OP2 0:G644 4.9 41.2 1.0 NE K:ARG8 4.9 46.3 1.0 N6 0:A1355 4.9 42.5 1.0

Sodium binding site 4 out of 86 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 Sodium with other atoms in the Na 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:Na8305 b:42.1 occ:1.00 O 0:HOH5035 2.2 65.4 1.0 O 0:HOH5632 2.4 51.5 1.0 O2' 0:A630 2.5 44.5 1.0 O 0:HOH6699 2.6 67.7 1.0 N3 0:A630 2.6 44.4 1.0 O2' 0:A631 2.8 39.7 1.0 C2 0:A630 3.4 45.1 1.0 C2' 0:A631 3.6 40.3 1.0 OP2 0:A2074 3.6 47.5 1.0 C1' 0:A630 3.6 43.9 1.0 C2' 0:A630 3.6 43.1 1.0 C4 0:A630 3.7 45.8 1.0 OP1 0:A632 4.0 46.4 1.0 C3' 0:A631 4.0 39.5 1.0 N2 0:G2070 4.1 43.2 1.0 N9 0:A630 4.1 45.5 1.0 O3' 0:A630 4.1 41.3 1.0 O3' 0:A631 4.2 41.5 1.0 OP2 0:G2072 4.4 57.4 1.0 O 0:HOH3395 4.4 24.6 1.0 O 0:HOH4051 4.5 74.0 1.0 P 0:A632 4.5 44.9 1.0 C3' 0:A630 4.5 41.2 1.0 N1 0:A629 4.7 40.7 1.0 N1 0:A630 4.7 45.3 1.0 OP2 0:A632 4.7 46.2 1.0 C2 0:G2070 4.8 42.2 1.0 C2 0:A629 4.8 42.1 1.0 O4' 0:A630 4.8 45.6 1.0 C2 0:A628 4.9 46.0 1.0 C5 0:A630 5.0 44.7 1.0

Sodium binding site 5 out of 86 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 Sodium with other atoms in the Na 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:Na8306 b:59.1 occ:1.00 N7 0:G2093 2.8 40.3 1.0 N7 0:G2094 2.8 43.2 1.0 N1 0:A2649 3.0 55.2 1.0 C5 0:G2093 3.2 41.0 1.0 N3 0:G2092 3.3 50.2 1.0 O6 0:G2094 3.3 41.7 1.0 O2' 0:G2092 3.3 48.1 1.0 O 0:HOH3119 3.3 58.3 1.0 O6 0:G2093 3.4 43.7 1.0 C2 0:A2649 3.4 54.6 1.0 C6 0:G2093 3.5 42.9 1.0 C5 0:G2094 3.5 43.0 1.0 N2 0:G2092 3.6 50.2 1.0 C8 0:G2093 3.6 38.1 1.0 C2 0:G2092 3.7 50.4 1.0 C6 0:G2094 3.7 42.0 1.0 C8 0:G2094 3.8 43.3 1.0 C6 0:A2649 4.2 55.5 1.0 C4 0:G2092 4.2 49.8 1.0 C4 0:G2093 4.2 39.4 1.0 N6 0:A2612 4.2 39.0 1.0 N9 0:G2093 4.4 39.7 1.0 C2' 0:G2092 4.4 46.2 1.0 C1' 0:G2092 4.4 47.2 1.0 N6 0:A2649 4.5 56.6 1.0 C6 0:A2612 4.5 43.2 1.0 N1 0:G2093 4.6 42.4 1.0 N9 0:G2092 4.7 49.6 1.0 N3 0:A2649 4.7 53.7 1.0 C4 0:G2094 4.8 43.3 1.0 N1 0:G2092 4.8 49.6 1.0 O3' 0:G2092 4.9 44.3 1.0 N9 0:G2094 4.9 42.6 1.0 N1 0:A2612 4.9 44.1 1.0

Sodium binding site 6 out of 86 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 Sodium with other atoms in the Na 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:Na8307 b:71.7 occ:1.00 O2' 0:C40 2.7 69.0 1.0 O2 0:C40 2.8 67.4 1.0 O2 0:C443 2.9 77.1 1.0 O4' 0:G41 3.2 62.8 1.0 C2' 0:C40 3.3 69.8 1.0 N1 0:A442 3.3 73.8 1.0 C1' 0:C40 3.6 68.9 1.0 C2 0:A442 3.7 73.3 1.0 C2 0:C443 3.8 76.2 1.0 C2 0:C40 3.8 68.8 1.0 N2 0:G39 4.0 63.2 1.0 C1' 0:G41 4.1 62.8 1.0 N1 0:C40 4.2 68.9 1.0 O 0:HOH6778 4.3 78.9 1.0 C4' 0:G41 4.3 63.8 1.0 C6 0:A442 4.4 74.1 1.0 C5' 0:G41 4.4 64.3 1.0 N9 0:G41 4.4 64.3 1.0 N3 0:C443 4.5 76.7 1.0 C1' 0:C443 4.5 75.6 1.0 N1 0:C443 4.5 75.7 1.0 C2 0:G39 4.6 62.7 1.0 N6 0:A442 4.6 74.9 1.0 N1 0:G39 4.7 63.4 1.0 C8 0:G41 4.8 63.8 1.0 O 0:HOH7874 4.8 74.3 1.0 C3' 0:C40 4.8 70.0 1.0 O4' 0:C40 4.8 68.8 1.0 O5' 0:G41 4.8 67.2 1.0 N3 0:A442 4.9 73.6 1.0

Sodium binding site 7 out of 86 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 Sodium with other atoms in the Na 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:Na8308 b:77.3 occ:1.00 O2 0:U1724 2.3 59.4 1.0 O2 0:C1394 2.4 59.2 1.0 O 0:HOH4370 2.5 58.8 1.0 O4 0:U1432 3.0 56.2 1.0 O 0:HOH8848 3.5 75.6 1.0 C2 0:U1724 3.5 57.5 1.0 C2 0:C1394 3.6 58.8 1.0 O2' 0:C1394 3.6 56.0 1.0 C2' 0:C1394 3.9 56.5 1.0 O6 0:G1433 4.0 62.6 1.0 O2' 0:U1724 4.1 54.9 1.0 O 0:HOH6384 4.1 84.0 1.0 C1' 0:U1724 4.2 55.4 1.0 C4 0:U1432 4.2 56.6 1.0 C1' 0:C1394 4.2 57.2 1.0 O 0:HOH3284 4.3 58.9 1.0 N1 0:U1724 4.4 57.1 1.0 N1 0:C1394 4.4 58.5 1.0 C2' 0:U1724 4.4 54.2 1.0 OP2 0:U1722 4.5 58.0 1.0 N3 0:C1394 4.5 58.4 1.0 N3 0:U1724 4.5 57.9 1.0 C6 0:G1433 4.6 60.2 1.0 N3 0:U1432 4.7 57.1 1.0 O2' 0:C1725 4.8 51.9 1.0 N1 0:G1433 4.9 60.4 1.0

Sodium binding site 8 out of 86 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 Sodium with other atoms in the Na 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:Na8310 b:46.1 occ:1.00 O 0:HOH5437 2.6 61.2 1.0 O6 0:G2579 2.8 59.1 1.0 O4' 0:A2577 3.0 57.6 1.0 N7 0:G2579 3.0 59.0 1.0 N3 0:A2577 3.1 52.8 1.0 N7 0:G2578 3.3 61.9 1.0 C6 0:G2579 3.4 59.8 1.0 O6 0:G2578 3.4 62.1 1.0 C5 0:G2579 3.6 59.0 1.0 O 0:HOH8634 3.6 98.2 1.0 C5 0:G2578 3.6 61.6 1.0 C1' 0:A2577 3.7 55.2 1.0 C6 0:G2578 3.7 61.8 1.0 O 0:HOH7194 3.8 80.7 1.0 C4 0:A2577 3.9 51.4 1.0 C2 0:A2577 4.0 52.4 1.0 C4' 0:A2577 4.0 58.4 1.0 N9 0:A2577 4.1 52.1 1.0 C8 0:G2578 4.2 60.0 1.0 C8 0:G2579 4.2 57.5 1.0 C4 0:G2578 4.7 61.0 1.0 N4 0:C2556 4.7 53.8 1.0 N1 0:G2578 4.8 63.1 1.0 N1 0:G2579 4.8 59.6 1.0 N3 0:U2554 4.9 51.0 1.0 C4 0:G2579 4.9 58.0 1.0 O3' 0:A2577 4.9 59.5 1.0 C5' 0:A2577 4.9 59.3 1.0 C3' 0:A2577 4.9 58.4 1.0 N9 0:G2578 4.9 59.5 1.0 O6 0:G2580 4.9 59.3 1.0 O 0:HOH6882 5.0 86.2 1.0 C2' 0:A2577 5.0 56.5 1.0

Sodium binding site 9 out of 86 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 Sodium with other atoms in the Na 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:Na8311 b:73.9 occ:1.00 O 0:HOH4525 2.3 47.7 1.0 O 0:HOH5585 2.4 69.7 1.0 O6 0:G2525 2.5 52.0 1.0 N7 0:G2524 3.1 45.2 1.0 O 0:HOH3172 3.5 86.3 1.0 C6 0:G2525 3.6 53.5 1.0 O 0:HOH4569 3.7 56.2 1.0 C5 0:U2523 3.8 49.7 1.0 O 0:HOH7273 3.9 76.4 1.0 O6 0:G2524 4.0 41.4 1.0 C4 0:U2523 4.1 50.5 1.0 C8 0:G2524 4.1 46.4 1.0 C5 0:G2524 4.1 43.9 1.0 O4 0:U2523 4.2 52.8 1.0 O2' 0:C2493 4.4 50.5 1.0 C6 0:U2523 4.4 49.2 1.0 C6 0:G2524 4.4 43.4 1.0 N1 0:G2525 4.5 53.4 1.0 C5 0:G2525 4.5 51.8 1.0 C2' 0:C2493 4.6 51.3 1.0 OP2 0:G2524 4.7 56.8 1.0 N7 0:G2525 4.7 51.4 1.0 OP2 0:U2523 4.7 51.8 1.0 N3 0:U2523 4.8 51.0 1.0

Sodium binding site 10 out of 86 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 Sodium with other atoms in the Na 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:Na8313 b:89.3 occ:1.00 O 0:HOH6050 2.4 85.0 1.0 O 0:HOH4783 2.4 69.8 1.0 O 0:HOH3923 2.5 61.4 1.0 O6 0:G2399 2.7 55.8 1.0 O 0:HOH6973 2.9 82.8 1.0 O 0:HOH7408 3.2 88.8 1.0 O 0:HOH6001 3.2 67.1 1.0 N7 0:G2399 3.4 56.8 1.0 C6 0:G2399 3.5 55.0 1.0 C5 0:G2399 3.8 55.9 1.0 O 0:HOH4352 3.8 62.4 1.0 O4 0:U2389 4.0 55.1 1.0 OP2 0:A2398 4.0 64.2 1.0 O6 0:G2400 4.1 50.1 1.0 O 0:HOH7187 4.2 81.9 1.0 N3 0:U2389 4.6 52.5 1.0 C8 0:G2399 4.7 56.3 1.0 N7 0:G2400 4.7 51.4 1.0 C4 0:U2389 4.7 53.1 1.0 N1 0:G2399 4.8 53.3 1.0 C6 0:G2400 4.8 49.6 1.0 O2 0:U2390 5.0 52.8 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