Sodium in PDB 3cpw: The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw was solved by J.A.Ippolito, Z.K.Kanyo, D.Wang, F.J.Franceschi, P.B.Moore, T.A.Steitz, E.M.Duffy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.730, 298.580, 575.290, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Strontium	(Sr)	108 atoms
Magnesium	(Mg)	92 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 - 75;

Binding sites:

The binding sites of Sodium atom in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cpw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8501 b:46.4 occ:1.00 O 0:HOH5377 2.7 76.4 1.0 OP2 0:C1069 2.7 34.6 1.0 O6 0:G1087 2.9 42.5 1.0 N7 0:G1072 3.0 33.8 1.0 O6 0:G1072 3.0 36.2 1.0 O 0:HOH3651 3.1 35.8 1.0 O 0:HOH3618 3.2 48.6 1.0 C5 0:G1072 3.4 32.7 1.0 C6 0:G1072 3.5 33.1 1.0 O 0:HOH9565 3.7 40.3 1.0 C6 0:G1087 3.9 40.1 1.0 C8 0:G1072 4.0 33.0 1.0 P 0:C1069 4.1 38.7 1.0 C5' 0:C1068 4.3 41.8 1.0 O 0:HOH3980 4.5 38.6 1.0 N1 0:G1087 4.6 38.4 1.0 C3' 0:C1068 4.6 39.3 1.0 O3' 0:C1068 4.6 39.0 1.0 OP2 0:C1068 4.7 46.5 1.0 O 0:HOH4691 4.7 57.2 1.0 C4 0:G1072 4.7 34.2 1.0 O 0:HOH5737 4.7 55.2 1.0 N1 0:G1072 4.7 30.6 1.0 OP1 0:C1069 4.8 35.7 1.0 C5 0:G1087 4.9 40.9 1.0 N9 0:G1072 5.0 33.7 1.0

Sodium binding site 2 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8502 b:75.9 occ:1.00 O 0:HOH8223 2.6 69.0 1.0 OP2 0:U1120 2.9 51.5 1.0 N7 0:G1121 3.0 44.0 1.0 O 0:HOH6085 3.0 89.6 1.0 O6 0:G1121 3.1 43.4 1.0 O2' 0:G1119 3.1 45.7 1.0 O 0:HOH4962 3.1 75.5 1.0 O3' 0:G1119 3.2 47.0 1.0 O4 0:U1122 3.5 45.3 1.0 O 0:HOH4590 3.6 54.2 1.0 C5 0:G1121 3.6 42.5 1.0 P 0:U1120 3.7 49.8 1.0 C6 0:G1121 3.7 43.5 1.0 C2' 0:G1119 4.1 44.7 1.0 MG 0:MG8018 4.1 44.1 1.0 C8 0:G1121 4.1 45.0 1.0 C4 0:U1122 4.2 45.8 1.0 C3' 0:G1119 4.2 45.4 1.0 C5 0:U1122 4.3 44.4 1.0 C1' 0:G1119 4.5 41.8 1.0 O 0:HOH7305 4.5 70.6 1.0 OP1 0:U1120 4.7 51.8 1.0 O5' 0:U1120 4.8 46.6 1.0 C5' 0:U1120 4.9 46.8 1.0 C4 0:G1121 5.0 43.6 1.0

Sodium binding site 3 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8504 b:42.9 occ:1.00 O 0:HOH4510 2.5 45.6 1.0 O 0:HOH5118 2.5 40.8 1.0 N3 0:A630 2.9 46.9 1.0 O2' 0:A631 2.9 42.1 1.0 O2' 0:A630 3.0 45.1 1.0 OP2 0:A2074 3.2 47.8 1.0 O 0:HOH6184 3.2 41.9 1.0 C2' 0:A631 3.5 41.4 1.0 C1' 0:A630 3.5 45.9 1.0 N2 0:G2070 3.7 43.1 1.0 C2 0:A630 3.8 46.5 1.0 C4 0:A630 3.8 46.8 1.0 C2' 0:A630 3.9 45.8 1.0 C3' 0:A631 4.0 41.9 1.0 O3' 0:A630 4.0 43.4 1.0 N1 0:A629 4.1 40.3 1.0 N9 0:A630 4.1 46.8 1.0 C2 0:A629 4.2 40.5 1.0 O3' 0:A631 4.4 42.1 1.0 OP1 0:A632 4.5 41.7 1.0 C2 0:G2070 4.6 44.7 1.0 C3' 0:A630 4.6 43.5 1.0 P 0:A2074 4.6 46.2 1.0 O4' 0:A630 4.6 44.8 1.0 O 0:HOH9881 4.6 43.2 1.0 OP2 0:G2072 4.7 64.8 1.0 O 0:HOH3533 4.9 54.6 1.0 C1' 0:A631 4.9 40.0 1.0 P 0:A632 5.0 43.9 1.0 C6 0:A629 5.0 40.3 1.0

Sodium binding site 4 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8505 b:51.6 occ:1.00 N7 0:G2094 2.8 36.5 1.0 N1 0:A2649 2.9 40.0 1.0 N7 0:G2093 3.0 37.5 1.0 O 0:HOH9619 3.2 48.9 1.0 O2' 0:G2092 3.2 39.4 1.0 N3 0:G2092 3.2 37.2 1.0 O6 0:G2094 3.2 41.2 1.0 C2 0:A2649 3.3 37.2 1.0 O6 0:G2093 3.3 41.6 1.0 C5 0:G2093 3.4 38.3 1.0 N2 0:G2092 3.5 38.5 1.0 C6 0:G2093 3.6 39.8 1.0 C5 0:G2094 3.6 38.6 1.0 C2 0:G2092 3.7 37.8 1.0 C6 0:G2094 3.8 38.9 1.0 C8 0:G2093 3.9 37.6 1.0 C8 0:G2094 3.9 36.5 1.0 C6 0:A2649 4.0 39.6 1.0 C4 0:G2092 4.2 38.2 1.0 N6 0:A2649 4.3 40.4 1.0 C2' 0:G2092 4.4 36.7 1.0 C1' 0:G2092 4.4 37.8 1.0 C4 0:G2093 4.5 37.8 1.0 N6 0:A2612 4.5 42.1 1.0 N3 0:A2649 4.5 37.6 1.0 C6 0:A2612 4.5 44.0 1.0 N9 0:G2092 4.6 37.5 1.0 N1 0:A2612 4.7 43.3 1.0 N1 0:G2093 4.7 39.0 1.0 N9 0:G2093 4.7 36.1 1.0 N1 0:G2092 4.8 35.9 1.0 C4 0:G2094 4.9 37.8 1.0 O3' 0:G2092 4.9 37.0 1.0

Sodium binding site 5 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8506 b:66.1 occ:1.00 O2 0:C40 2.7 66.7 1.0 O2' 0:C40 2.7 66.2 1.0 O2 0:C443 2.8 70.2 1.0 C2' 0:C40 3.3 66.0 1.0 C1' 0:C40 3.4 66.9 1.0 N1 0:A442 3.4 69.9 1.0 O4' 0:G41 3.4 59.6 1.0 C2 0:C40 3.7 67.5 1.0 C2 0:C443 3.8 69.4 1.0 C2 0:A442 3.9 69.2 1.0 N2 0:G39 4.0 56.5 1.0 N1 0:C40 4.1 67.6 1.0 C1' 0:G41 4.3 58.3 1.0 O 0:HOH6262 4.3 53.5 1.0 C6 0:A442 4.3 69.3 1.0 N3 0:C443 4.4 68.7 1.0 C4' 0:G41 4.5 58.8 1.0 O4' 0:C40 4.5 66.9 1.0 N6 0:A442 4.6 69.3 1.0 C5' 0:G41 4.6 59.5 1.0 N9 0:G41 4.6 57.5 1.0 N1 0:C443 4.6 69.4 1.0 C1' 0:C443 4.6 69.0 1.0 C2 0:G39 4.6 58.0 1.0 O 0:HOH7343 4.7 68.1 1.0 C3' 0:C40 4.8 65.1 1.0 N1 0:G39 4.9 57.1 1.0 N3 0:C40 5.0 68.2 1.0 C8 0:G41 5.0 56.8 1.0

Sodium binding site 6 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8507 b:51.6 occ:1.00 O2 0:U1724 2.3 65.9 1.0 O2 0:C1394 2.5 39.0 1.0 O4 0:U1432 2.5 49.0 1.0 O 0:HOH3854 2.8 49.5 1.0 SR 0:SR8962 3.0 0.9 1.0 O6 0:G1433 3.3 51.8 1.0 C2 0:U1724 3.5 63.7 1.0 C2 0:C1394 3.6 41.0 1.0 C4 0:U1432 3.7 45.9 1.0 O2' 0:C1394 3.9 40.3 1.0 C6 0:G1433 3.9 49.5 1.0 C2' 0:C1394 4.0 42.2 1.0 O 0:HOH7509 4.1 75.9 1.0 O2' 0:U1724 4.2 63.0 1.0 N3 0:U1724 4.3 62.6 1.0 N1 0:G1433 4.3 50.1 1.0 N3 0:U1432 4.4 44.0 1.0 C1' 0:C1394 4.4 40.9 1.0 N3 0:C1394 4.4 39.3 1.0 O 0:HOH5246 4.4 87.4 1.0 N1 0:C1394 4.5 41.9 1.0 C1' 0:U1724 4.5 61.4 1.0 N1 0:U1724 4.5 63.1 1.0 C2' 0:U1724 4.5 60.9 1.0 C5 0:G1433 4.8 48.1 1.0 C5 0:U1432 4.8 44.4 1.0 O 0:HOH5868 4.9 51.7 1.0

Sodium binding site 7 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8508 b:55.8 occ:1.00 O 0:HOH4920 2.8 49.3 1.0 O6 0:G2579 2.9 37.8 1.0 N7 0:G2578 3.0 41.8 1.0 N7 0:G2579 3.1 37.6 1.0 O4' 0:A2577 3.1 46.0 1.0 N3 0:A2577 3.2 41.9 1.0 O6 0:G2578 3.4 42.4 1.0 C5 0:G2578 3.5 42.9 1.0 C6 0:G2579 3.5 37.8 1.0 O 0:HOH8169 3.6 81.0 1.0 C5 0:G2579 3.6 39.0 1.0 C6 0:G2578 3.6 42.6 1.0 C1' 0:A2577 3.7 45.5 1.0 C8 0:G2578 3.9 41.4 1.0 C4' 0:A2577 3.9 46.4 1.0 C2 0:A2577 4.0 41.3 1.0 C4 0:A2577 4.0 42.2 1.0 C8 0:G2579 4.3 39.4 1.0 N9 0:A2577 4.3 43.4 1.0 C4 0:G2578 4.5 42.0 1.0 O 0:HOH6363 4.6 65.0 1.0 N4 0:C2556 4.7 45.5 1.0 N9 0:G2578 4.7 41.6 1.0 O 0:HOH6680 4.8 76.7 1.0 N1 0:G2578 4.8 41.2 1.0 O3' 0:A2577 4.8 45.6 1.0 C3' 0:A2577 4.9 46.5 1.0 N1 0:G2579 4.9 37.8 1.0 N3 0:U2554 4.9 40.0 1.0 C5' 0:A2577 4.9 45.8 1.0 C4 0:G2579 4.9 40.2 1.0

Sodium binding site 8 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8509 b:83.9 occ:1.00 O 0:HOH5068 2.7 54.4 1.0 O 0:HOH4019 3.0 49.9 1.0 N7 0:G2524 3.2 52.6 1.0 O 0:HOH6754 3.3 67.1 1.0 O6 0:G2525 3.3 57.6 1.0 O 0:HOH9673 3.5 63.0 1.0 OP2 0:G2524 3.6 54.8 1.0 C5 0:U2523 3.7 52.7 1.0 C8 0:G2524 3.8 52.5 1.0 C6 0:U2523 4.0 53.2 1.0 O 0:HOH4059 4.1 31.6 1.0 C4 0:U2523 4.1 54.0 1.0 OP2 0:U2523 4.2 60.1 1.0 C6 0:G2525 4.2 57.2 1.0 C5 0:G2524 4.4 51.8 1.0 O4 0:U2523 4.5 55.6 1.0 O5' 0:U2523 4.5 59.3 1.0 N1 0:U2523 4.6 54.6 1.0 N3 0:U2523 4.7 53.9 1.0 O6 0:G2524 4.8 50.7 1.0 C3' 0:U2523 4.8 55.8 1.0 N7 0:G2525 4.8 57.4 1.0 C5 0:G2525 4.8 57.4 1.0 P 0:G2524 5.0 57.0 1.0 C2 0:U2523 5.0 54.6 1.0 C6 0:G2524 5.0 51.1 1.0

Sodium binding site 9 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8511 b:71.5 occ:1.00 O 0:HOH4266 2.5 66.0 1.0 O 0:HOH5527 2.5 59.1 1.0 O 0:HOH3405 2.6 40.6 1.0 O 0:HOH5478 2.8 55.3 1.0 O6 0:G2399 2.9 53.0 1.0 O 0:HOH6449 3.1 49.1 1.0 N7 0:G2399 3.2 51.4 1.0 C6 0:G2399 3.6 52.2 1.0 C5 0:G2399 3.7 51.7 1.0 O 0:HOH6896 3.9 91.1 1.0 OP2 0:A2398 4.0 53.8 1.0 O 0:HOH3833 4.1 43.3 1.0 O 0:HOH6672 4.1 47.3 1.0 O6 0:G2400 4.1 50.5 1.0 O4 0:U2389 4.4 48.9 1.0 C8 0:G2399 4.4 50.7 1.0 N7 0:G2400 4.5 50.6 1.0 N3 0:U2389 4.7 48.3 1.0 C6 0:G2400 4.8 50.1 1.0 C5 0:G2400 4.9 50.0 1.0 N1 0:G2399 4.9 51.5 1.0

Sodium binding site 10 out of 75 in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula 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 the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8512 b:72.5 occ:1.00 O 0:HOH3579 2.6 59.9 1.0 O2' 0:U2607 2.9 44.9 1.0 O 0:HOH4300 2.9 57.2 1.0 OP1 0:U2541 3.0 63.2 1.0 O 0:HOH9955 3.0 64.5 1.0 OP1 0:U2610 3.3 40.7 1.0 OP2 0:U2541 3.5 61.6 1.0 O 0:HOH9808 3.6 45.5 1.0 CZ3 B:TRP242 3.6 39.3 1.0 P 0:U2541 3.7 60.9 1.0 O 0:HOH8224 3.7 37.8 1.0 OP2 0:C2608 3.9 40.7 1.0 NA 0:NA8549 4.1 75.4 1.0 O 0:HOH9870 4.2 43.2 1.0 O 0:HOH8097 4.3 61.6 1.0 C2' 0:U2607 4.3 44.5 1.0 O2 0:U2607 4.3 52.0 1.0 CE3 B:TRP242 4.4 38.0 1.0 CH2 B:TRP242 4.4 38.0 1.0 O 0:HOH7858 4.6 65.0 1.0 P 0:U2610 4.7 41.2 1.0 P 0:C2608 4.7 42.8 1.0 O3' 0:U2607 4.8 44.2 1.0 O3' 0:G2540 4.9 62.5 1.0 O5' 0:U2541 4.9 58.6 1.0 OP1 0:C2608 4.9 45.5 1.0 O 0:HOH9816 4.9 52.7 1.0

J.A.Ippolito, Z.K.Kanyo, D.Wang, F.J.Franceschi, P.B.Moore, T.A.Steitz, E.M.Duffy. Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit J.Med.Chem. V. 51 3353 2008.
ISSN: ISSN 0022-2623
PubMed: 18494460
DOI: 10.1021/JM800379D