Magnesium 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
Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 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 - 92;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 92 binding sites of Magnesium where determined in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8001 b:31.7 occ:1.00 OP2 0:C2533 2.1 57.9 1.0 O 0:HOH8209 2.3 41.5 1.0 O 0:HOH4056 2.4 52.3 1.0 OP2 0:A2483 2.6 53.2 1.0 OP2 0:C2534 2.6 51.5 1.0 O2' 0:A2532 3.0 57.8 1.0 P 0:C2533 3.4 56.0 1.0 O 0:HOH9666 3.5 68.9 1.0 O3' 0:G2482 3.5 51.8 1.0 O3' 0:A2532 3.6 55.0 1.0 P 0:A2483 3.7 51.6 1.0 OP2 0:U2484 3.7 62.8 1.0 P 0:C2534 4.0 53.8 1.0 C2' 0:A2532 4.2 56.5 1.0 O5' 0:C2533 4.2 52.6 1.0 O 0:HOH4744 4.3 31.7 1.0 O 0:HOH6758 4.3 97.9 1.0 C3' 0:A2532 4.4 55.3 1.0 O2' 0:G2482 4.5 51.0 1.0 OP1 0:C2533 4.6 57.0 1.0 OP1 0:C2534 4.6 53.0 1.0 C5' 0:A2483 4.7 52.2 1.0 O5' 0:A2483 4.7 53.5 1.0 OP2 0:A2485 4.7 61.9 1.0 O3' 0:C2533 4.7 52.0 1.0 OP1 0:A2483 4.8 50.8 1.0 C3' 0:G2482 4.9 51.0 1.0 O 0:HOH7831 4.9 76.6 1.0 C3' 0:C2533 4.9 50.3 1.0

Magnesium binding site 2 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8002 b:82.7 occ:1.00 O 0:HOH8188 2.1 33.4 1.0 OP1 0:A2483 2.1 50.8 1.0 O6 0:G627 2.2 41.9 1.0 O 0:HOH8187 2.8 56.6 1.0 O 0:HOH7464 3.0 69.6 1.0 O 0:HOH4744 3.0 31.7 1.0 OP1 0:C2534 3.1 53.0 1.0 C6 0:G627 3.4 40.7 1.0 P 0:A2483 3.5 51.6 1.0 O 0:HOH6268 3.5 68.2 1.0 O2' 0:U625 3.7 41.6 1.0 O 0:HOH9745 3.8 56.5 1.0 O 0:HOH3972 4.0 57.2 1.0 OP2 0:A2483 4.1 53.2 1.0 C5 0:G627 4.2 40.8 1.0 O5' 0:A2483 4.3 53.5 1.0 N1 0:G627 4.4 41.6 1.0 O 0:HOH3573 4.4 50.0 1.0 N7 0:G627 4.4 38.7 1.0 O4 0:U626 4.5 42.6 1.0 P 0:C2534 4.6 53.8 1.0 O3' 0:G2482 4.6 51.8 1.0 OP2 0:U2535 4.6 59.6 1.0 C5 0:U626 4.7 42.5 1.0 C3' 0:G2482 4.9 51.0 1.0 C2' 0:U625 4.9 39.1 1.0 C4 0:U626 4.9 42.9 1.0

Magnesium binding site 3 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8003 b:35.6 occ:1.00 O 0:HOH4101 2.1 47.5 1.0 O A:HOH8980 2.1 30.8 1.0 OP1 0:A2624 2.2 37.2 1.0 OP2 0:A876 2.2 34.3 1.0 OP2 0:G877 2.3 32.1 1.0 O A:HOH9011 2.5 41.8 1.0 P 0:A876 3.6 36.9 1.0 P 0:G877 3.6 36.7 1.0 P 0:A2624 3.7 36.6 1.0 O 0:HOH6664 4.0 48.6 1.0 O A:ALA193 4.0 39.9 1.0 OD1 A:ASN195 4.0 35.1 1.0 OP1 0:G877 4.1 37.8 1.0 O3' 0:A875 4.1 35.8 1.0 O5' 0:A876 4.1 33.4 1.0 O A:HOH9096 4.2 71.6 1.0 O 0:HOH4895 4.3 59.6 1.0 O3' 0:G2623 4.3 37.9 1.0 OP2 0:A2624 4.5 38.8 1.0 O3' 0:A876 4.5 36.4 1.0 O5' 0:A2624 4.6 39.1 1.0 C5' 0:A876 4.7 35.8 1.0 O 0:HOH9517 4.7 25.2 1.0 O A:HOH9022 4.7 55.9 1.0 O5' 0:G877 4.7 34.4 1.0 C5' 0:A2624 4.7 39.5 1.0 OP1 0:A876 4.8 37.9 1.0 CG A:ASN195 4.9 33.8 1.0 C3' 0:A876 5.0 36.3 1.0

Magnesium binding site 4 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8004 b:36.2 occ:1.00 O 0:HOH3235 2.1 37.2 1.0 O 0:HOH4215 2.1 37.6 1.0 O 0:HOH8194 2.1 39.9 1.0 OP1 0:A459 2.1 37.4 1.0 O6 0:G456 2.2 46.0 1.0 O 0:HOH9543 2.2 37.1 1.0 C6 0:G456 3.2 47.2 1.0 P 0:A459 3.5 38.7 1.0 O 0:HOH6351 3.7 83.6 1.0 C5 0:G456 4.0 46.7 1.0 N7 0:G456 4.0 45.6 1.0 O 0:HOH3958 4.1 53.1 1.0 O 0:HOH4139 4.1 43.1 1.0 OP2 0:A459 4.2 40.6 1.0 O5' 0:A459 4.2 38.7 1.0 NZ C:LYS85 4.3 31.4 1.0 C5' 0:A459 4.3 40.4 1.0 N1 0:G456 4.4 46.4 1.0 CE C:LYS85 4.4 32.0 1.0 N7 0:A455 4.4 39.1 1.0 OP2 0:A455 4.4 41.6 1.0 OP1 0:A460 4.5 41.5 1.0 O 0:HOH9809 4.6 27.7 1.0 O3' 0:G458 4.6 38.1 1.0 OP1 0:A477 4.7 39.3 1.0 C5' 0:U454 4.8 37.0 1.0 CD C:LYS85 4.8 32.7 1.0 N6 0:A455 5.0 40.4 1.0

Magnesium binding site 5 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8005 b:39.2 occ:1.00 OP1 0:A1836 2.1 36.4 1.0 OP1 0:U1838 2.1 37.4 1.0 OP2 0:A1839 2.1 39.6 1.0 O 0:HOH8210 2.2 54.5 1.0 O 0:HOH8211 2.2 47.8 1.0 O 0:HOH4053 2.3 35.0 1.0 P 0:A1836 3.5 34.6 1.0 P 0:U1838 3.5 37.1 1.0 P 0:A1839 3.6 37.9 1.0 O 0:HOH5899 3.8 47.6 1.0 C2' 0:U1835 4.2 37.9 1.0 O5' 0:A1839 4.2 38.1 1.0 O 0:HOH9980 4.2 53.4 1.0 O5' 0:A1836 4.3 39.1 1.0 O 0:HOH5957 4.3 39.7 1.0 OP2 0:A1836 4.3 36.2 1.0 O5' 0:U1838 4.3 38.6 1.0 OP2 0:U1838 4.3 37.0 1.0 N7 0:A1839 4.4 35.6 1.0 O3' 0:U1835 4.4 36.4 1.0 O3' 0:U1838 4.4 40.9 1.0 C3' 0:G1837 4.4 41.1 1.0 O 0:HOH3100 4.5 42.8 1.0 C3' 0:U1835 4.5 36.8 1.0 C3' 0:U1838 4.5 38.7 1.0 O3' 0:G1837 4.5 39.0 1.0 O2' 0:U1835 4.5 38.8 1.0 C8 0:A1839 4.5 37.5 1.0 C5' 0:U1838 4.5 36.9 1.0 OP1 0:A1839 4.6 41.3 1.0 OP2 0:G1837 4.7 37.0 1.0 O 0:HOH8280 4.7 47.5 1.0

Magnesium binding site 6 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8006 b:27.5 occ:1.00 O 0:HOH4068 2.2 44.0 1.0 OP1 0:A2465 2.2 50.9 1.0 O 0:HOH8281 2.2 62.8 1.0 OP1 0:C2464 2.3 46.6 1.0 OP1 0:U919 2.3 40.3 1.0 O 0:HOH8203 2.6 39.0 1.0 P 0:U919 3.3 39.9 1.0 P 0:A2465 3.4 50.9 1.0 OP2 0:U919 3.4 39.8 1.0 P 0:C2464 3.5 46.7 1.0 OP2 0:A2465 3.8 54.5 1.0 O5' 0:U919 4.1 39.7 1.0 O5' 0:C2464 4.1 48.5 1.0 O 0:HOH3016 4.1 63.6 1.0 O5' 0:A2465 4.1 50.7 1.0 O 0:HOH6281 4.2 55.6 1.0 OP2 0:C2464 4.2 49.0 1.0 C5' 0:C2464 4.2 50.8 1.0 O 0:HOH9920 4.3 57.3 1.0 O 0:HOH3794 4.5 40.7 1.0 O3' 0:G918 4.6 41.6 1.0 OP1 0:G2466 4.6 53.3 1.0 C5' 0:U919 4.6 39.9 1.0 O 0:HOH3376 4.7 68.8 1.0 O3' 0:C2464 4.7 51.6 1.0 O3' 0:A2463 4.7 48.8 1.0 C3' 0:A2465 4.8 51.2 1.0 OP1 0:G2293 4.9 55.2 1.0 C3' 0:C2464 5.0 51.8 1.0 C5' 0:G2293 5.0 52.5 1.0

Magnesium binding site 7 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8007 b:53.4 occ:1.00 OP1 0:G2611 2.5 49.1 1.0 O 0:HOH8204 2.7 46.0 1.0 OP1 0:A2612 2.7 43.5 1.0 O 0:HOH4172 3.0 59.4 1.0 O 0:HOH9810 3.0 45.4 1.0 O 0:HOH8205 3.1 57.2 1.0 NA 0:NA8549 3.2 75.4 1.0 O3' 0:U2610 3.3 45.0 1.0 P 0:G2611 3.5 47.1 1.0 OP1 0:G2094 3.8 38.9 1.0 O 0:HOH8219 4.1 59.5 1.0 P 0:A2612 4.1 42.5 1.0 O 0:HOH7786 4.2 26.6 1.0 C5' 0:G2611 4.2 41.1 1.0 O 0:HOH9938 4.2 41.5 1.0 OP2 0:G2094 4.3 37.8 1.0 O5' 0:G2611 4.4 43.0 1.0 C4' 0:U2610 4.4 41.2 1.0 C3' 0:U2610 4.4 41.1 1.0 P 0:G2094 4.5 36.9 1.0 OP2 0:A2612 4.7 45.0 1.0 C5' 0:U2610 4.7 39.0 1.0 OP2 0:G2611 4.7 43.9 1.0 OP2 0:G2093 4.8 37.9 1.0 O3' 0:G2611 4.8 42.3 1.0 C3' 0:G2611 4.8 41.1 1.0 O2' 0:U2610 5.0 40.6 1.0

Magnesium binding site 8 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8008 b:34.3 occ:1.00 O 0:HOH3101 2.1 31.6 1.0 O 0:HOH8282 2.2 61.9 1.0 OP1 0:G28 2.3 43.0 1.0 O 0:HOH9535 2.3 26.9 1.0 O 0:HOH3678 2.7 45.6 1.0 O 0:HOH4085 2.7 28.1 1.0 P 0:G28 3.5 43.2 1.0 OP1 0:U1304 3.8 42.1 1.0 O 0:HOH3936 3.8 65.9 1.0 O3' 0:U27 3.8 41.3 1.0 OP2 0:G1344 3.9 51.6 1.0 OP2 0:G28 4.2 44.7 1.0 OP1 0:C1343 4.2 47.4 1.0 O 0:HOH3572 4.6 34.6 1.0 P 0:G1344 4.7 51.9 1.0 O5' 0:G28 4.7 43.0 1.0 OP1 0:G1344 4.8 53.7 1.0 OP1 0:C1305 4.8 36.4 1.0 O 0:HOH4446 4.9 67.5 1.0 OP2 0:C1305 4.9 39.9 1.0

Magnesium binding site 9 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8009 b:23.6 occ:1.00 O 0:HOH9517 1.9 25.2 1.0 OP1 0:G877 2.2 37.8 1.0 OP1 0:G2623 2.2 43.3 1.0 O A:HOH9103 2.2 38.5 1.0 O 0:HOH4080 2.4 40.6 1.0 O 0:HOH4092 2.7 36.6 1.0 OP2 0:A2624 3.3 38.8 1.0 O A:HOH9011 3.3 41.8 1.0 P 0:G877 3.6 36.7 1.0 P 0:G2623 3.6 42.5 1.0 O 0:HOH8217 3.9 75.8 1.0 P 0:A2624 4.1 36.6 1.0 OP2 0:G877 4.3 32.1 1.0 OP1 0:A2624 4.3 37.2 1.0 O5' 0:G2623 4.3 41.9 1.0 O5' 0:G877 4.3 34.4 1.0 C5' 0:G2623 4.4 40.1 1.0 O3' 0:G2623 4.4 37.9 1.0 OP2 0:G2623 4.5 43.7 1.0 C5' 0:G877 4.5 36.0 1.0 O3' 0:A876 4.5 36.4 1.0 OD1 A:ASN195 4.6 35.1 1.0 O3' 0:A2622 4.6 40.5 1.0 OP2 0:C2475 4.7 47.3 1.0 O6 0:G885 4.7 34.5 1.0 O 0:HOH9722 4.7 39.1 1.0 O 0:HOH6271 4.8 0.7 1.0 C3' 0:G2623 4.9 38.9 1.0

Magnesium binding site 10 out of 92 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 Magnesium with other atoms in the Mg 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:Mg8010 b:70.6 occ:1.00 O 0:HOH4095 2.6 61.4 1.0 O 0:HOH4055 2.6 45.1 1.0 O5' 0:G2102 2.6 70.3 1.0 O3' 0:A2101 2.8 68.9 1.0 OP2 0:G2102 2.9 71.3 1.0 O 0:HOH4228 3.0 64.3 1.0 P 0:G2102 3.0 71.8 1.0 O2' 0:A2101 3.0 65.1 1.0 OP2 0:G2537 3.1 56.7 1.0 O 0:HOH8185 3.4 55.9 1.0 O 0:HOH9529 3.7 58.0 1.0 OP1 0:A2103 3.7 68.3 1.0 C3' 0:A2101 3.8 66.1 1.0 C3' 0:G2102 3.9 66.2 1.0 C2' 0:A2101 3.9 64.5 1.0 C5' 0:G2102 4.0 67.5 1.0 O C:HOH8522 4.1 53.0 1.0 O 0:HOH3282 4.2 47.4 1.0 OP1 0:G2102 4.4 71.3 1.0 C4' 0:G2102 4.5 65.8 1.0 O 0:HOH9961 4.5 48.7 1.0 P 0:G2537 4.6 56.0 1.0 C1' 0:A2101 4.6 63.2 1.0 P 0:A2103 4.6 67.2 1.0 C5' 0:G2537 4.7 62.1 1.0 C2' 0:G2102 4.7 65.0 1.0 O3' 0:G2102 4.8 67.9 1.0 OP2 0:A2479 4.8 34.5 1.0 OP2 0:A2103 5.0 66.0 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