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

Protein crystallography data

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

Other elements in 3cpw:

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

Strontium Binding Sites:

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 - 108;

Binding sites:

The binding sites of Strontium 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 Strontium atom.
In total 108 binding sites of Strontium where determined in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 3cpw

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Strontium binding site 1 out of 108 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 Strontium with other atoms in the Sr 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:Sr8901

b:75.3
occ:1.00
N7 0:G854 2.5 38.7 1.0
O 0:HOH4841 2.5 63.0 1.0
O 0:HOH4710 2.5 70.9 1.0
N7 0:G824 2.6 41.9 1.0
O 0:HOH4388 2.6 0.7 1.0
O 0:HOH4944 2.6 70.9 1.0
C8 0:G854 3.2 39.8 1.0
C8 0:G824 3.3 43.2 1.0
OP2 0:G854 3.6 43.0 1.0
C5 0:G854 3.6 39.1 1.0
C5 0:G824 3.7 40.0 1.0
O6 0:G854 4.0 42.3 1.0
O6 0:G824 4.1 39.4 1.0
OP2 0:U823 4.2 44.8 1.0
OP2 0:G824 4.2 47.8 1.0
C6 0:G854 4.2 40.4 1.0
C6 0:G824 4.2 39.5 1.0
N9 0:G824 4.5 41.9 1.0
OP2 0:C853 4.5 45.0 1.0
N9 0:G854 4.5 39.7 1.0
C4 0:G824 4.7 40.8 1.0
C4 0:G854 4.7 39.3 1.0
C5 0:U823 4.7 38.0 1.0
O5' 0:G854 4.8 38.8 1.0
P 0:G854 4.8 40.4 1.0
C5 0:C853 4.9 33.8 1.0
C6 0:U823 4.9 38.4 1.0

Strontium binding site 2 out of 108 in 3cpw

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Strontium binding site 2 out of 108 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 Strontium with other atoms in the Sr 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:Sr8902

b:49.5
occ:1.00
OP1 0:G836 2.5 37.4 1.0
O 0:HOH9836 2.5 48.4 1.0
OP1 0:U2615 2.6 34.9 1.0
O B:HOH8997 2.7 52.8 1.0
OE1 B:GLN230 2.8 36.7 1.0
O 0:HOH5448 3.1 45.6 1.0
CD B:GLN230 3.8 36.3 1.0
P 0:U2615 3.9 37.0 1.0
CB B:GLN230 4.0 36.6 1.0
P 0:G836 4.0 42.3 1.0
O 0:HOH4269 4.0 73.1 1.0
CG B:GLN230 4.1 34.2 1.0
O 0:HOH4419 4.1 65.5 1.0
O 0:HOH7195 4.2 44.0 1.0
O 0:HOH3018 4.3 55.9 1.0
C5' 0:G836 4.5 37.6 1.0
OP2 0:U2615 4.5 36.7 1.0
O3' 0:C2614 4.5 33.2 1.0
CA B:GLN230 4.6 36.6 1.0
O5' 0:G836 4.6 37.6 1.0
O 0:HOH9695 4.6 44.7 1.0
C3' 0:U835 4.7 35.7 1.0
O B:GLN230 4.7 33.8 1.0
O3' 0:U835 4.8 36.4 1.0
O 0:HOH9558 4.9 35.0 1.0
OP2 0:G836 4.9 40.4 1.0
OP2 0:G2616 4.9 38.0 1.0
O5' 0:U2615 5.0 32.9 1.0
NE2 B:GLN230 5.0 36.2 1.0

Strontium binding site 3 out of 108 in 3cpw

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Strontium binding site 3 out of 108 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 Strontium with other atoms in the Sr 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:Sr8903

b:59.9
occ:1.00
O 0:HOH4071 2.6 61.3 1.0
O 0:HOH4386 2.6 79.6 1.0
O6 0:G1491 2.6 51.2 1.0
O 0:HOH9869 2.7 47.2 1.0
O 0:HOH6563 2.8 63.3 1.0
OP2 0:G1489 2.8 52.6 1.0
C6 0:G1491 3.8 48.0 1.0
P 0:G1489 3.8 52.7 1.0
OP1 0:G1489 3.9 54.9 1.0
N7 0:G1491 4.4 46.1 1.0
OP2 0:A1487 4.4 48.7 1.0
O 0:HOH6677 4.4 38.4 1.0
C5 0:G1491 4.5 46.5 1.0
O5' 0:G1489 4.7 50.6 1.0
N7 0:G1490 4.7 35.2 1.0
OP2 0:G1490 4.8 44.3 1.0
N1 0:G1491 4.9 45.8 1.0
OP1 0:G1453 4.9 50.7 1.0
O 0:HOH9651 4.9 50.2 1.0

Strontium binding site 4 out of 108 in 3cpw

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Strontium binding site 4 out of 108 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 Strontium with other atoms in the Sr 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:Sr8904

b:52.3
occ:1.00
O 0:HOH9902 2.5 44.4 1.0
O 0:HOH6964 2.6 35.9 1.0
OP1 0:G1354 2.7 40.1 1.0
OP2 0:A643 3.0 32.9 1.0
OP1 0:C1353 3.2 51.7 1.0
OP1 0:A643 3.7 38.5 1.0
P 0:G1354 3.7 35.5 1.0
O3' 0:C1353 3.7 38.2 1.0
P 0:A643 3.8 36.5 1.0
O5' 0:C1353 4.2 51.3 1.0
P 0:C1353 4.4 55.4 1.0
OP2 0:G1354 4.5 33.6 1.0
C5' 0:C1353 4.5 44.8 1.0
O4 0:U904 4.5 40.7 1.0
OP1 0:G642 4.6 35.8 1.0
N3 0:U904 4.6 36.7 1.0
OP2 0:G642 4.6 32.5 1.0
C3' 0:C1353 4.6 39.2 1.0
O5' 0:A643 4.7 31.6 1.0
N1 0:A1355 4.8 34.1 1.0
O5' 0:G642 4.8 33.8 1.0
O2' 0:A1352 4.9 61.3 1.0
P 0:G642 4.9 36.8 1.0
O5' 0:G1354 4.9 36.8 1.0

Strontium binding site 5 out of 108 in 3cpw

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Strontium binding site 5 out of 108 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 Strontium with other atoms in the Sr 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:Sr8905

b:59.0
occ:1.00
OP1 0:A1755 2.8 43.7 1.0
O 0:HOH7528 2.9 56.0 1.0
O 0:HOH7945 2.9 47.7 1.0
O 0:HOH6972 3.2 55.8 1.0
O3' 0:A1754 3.6 41.5 1.0
P 0:A1755 3.8 41.5 1.0
O 0:HOH7611 4.3 66.2 1.0
O 0:HOH3481 4.5 57.7 1.0
OP1 0:C1738 4.6 49.2 1.0
OP2 0:C1738 4.6 49.0 1.0
N2 0:G834 4.7 39.4 1.0
C5' 0:A1755 4.8 41.0 1.0
O2' 0:G834 4.8 34.1 1.0
O5' 0:A1755 4.8 42.5 1.0
OP2 0:A1755 4.8 42.7 1.0
N3 0:G834 5.0 37.2 1.0
C3' 0:A1754 5.0 39.1 1.0

Strontium binding site 6 out of 108 in 3cpw

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Strontium binding site 6 out of 108 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 Strontium with other atoms in the Sr 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:Sr8906

b:56.5
occ:1.00
O C:HOH8549 2.7 66.2 1.0
O 0:HOH6027 2.7 33.0 1.0
O2 0:C893 2.8 38.5 1.0
O2' 0:C893 2.8 38.7 1.0
O 0:HOH6660 3.5 35.7 1.0
C2 0:C893 3.9 34.8 1.0
C2' 0:C893 3.9 36.8 1.0
C1' 0:C893 3.9 36.2 1.0
O3' 0:C893 4.2 35.2 1.0
O C:HOH8518 4.3 35.6 1.0
O 0:HOH4822 4.4 56.1 1.0
N1 0:C893 4.4 35.0 1.0
N7 0:G892 4.5 33.8 1.0
O C:HOH8614 4.6 45.4 1.0
OP2 0:G892 4.7 38.7 1.0
C3' 0:C893 4.7 36.5 1.0
O 0:HOH6767 4.7 54.8 1.0
OP2 0:A895 4.8 38.0 1.0
NZ Z:LYS53 4.8 42.7 1.0
O 0:HOH4321 4.8 47.3 1.0
N3 0:C893 4.9 33.9 1.0

Strontium binding site 7 out of 108 in 3cpw

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Strontium binding site 7 out of 108 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 Strontium with other atoms in the Sr 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:Sr8907

b:63.5
occ:1.00
O H:ASP10 2.5 40.1 1.0
O 0:HOH5240 2.6 64.5 1.0
O H:HOH8992 2.6 75.7 1.0
O 0:HOH6721 2.7 51.7 1.0
O 0:HOH4258 2.7 61.2 1.0
O6 0:G1055 2.9 55.2 1.0
C H:ASP10 3.7 43.4 1.0
C6 0:G1055 3.9 51.1 1.0
CB H:ASP10 4.1 47.8 1.0
CG H:LYS11 4.2 44.9 1.0
O 0:HOH3731 4.3 49.2 1.0
N7 0:G1055 4.3 49.9 1.0
CA H:ASP10 4.4 45.0 1.0
C5 0:G1055 4.5 50.7 1.0
CG H:ASP10 4.6 49.9 1.0
OD1 H:ASP10 4.6 50.8 1.0
N7 0:G1054 4.6 55.6 1.0
N H:LYS11 4.7 43.3 1.0
OP2 0:G1054 4.7 48.0 1.0
CA H:LYS11 4.7 43.6 1.0
CE H:LYS11 4.9 45.7 1.0
OP2 0:G1053 5.0 46.9 1.0

Strontium binding site 8 out of 108 in 3cpw

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Strontium binding site 8 out of 108 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 Strontium with other atoms in the Sr 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:Sr8908

b:90.6
occ:1.00
OD2 L:ASP157 2.6 52.2 1.0
OP1 0:G147 2.7 44.2 1.0
OP1 0:A183 2.7 54.0 1.0
O L:HOH8951 2.8 84.5 1.0
O3' 0:U146 3.4 39.5 1.0
O3' 0:G182 3.5 48.6 1.0
CG L:ASP157 3.6 48.8 1.0
P 0:G147 3.7 40.8 1.0
P 0:A183 3.7 51.5 1.0
OD1 L:ASP157 3.9 48.9 1.0
O 0:HOH7229 4.1 72.4 1.0
C5' 0:G147 4.3 42.1 1.0
O 0:HOH3557 4.4 50.8 1.0
O5' 0:G147 4.5 42.7 1.0
C3' 0:U146 4.7 43.6 1.0
C3' 0:G182 4.7 48.9 1.0
C5' 0:A183 4.8 48.4 1.0
O5' 0:A183 4.8 50.8 1.0
OP2 0:A183 4.8 51.3 1.0
O2' 0:U146 4.8 44.3 1.0
OP2 0:G147 4.9 40.0 1.0
C5' 0:G182 4.9 49.0 1.0
CB L:ASP157 4.9 45.7 1.0
C4' 0:U146 5.0 44.1 1.0

Strontium binding site 9 out of 108 in 3cpw

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Strontium binding site 9 out of 108 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 Strontium with other atoms in the Sr 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:Sr8909

b:74.8
occ:1.00
O 0:HOH5909 2.6 71.1 1.0
O 0:HOH6544 2.6 79.5 1.0
O 0:HOH8278 2.6 70.6 1.0
O 0:HOH6976 2.7 84.2 1.0
O 0:HOH4199 2.7 0.1 1.0
O 0:HOH7266 2.9 47.4 1.0
O 0:HOH8279 3.7 67.6 1.0
O 0:HOH4475 4.2 54.8 1.0
O 0:HOH4118 4.2 42.9 1.0
O 0:HOH6569 4.3 92.7 1.0
OP2 0:C2077 4.4 43.1 1.0
O6 0:G2080 4.4 46.1 1.0
N7 0:G2079 4.8 40.6 1.0
O 0:HOH6476 4.9 66.0 1.0
N6 0:A536 5.0 49.9 1.0

Strontium binding site 10 out of 108 in 3cpw

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Strontium binding site 10 out of 108 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 Strontium with other atoms in the Sr 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:Sr8910

b:59.4
occ:1.00
OP2 0:A1747 2.6 39.1 1.0
OP1 0:G2585 2.6 44.0 1.0
OP2 0:U1748 2.7 40.1 1.0
O 0:HOH4246 2.7 73.0 1.0
O4 0:U1749 2.7 39.6 1.0
O 0:HOH3138 3.0 58.7 1.0
C4 0:U1749 3.7 40.9 1.0
P 0:G2585 3.7 43.4 1.0
OP2 0:G2585 3.9 41.6 1.0
P 0:A1747 4.0 38.1 1.0
P 0:U1748 4.0 39.5 1.0
C5 0:U1749 4.0 41.9 1.0
O 0:HOH8197 4.1 46.1 1.0
SR 0:SR8982 4.3 0.1 1.0
OP2 0:U2586 4.3 46.8 1.0
O5' 0:A1747 4.5 40.5 1.0
C5' 0:A1747 4.5 39.4 1.0
O 0:HOH5342 4.5 63.9 1.0
OP1 0:U1748 4.6 35.0 1.0
OP1 0:U2586 4.6 44.9 1.0
O5' 0:G2585 4.7 44.4 1.0
P 0:U2586 4.8 45.0 1.0
O3' 0:G2584 4.8 43.5 1.0
OP1 0:G1751 4.8 42.4 1.0
O3' 0:A1746 4.9 38.5 1.0
O3' 0:A1747 4.9 39.9 1.0
C5' 0:G2585 4.9 43.6 1.0
OP1 0:A1747 4.9 38.2 1.0
O 0:HOH3237 4.9 83.7 1.0
N3 0:U1749 4.9 40.1 1.0
O5' 0:U1748 5.0 38.6 1.0

Reference:

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
Page generated: Mon Jan 25 16:03:25 2021

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