Sodium in PDB 3g6e: Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e was solved by G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.90 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.863, 299.418, 574.087, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.9

The structure of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium	(Sr)	108 atoms
Magnesium	(Mg)	93 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 Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit (pdb code 3g6e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e:
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 Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8501 b:43.8 occ:1.00 OP2 0:C1069 2.7 29.9 1.0 N7 0:G1072 2.8 32.5 1.0 O 0:HOH7345 2.9 44.1 1.0 O 0:HOH3877 3.0 83.8 1.0 O6 0:G1087 3.2 39.7 1.0 O6 0:G1072 3.2 35.6 1.0 O 0:HOH3164 3.4 41.7 1.0 C5 0:G1072 3.5 32.8 1.0 O 0:HOH7450 3.6 55.3 1.0 C6 0:G1072 3.6 31.4 1.0 C8 0:G1072 3.9 32.0 1.0 P 0:C1069 4.0 34.0 1.0 C6 0:G1087 4.1 37.5 1.0 C5' 0:C1068 4.3 41.7 1.0 C3' 0:C1068 4.5 38.2 1.0 O3' 0:C1068 4.5 34.1 1.0 O 0:HOH8214 4.6 43.2 1.0 OP1 0:C1069 4.7 29.6 1.0 C4 0:G1072 4.7 33.4 1.0 N1 0:G1087 4.8 35.9 1.0 OP2 0:C1068 4.9 45.9 1.0 N9 0:G1072 4.9 33.1 1.0 N1 0:G1072 5.0 30.3 1.0

Sodium binding site 2 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8502 b:70.0 occ:1.00 O2' 0:G1119 2.9 39.0 1.0 OP2 0:U1120 3.0 44.3 1.0 O 0:HOH7759 3.0 70.9 1.0 O6 0:G1121 3.0 35.7 1.0 O 0:HOH3297 3.1 36.9 1.0 O3' 0:G1119 3.2 43.0 1.0 N7 0:G1121 3.3 35.2 1.0 O 0:HOH9032 3.4 41.5 1.0 O4 0:U1122 3.5 41.0 1.0 P 0:U1120 3.7 43.8 1.0 C6 0:G1121 3.7 32.3 1.0 O 0:HOH6604 3.8 83.0 1.0 C5 0:G1121 3.8 33.2 1.0 O 0:HOH4850 3.9 72.4 1.0 C2' 0:G1119 3.9 39.0 1.0 C3' 0:G1119 4.1 41.3 1.0 C4 0:U1122 4.2 39.7 1.0 MG 0:MG8018 4.2 39.6 1.0 C1' 0:G1119 4.3 36.6 1.0 C8 0:G1121 4.4 34.4 1.0 C5 0:U1122 4.4 39.1 1.0 OP1 0:U1120 4.6 46.6 1.0 N4 0:C1243 4.8 34.0 1.0 N6 0:A1242 4.9 38.9 1.0 O5' 0:U1120 4.9 41.6 1.0

Sodium binding site 3 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8504 b:34.8 occ:1.00 O2' 0:A631 2.8 31.1 1.0 O2' 0:A630 2.8 33.4 1.0 O 0:HOH3514 2.8 37.9 1.0 N3 0:A630 2.8 35.5 1.0 O 0:HOH8857 2.9 51.3 1.0 O 0:HOH4986 2.9 58.1 1.0 OP2 0:A2074 3.3 36.4 1.0 C1' 0:A630 3.5 34.3 1.0 C2' 0:A631 3.5 31.5 1.0 C2' 0:A630 3.7 34.4 1.0 C2 0:A630 3.7 34.8 1.0 N2 0:G2070 3.8 36.0 1.0 C4 0:A630 3.8 34.5 1.0 O3' 0:A630 3.9 32.3 1.0 C3' 0:A631 4.0 31.2 1.0 N9 0:A630 4.0 35.0 1.0 N1 0:A629 4.2 38.1 1.0 C2 0:A629 4.3 38.2 1.0 O3' 0:A631 4.4 31.4 1.0 OP1 0:A632 4.4 33.3 1.0 C3' 0:A630 4.5 32.0 1.0 O 0:HOH4575 4.6 34.0 1.0 C2 0:G2070 4.6 35.1 1.0 O4' 0:A630 4.6 34.1 1.0 OP2 0:G2072 4.7 51.2 1.0 P 0:A2074 4.7 36.2 1.0 C1' 0:A631 4.9 31.9 1.0 P 0:A632 4.9 33.0 1.0

Sodium binding site 4 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8505 b:42.9 occ:1.00 N1 0:A2649 2.9 39.5 1.0 N7 0:G2094 2.9 35.7 1.0 O 0:HOH3401 3.0 28.1 1.0 N7 0:G2093 3.0 32.1 1.0 N3 0:G2092 3.1 32.4 1.0 O2' 0:G2092 3.2 31.5 1.0 O6 0:G2094 3.2 41.6 1.0 C2 0:A2649 3.3 39.6 1.0 C5 0:G2093 3.5 33.3 1.0 N2 0:G2092 3.6 33.0 1.0 C2 0:G2092 3.6 32.3 1.0 O6 0:G2093 3.6 40.2 1.0 C5 0:G2094 3.7 36.7 1.0 C6 0:G2093 3.8 35.9 1.0 C6 0:G2094 3.8 38.3 1.0 C8 0:G2093 3.9 33.6 1.0 C6 0:A2649 3.9 39.0 1.0 N6 0:A2612 4.0 37.5 1.0 C4 0:G2092 4.0 33.1 1.0 C8 0:G2094 4.0 35.7 1.0 C6 0:A2612 4.2 39.7 1.0 N6 0:A2649 4.2 40.7 1.0 C2' 0:G2092 4.3 31.4 1.0 C1' 0:G2092 4.3 30.7 1.0 N9 0:G2092 4.5 32.1 1.0 C4 0:G2093 4.5 31.6 1.0 N3 0:A2649 4.6 39.2 1.0 N1 0:A2612 4.6 37.9 1.0 C5 0:A2612 4.6 40.4 1.0 N1 0:G2092 4.7 28.8 1.0 N9 0:G2093 4.7 31.8 1.0 O3' 0:G2092 4.8 32.3 1.0 N1 0:G2093 4.9 35.3 1.0 C4 0:G2094 5.0 36.2 1.0 N7 0:A2612 5.0 40.6 1.0

Sodium binding site 5 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8506 b:66.0 occ:1.00 O2 0:C40 2.9 61.8 1.0 O4' 0:G41 2.9 53.7 1.0 O2' 0:C40 2.9 61.5 1.0 O2 0:C443 3.0 61.3 1.0 N1 0:A442 3.1 60.1 1.0 C2 0:A442 3.4 58.8 1.0 C2' 0:C40 3.5 61.4 1.0 C1' 0:G41 3.7 52.3 1.0 C1' 0:C40 3.8 61.9 1.0 C2 0:C443 3.9 60.8 1.0 C2 0:C40 3.9 62.4 1.0 C4' 0:G41 4.0 52.7 1.0 N9 0:G41 4.3 52.2 1.0 C6 0:A442 4.3 60.0 1.0 N1 0:C40 4.3 62.7 1.0 C5' 0:G41 4.4 54.2 1.0 N2 0:G39 4.4 55.4 1.0 C1' 0:C443 4.5 59.7 1.0 N1 0:C443 4.6 60.4 1.0 N3 0:A442 4.6 59.5 1.0 N6 0:A442 4.7 60.3 1.0 N3 0:C443 4.7 60.5 1.0 C8 0:G41 4.8 53.0 1.0 O5' 0:G41 4.9 57.8 1.0 C4 0:G41 4.9 52.5 1.0 O 0:HOH6666 4.9 63.3 1.0 C3' 0:C40 5.0 61.2 1.0

Sodium binding site 6 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8507 b:49.6 occ:1.00 O2 0:U1724 2.5 47.1 1.0 O2 0:C1394 2.5 39.7 1.0 O4 0:U1432 2.7 45.9 1.0 O 0:HOH8054 3.0 42.9 1.0 O6 0:G1433 3.1 54.0 1.0 C2 0:C1394 3.6 39.8 1.0 O2' 0:C1394 3.6 41.5 1.0 C2 0:U1724 3.6 43.6 1.0 C2' 0:C1394 3.7 41.8 1.0 O 0:HOH6898 3.8 70.1 1.0 C6 0:G1433 3.8 49.9 1.0 SR 0:SR8962 3.8 0.2 1.0 C4 0:U1432 3.9 43.5 1.0 O 0:HOH3689 3.9 45.7 1.0 C1' 0:C1394 4.1 40.8 1.0 N1 0:G1433 4.2 50.7 1.0 N1 0:C1394 4.3 40.4 1.0 N3 0:U1724 4.3 42.2 1.0 N3 0:C1394 4.4 39.0 1.0 N3 0:U1432 4.4 44.6 1.0 C5 0:G1433 4.7 47.0 1.0 N1 0:U1724 4.7 42.3 1.0 O2' 0:U1724 4.8 41.0 1.0 C1' 0:U1724 4.8 40.3 1.0 C2' 0:U1724 4.9 40.5 1.0 OP2 0:C1395 4.9 41.1 1.0 OP2 0:U1722 5.0 48.9 1.0

Sodium binding site 7 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8508 b:46.6 occ:1.00 O6 0:G2579 2.9 35.6 1.0 N7 0:G2579 3.0 40.0 1.0 O4' 0:A2577 3.1 40.1 1.0 N3 0:A2577 3.1 35.7 1.0 O 0:HOH3242 3.1 46.3 1.0 N7 0:G2578 3.2 40.9 1.0 O 0:HOH5700 3.5 79.6 1.0 C6 0:G2579 3.5 38.5 1.0 C5 0:G2579 3.6 38.8 1.0 C1' 0:A2577 3.6 38.4 1.0 O6 0:G2578 3.6 41.7 1.0 C5 0:G2578 3.6 40.0 1.0 C6 0:G2578 3.8 41.4 1.0 C2 0:A2577 3.9 35.7 1.0 C4 0:A2577 3.9 36.3 1.0 O 0:HOH7700 4.0 77.4 1.0 C4' 0:A2577 4.0 41.5 1.0 C8 0:G2578 4.0 39.9 1.0 N9 0:A2577 4.1 35.9 1.0 C8 0:G2579 4.2 41.0 1.0 C4 0:G2578 4.6 40.5 1.0 O3' 0:A2577 4.8 41.2 1.0 N4 0:C2556 4.8 36.4 1.0 N9 0:G2578 4.8 41.0 1.0 C3' 0:A2577 4.9 41.8 1.0 N1 0:G2579 4.9 38.5 1.0 N1 0:G2578 4.9 40.5 1.0 C4 0:G2579 4.9 38.8 1.0 C2' 0:A2577 4.9 40.5 1.0 O6 0:G2580 5.0 39.5 1.0 N3 0:U2554 5.0 33.7 1.0 C5' 0:A2577 5.0 41.2 1.0

Sodium binding site 8 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8509 b:71.2 occ:1.00 N7 0:G2524 2.9 39.1 1.0 O6 0:G2525 2.9 48.6 1.0 O 0:HOH8253 3.0 37.0 1.0 O 0:HOH3615 3.0 47.2 1.0 O 0:HOH3440 3.1 53.1 1.0 O 0:HOH5803 3.5 77.9 1.0 C8 0:G2524 3.6 38.0 1.0 C5 0:U2523 3.7 39.2 1.0 C6 0:G2525 3.9 46.8 1.0 C4 0:U2523 4.0 40.4 1.0 OP2 0:G2524 4.0 39.5 1.0 O 0:HOH8299 4.1 27.9 1.0 C5 0:G2524 4.1 37.3 1.0 C6 0:U2523 4.1 37.6 1.0 OP2 0:U2523 4.3 49.5 1.0 O4 0:U2523 4.3 43.1 1.0 O6 0:G2524 4.4 33.9 1.0 N3 0:U2523 4.6 38.4 1.0 C5 0:G2525 4.6 45.6 1.0 N7 0:G2525 4.6 45.8 1.0 C6 0:G2524 4.7 36.1 1.0 N1 0:U2523 4.8 38.5 1.0 O5' 0:U2523 4.9 46.9 1.0 O2' 0:C2493 4.9 41.8 1.0 N1 0:G2525 4.9 45.3 1.0 N9 0:G2524 4.9 38.7 1.0 C2 0:U2523 5.0 39.1 1.0

Sodium binding site 9 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8511 b:91.3 occ:1.00 O 0:HOH4089 2.9 77.6 1.0 O6 0:G2399 2.9 43.7 1.0 O 0:HOH6542 3.1 36.6 1.0 O 0:HOH8593 3.1 63.4 1.0 O 0:HOH4019 3.2 72.1 1.0 O4 0:U2389 3.3 42.8 1.0 O 0:HOH5380 3.5 70.7 1.0 O6 0:G2400 3.5 43.8 1.0 O 0:HOH7982 3.9 51.3 1.0 C6 0:G2399 3.9 42.6 1.0 N3 0:U2389 4.0 41.9 1.0 C4 0:U2389 4.1 41.6 1.0 O 0:HOH7917 4.2 48.3 1.0 N4 0:C2388 4.2 40.8 1.0 O 0:HOH6003 4.2 91.7 1.0 N7 0:G2399 4.2 45.6 1.0 C6 0:G2400 4.3 43.4 1.0 C5 0:G2399 4.5 43.6 1.0 OP2 0:A2398 4.7 46.7 1.0 N7 0:G2400 4.7 43.6 1.0 O 0:HOH5766 4.7 46.1 1.0 O 0:HOH5689 4.8 69.2 1.0 C5 0:G2400 4.8 43.8 1.0

Sodium binding site 10 out of 75 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8512 b:48.3 occ:1.00 O2' 0:U2607 2.6 32.6 1.0 O 0:HOH4204 2.8 27.2 1.0 O 0:HOH4810 2.9 53.7 1.0 O2 0:U2607 3.0 37.1 1.0 O 0:HOH7223 3.0 69.4 1.0 OP1 0:U2541 3.2 46.0 1.0 CZ3 B:TRP242 3.4 32.1 1.0 OP2 0:C2608 3.7 31.6 1.0 O 0:HOH3493 3.8 37.5 1.0 O 0:HOH7760 3.9 36.8 1.0 C2' 0:U2607 3.9 32.6 1.0 C2 0:U2607 3.9 39.3 1.0 CH2 B:TRP242 4.1 33.9 1.0 OP1 0:U2610 4.1 31.4 1.0 C1' 0:U2607 4.1 35.0 1.0 O 0:HOH6125 4.2 33.7 1.0 P 0:U2541 4.2 46.1 1.0 O3' 0:U2607 4.3 30.9 1.0 OP2 0:U2541 4.3 44.6 1.0 CE3 B:TRP242 4.3 29.9 1.0 N1 0:U2607 4.4 39.0 1.0 P 0:C2608 4.4 33.1 1.0 O 0:HOH3511 4.5 46.1 1.0 O 0:HOH4245 4.7 26.8 1.0 C3' 0:U2607 4.7 31.8 1.0 OP1 0:C2608 4.9 34.5 1.0 N3 0:U2607 4.9 40.8 1.0

G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: the Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. J.Mol.Biol. V. 389 146 2009.
ISSN: ISSN 0022-2836
PubMed: 19362093
DOI: 10.1016/J.JMB.2009.04.005