Potassium 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
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit, PDB code: 3g6e:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Co-Crystal Structure of Homoharringtonine Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K8401 b:0.6 occ:1.00 O6 0:G2102 3.2 54.6 1.0 OP1 0:U2539 3.4 39.5 1.0 N7 0:G2482 3.5 38.9 1.0 O6 0:G2482 3.5 41.3 1.0 O4' 0:C2536 3.6 35.9 1.0 N7 0:G2102 3.6 54.5 1.0 O 0:HOH3785 3.7 0.8 1.0 O2 0:U2535 3.7 43.5 1.0 C12 0:HMT9101 3.8 75.1 1.0 O 0:HOH3610 3.9 0.1 1.0 C2' 0:U2535 4.0 39.6 1.0 C4' 0:C2536 4.0 35.5 1.0 C6 0:G2102 4.0 54.6 1.0 O2' 0:U2535 4.1 41.2 1.0 C5' 0:C2536 4.2 36.1 1.0 C5 0:G2102 4.2 54.8 1.0 C5 0:G2482 4.2 38.4 1.0 C2 0:U2535 4.2 39.9 1.0 C6 0:G2482 4.2 38.7 1.0 C1' 0:C2536 4.4 35.4 1.0 O2 0:C2536 4.5 32.8 1.0 C8 0:G2482 4.6 38.3 1.0 N1 0:U2535 4.7 39.3 1.0 C1' 0:U2535 4.8 38.7 1.0 P 0:U2539 4.8 43.5 1.0 C11 0:HMT9101 4.8 75.6 1.0 N3 0:U2535 4.8 36.9 1.0 O4' 0:A2538 4.8 50.3 1.0 C8 0:G2102 4.8 53.7 1.0 O5' 0:C2536 4.9 37.0 1.0 N1 0:C2536 4.9 35.7 1.0 C2 0:C2536 5.0 34.7 1.0 N6 0:A2486 5.0 47.9 1.0

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K8402 b:65.2 occ:1.00 O4 0:U163 3.1 33.0 1.0 O 0:HOH2991 3.1 23.2 1.0 OP2 0:C162 3.1 28.7 1.0 O4 0:U172 3.2 42.5 1.0 O 0:HOH3347 3.3 44.3 1.0 O 0:HOH3817 3.4 65.4 1.0 O 0:HOH3483 3.4 26.8 1.0 O 0:HOH7790 3.6 25.6 1.0 CD M:ARG82 3.7 50.4 1.0 O 0:HOH7789 3.8 46.7 1.0 O 0:HOH4189 3.9 39.9 1.0 C4 0:U172 4.1 40.6 1.0 C4 0:U163 4.1 31.4 1.0 N3 0:U172 4.1 40.3 1.0 P 0:C162 4.3 30.5 1.0 N4 0:C171 4.4 36.4 1.0 OP2 0:A169 4.5 28.9 1.0 C5 0:U163 4.5 30.4 1.0 NE M:ARG82 4.6 51.7 1.0 OP1 0:C162 4.6 26.9 1.0 O6 0:G164 4.7 30.3 1.0 CG M:ARG82 4.7 49.0 1.0 CB M:ARG82 4.7 46.7 1.0 OP1 0:A169 4.8 28.9 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