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Potassium in PDB 3i56: Co-Crystal Structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit, PDB code: 3i56 was solved by G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.430, 300.773, 575.414, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.3

Other elements in 3i56:

The structure of Co-Crystal Structure of Triacetyloleandomcyin 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

Potassium Binding Sites:

The binding sites of Potassium atom in the Co-Crystal Structure of Triacetyloleandomcyin Bound to the Large Ribosomal Subunit (pdb code 3i56). 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit, PDB code: 3i56:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 3i56

Go back to Potassium Binding Sites List in 3i56
Potassium binding site 1 out of 2 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8401

b:0.7
occ:1.00
O6 0:G2102 3.0 40.6 1.0
OP1 0:U2539 3.2 24.6 1.0
O2 0:U2535 3.4 30.1 1.0
O6 0:G2482 3.5 26.3 1.0
C6 0:G2102 4.0 39.7 1.0
N7 0:G2102 4.0 38.4 1.0
C2 0:U2535 4.1 27.9 1.0
O 0:HOH3782 4.3 17.2 1.0
C2' 0:U2535 4.3 25.7 1.0
O2' 0:U2535 4.3 25.1 1.0
N7 0:G2482 4.4 27.6 1.0
C5 0:G2102 4.4 39.1 1.0
P 0:U2539 4.4 28.8 1.0
O3' 0:A2538 4.5 31.3 1.0
C6 0:G2482 4.5 25.4 1.0
O4' 0:C2536 4.5 28.4 1.0
N3 0:U2535 4.7 25.9 1.0
O 0:HOH3610 4.8 35.7 1.0
C5 0:G2482 4.8 26.1 1.0
C4' 0:C2536 4.8 28.4 1.0
N1 0:U2535 4.8 27.2 1.0
C1' 0:U2535 4.9 26.1 1.0
O4' 0:A2538 4.9 36.4 1.0
N6 0:A2486 5.0 41.9 1.0
O2 0:C2536 5.0 22.0 1.0

Potassium binding site 2 out of 2 in 3i56

Go back to Potassium Binding Sites List in 3i56
Potassium binding site 2 out of 2 in the Co-Crystal Structure of Triacetyloleandomcyin 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 Triacetyloleandomcyin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8402

b:78.8
occ:1.00
O4 0:U163 3.1 25.8 1.0
O4 0:U172 3.3 26.6 1.0
OP2 0:C162 3.4 15.2 1.0
O 0:HOH2986 3.4 99.8 1.0
O 0:HOH3347 3.5 38.0 1.0
O 0:HOH3483 3.5 26.8 1.0
O 0:HOH7789 3.5 0.1 1.0
O 0:HOH3817 3.5 76.5 1.0
O 0:HOH7790 3.8 0.7 1.0
CD M:ARG82 3.9 26.8 1.0
MG 0:MG8041 4.0 28.7 1.0
N3 0:U172 4.1 23.2 1.0
C4 0:U172 4.1 24.6 1.0
C4 0:U163 4.1 23.4 1.0
N4 0:C171 4.2 23.2 1.0
OP2 0:A169 4.3 17.9 1.0
O 0:HOH4195 4.3 22.8 1.0
P 0:C162 4.5 14.3 1.0
O6 0:G164 4.5 22.6 1.0
OP1 0:C162 4.6 13.6 1.0
C5 0:U163 4.6 21.6 1.0
NE M:ARG82 4.6 27.7 1.0
OP1 0:A169 4.7 16.0 1.0
CG M:ARG82 4.7 25.5 1.0
CB M:ARG82 4.8 24.0 1.0

Reference:

G.Gurel, G.Blaha, T.A.Steitz, P.B.Moore. Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula Marismortui. Antimicrob.Agents Chemother. V. 53 5010 2009.
ISSN: ISSN 0066-4804
PubMed: 19738021
DOI: 10.1128/AAC.00817-09
Page generated: Sun Dec 13 23:19:43 2020

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