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Potassium in PDB 2otj: 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.70 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.738, 299.519, 573.593, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 2otj:

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 117 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 2otj

Go back to Potassium Binding Sites List in 2otj
Potassium binding site 1 out of 2 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8401

b:84.8
occ:1.00
O6 0:G2102 2.5 62.4 1.0
O6 0:G2482 2.7 46.3 1.0
N7 0:G2482 2.8 44.8 1.0
O2 0:C2536 3.0 39.6 1.0
O4' 0:C2536 3.2 45.4 1.0
C6 0:G2482 3.3 45.4 1.0
C6 0:G2102 3.3 62.5 1.0
C5 0:G2482 3.4 44.9 1.0
C2 0:C2536 3.6 40.8 1.0
N7 0:G2102 3.6 61.6 1.0
C1' 0:C2536 3.7 44.5 1.0
N6 0:A2486 3.7 60.9 1.0
C5 0:G2102 3.8 62.0 1.0
N1 0:C2536 3.9 42.1 1.0
O2 0:U2535 3.9 49.6 1.0
C8 0:G2482 4.0 44.5 1.0
C4' 0:C2536 4.1 46.0 1.0
C2 0:U2535 4.2 49.8 1.0
N3 0:U2535 4.4 48.8 1.0
N3 0:C2536 4.5 40.6 1.0
N1 0:G2102 4.5 62.8 1.0
N1 0:G2482 4.7 45.2 1.0
C4 0:G2482 4.7 45.3 1.0
C5' 0:C2536 4.7 46.0 1.0
OP1 0:U2539 4.7 50.9 1.0
C2' 0:U2535 4.8 48.9 1.0
C8 0:G2102 4.8 61.3 1.0
C6 0:C2536 4.9 41.8 1.0

Potassium binding site 2 out of 2 in 2otj

Go back to Potassium Binding Sites List in 2otj
Potassium binding site 2 out of 2 in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8402

b:62.0
occ:1.00
O 0:HOH9014 2.7 21.9 1.0
O 0:HOH9113 2.8 27.0 1.0
O 0:HOH9149 2.9 24.1 1.0
O4 0:U172 2.9 36.6 1.0
O4 0:U163 2.9 35.2 1.0
OP2 0:C162 3.0 28.9 1.0
O 0:HOH4953 3.1 61.5 1.0
O 0:HOH7816 3.4 33.5 1.0
CD M:ARG82 3.5 44.1 1.0
C4 0:U172 3.8 35.4 1.0
O 0:HOH9328 3.9 20.4 1.0
N3 0:U172 4.0 34.5 1.0
C4 0:U163 4.0 34.4 1.0
O 0:HOH7815 4.1 44.7 1.0
NE M:ARG82 4.2 45.2 1.0
N4 0:C171 4.3 35.2 1.0
P 0:C162 4.4 29.4 1.0
C5 0:U163 4.5 34.7 1.0
OP2 0:A169 4.6 28.5 1.0
CG M:ARG82 4.6 44.0 1.0
O6 0:G164 4.7 28.4 1.0
OP1 0:C162 4.8 28.4 1.0
CB M:ARG82 4.8 43.0 1.0
OP1 0:A169 4.8 28.1 1.0
MG 0:MG8054 4.9 30.6 1.0
N3 0:C173 4.9 27.0 1.0
N4 0:C173 4.9 26.4 1.0

Reference:

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081
Page generated: Sun Dec 13 23:11:08 2020

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