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Potassium in PDB 2otl: Girodazole Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl 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) 49.36 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.077, 300.598, 575.055, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.8

Other elements in 2otl:

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

Magnesium (Mg) 116 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 23 atoms
Sodium (Na) 85 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 2 in 2otl

Go back to Potassium Binding Sites List in 2otl
Potassium binding site 1 out of 2 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8401

b:85.7
occ:1.00
O6 0:G2102 2.6 48.2 1.0
O6 0:G2482 2.7 38.9 1.0
N7 0:G2482 2.9 38.5 1.0
O2 0:C2536 3.2 30.5 1.0
O4' 0:C2536 3.2 34.7 1.0
N7 0:G2102 3.3 48.4 1.0
C6 0:G2482 3.4 37.6 1.0
C6 0:G2102 3.4 49.5 1.0
C5 0:G2482 3.4 38.0 1.0
C1' 0:C2536 3.6 32.8 1.0
C2 0:C2536 3.6 30.9 1.0
C5 0:G2102 3.7 49.5 1.0
N1 0:C2536 3.8 33.0 1.0
C4' 0:C2536 4.0 33.8 1.0
C8 0:G2482 4.1 38.1 1.0
O2 0:U2535 4.2 41.9 1.0
N6 0:A2486 4.2 48.7 1.0
OP1 0:U2539 4.3 40.1 1.0
C2 0:U2535 4.4 40.4 1.0
N3 0:C2536 4.5 30.4 1.0
C8 0:G2102 4.6 48.7 1.0
C5' 0:C2536 4.6 34.1 1.0
C2' 0:U2535 4.6 40.4 1.0
N1 0:G2102 4.7 49.1 1.0
N3 0:U2535 4.7 39.4 1.0
N1 0:G2482 4.7 37.7 1.0
C4 0:G2482 4.8 37.5 1.0
C6 0:C2536 4.9 32.2 1.0
N1 0:U2535 5.0 41.1 1.0

Potassium binding site 2 out of 2 in 2otl

Go back to Potassium Binding Sites List in 2otl
Potassium binding site 2 out of 2 in the Girodazole 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 Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:K8402

b:58.0
occ:1.00
O 0:HOH9013 2.8 24.4 1.0
O4 0:U172 2.9 39.1 1.0
O 0:HOH9108 2.9 38.0 1.0
O4 0:U163 2.9 32.7 1.0
O 0:HOH4946 3.1 75.6 1.0
O 0:HOH9143 3.2 35.7 1.0
OP2 0:C162 3.4 26.0 1.0
O 0:HOH7803 3.4 37.6 1.0
CD M:ARG82 3.6 36.5 1.0
C4 0:U172 3.7 37.5 1.0
N3 0:U172 3.9 37.4 1.0
C4 0:U163 4.0 32.6 1.0
O 0:HOH9323 4.1 36.3 1.0
N4 0:C171 4.2 32.7 1.0
NE M:ARG82 4.3 37.6 1.0
O6 0:G164 4.4 35.4 1.0
OP2 0:A169 4.4 32.8 1.0
O 0:HOH7802 4.4 40.1 1.0
C5 0:U163 4.5 32.7 1.0
P 0:C162 4.7 29.2 1.0
OP1 0:A169 4.7 33.6 1.0
CG M:ARG82 4.7 34.7 1.0
CB M:ARG82 4.8 34.4 1.0
N3 0:C173 4.8 31.3 1.0
N4 0:C173 4.9 32.8 1.0
MG 0:MG8054 5.0 37.7 1.0
OP1 0:C162 5.0 27.6 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 23:11:07 2020

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