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Magnesium in PDB 5dk4: Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp

Enzymatic activity of Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp

All present enzymatic activity of Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp:
6.1.1.2;

Protein crystallography data

The structure of Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp, PDB code: 5dk4 was solved by T.Williams, W.Y.Yin, C.W.Carter Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.02 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.041, 62.041, 219.058, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp (pdb code 5dk4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp, PDB code: 5dk4:

Magnesium binding site 1 out of 1 in 5dk4

Go back to Magnesium Binding Sites List in 5dk4
Magnesium binding site 1 out of 1 in the Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of Tryptophanyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Indolmycin and Mg*Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:23.4
occ:1.00
 O A:HOH589 2.0 29.5 1.0
O A:HOH525 2.1 23.5 1.0
O A:HOH591 2.1 28.6 1.0
O2A A:ATP401 2.2 19.5 1.0
O3G A:ATP401 2.2 19.7 1.0
O2B A:ATP401 2.2 19.2 1.0
HE21 A:GLN9 3.2 23.9 1.0
PB A:ATP401 3.3 19.4 1.0
PA A:ATP401 3.4 19.6 1.0
PG A:ATP401 3.5 20.0 1.0
HE22 A:GLN9 3.5 23.9 1.0
HZ2 A:LYS192 3.5 24.9 1.0
O3B A:ATP401 3.6 18.3 1.0
O06 A:5BX404 3.7 25.5 1.0
NE2 A:GLN9 3.7 19.9 1.0
HZ1 A:LYS111 3.7 58.9 1.0
O3A A:ATP401 3.8 21.3 1.0
O A:HOH619 3.9 27.9 1.0
N04 A:5BX404 3.9 26.6 1.0
O A:HOH541 4.0 37.5 1.0
H8 A:ATP401 4.1 30.9 1.0
O5' A:ATP401 4.1 20.6 1.0
C05 A:5BX404 4.2 30.6 1.0
HE2 A:LYS192 4.2 29.6 1.0
OD2 A:ASP146 4.3 31.0 1.0
NZ A:LYS192 4.3 20.8 1.0
O1G A:ATP401 4.4 21.8 1.0
O2G A:ATP401 4.5 18.1 1.0
NZ A:LYS111 4.6 49.1 1.0
HE3 A:LYS192 4.6 29.6 1.0
HZ1 A:LYS192 4.6 24.9 1.0
CE A:LYS192 4.6 24.6 1.0
O1B A:ATP401 4.7 18.5 1.0
O1A A:ATP401 4.7 17.7 1.0
H2' A:ATP401 4.7 24.7 1.0
HE21 A:GLN147 4.7 45.1 1.0
HE2 A:LYS111 4.8 76.5 1.0
HE22 A:GLN147 4.9 45.1 1.0
HZ3 A:LYS111 4.9 58.9 1.0
NE2 A:GLN147 5.0 37.6 1.0
HZ3 A:LYS192 5.0 24.9 1.0
CD A:GLN9 5.0 22.1 1.0

Reference:

T.L.Williams, Y.W.Yin, C.W.Carter. Selective Inhibition of Bacterial Tryptophanyl-Trna Synthetases By Indolmycin Is Mechanism-Based. J.Biol.Chem. V. 291 255 2016.
ISSN: ESSN 1083-351X
PubMed: 26555258
DOI: 10.1074/JBC.M115.690321
Page generated: Tue Aug 12 07:00:07 2025

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