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Cadmium in PDB 3a05: Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan

Enzymatic activity of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan

All present enzymatic activity of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan:
6.1.1.2;

Protein crystallography data

The structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan, PDB code: 3a05 was solved by W.Tsuchiya, Z.Fujimoto, T.Hasegawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.212, 102.919, 97.645, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.4

Other elements in 3a05:

The structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan (pdb code 3a05). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan, PDB code: 3a05:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 3a05

Go back to Cadmium Binding Sites List in 3a05
Cadmium binding site 1 out of 3 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd374

b:30.6
occ:1.00
OE2 A:GLU343 2.3 38.2 1.0
OE1 A:GLU343 2.4 37.7 1.0
OE1 A:GLU346 2.4 28.5 1.0
OE2 A:GLU346 2.6 37.9 1.0
CD A:GLU343 2.8 32.7 1.0
CD A:GLU346 2.8 34.8 1.0
NE1 A:TRP342 3.8 39.2 1.0
CD1 A:TRP342 4.3 36.7 1.0
CG A:GLU346 4.3 34.3 1.0
CG A:GLU343 4.3 30.2 1.0
NE2 A:GLN339 4.4 37.0 1.0
O A:HOH420 4.6 26.6 1.0
CB A:GLU346 4.8 30.9 1.0
CE2 A:TRP342 4.9 35.6 1.0

Cadmium binding site 2 out of 3 in 3a05

Go back to Cadmium Binding Sites List in 3a05
Cadmium binding site 2 out of 3 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd375

b:58.1
occ:1.00
O A:HOH583 2.2 53.0 1.0
O A:HOH584 2.5 42.1 1.0
NE2 A:HIS307 2.6 41.1 1.0
OE2 A:GLU13 2.9 91.2 1.0
O A:HOH585 3.0 46.2 1.0
OE1 A:GLU13 3.1 92.8 1.0
CD2 A:HIS307 3.4 40.2 1.0
CD A:GLU13 3.4 94.3 1.0
CE1 A:HIS307 3.6 40.9 1.0
O A:GLU301 4.4 43.5 1.0
CG A:HIS307 4.6 35.3 1.0
ND1 A:HIS307 4.7 42.0 1.0
CG A:GLU13 4.9 96.1 1.0
CE A:LYS247 4.9 53.2 1.0
NZ A:LYS247 4.9 56.5 1.0

Cadmium binding site 3 out of 3 in 3a05

Go back to Cadmium Binding Sites List in 3a05
Cadmium binding site 3 out of 3 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd376

b:53.2
occ:1.00
N A:TRP377 2.2 33.4 1.0
OE2 A:GLU112 2.5 34.0 1.0
OE1 A:GLU112 2.6 29.6 1.0
O A:HOH465 2.7 31.7 1.0
CD A:GLU112 2.9 32.2 1.0
O A:HOH526 2.9 45.4 1.0
CA A:TRP377 3.3 33.9 1.0
C A:TRP377 3.3 35.5 1.0
OE1 A:GLN192 3.7 46.4 1.0
OH A:TYR178 4.1 82.5 1.0
O A:HOH495 4.3 48.1 1.0
CG A:GLU112 4.3 27.3 1.0
CB A:TRP377 4.4 31.7 1.0
O A:TRP377 4.4 35.9 1.0
O A:HOH402 4.5 28.3 1.0
CD A:GLN192 4.9 37.0 1.0

Reference:

W.Tsuchiya, Z.Fujimoto, T.Hasegawa. Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 To Be Published.
Page generated: Wed Oct 28 10:00:50 2020
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