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Cadmium in PDB 3a04: Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1

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

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

Protein crystallography data

The structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1, PDB code: 3a04 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) 32.48 / 1.97
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.709, 103.194, 97.806, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23.5

Other elements in 3a04:

The structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 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 (pdb code 3a04). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1, PDB code: 3a04:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3a04

Go back to Cadmium Binding Sites List in 3a04
Cadmium binding site 1 out of 2 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd374

b:34.1
occ:1.00
OE1 A:GLU343 2.2 45.6 1.0
OE1 A:GLU346 2.3 31.7 1.0
OE2 A:GLU343 2.6 47.6 1.0
CD A:GLU343 2.8 41.4 1.0
OE2 A:GLU346 2.8 41.5 1.0
CD A:GLU346 2.9 39.5 1.0
NE1 A:TRP342 3.8 42.7 1.0
CG A:GLU343 4.3 32.3 1.0
CD1 A:TRP342 4.3 39.8 1.0
CG A:GLU346 4.4 36.3 1.0
NE2 A:GLN339 4.5 45.2 1.0
O A:HOH432 4.5 31.6 1.0
CB A:GLU346 4.8 34.3 1.0
CE2 A:TRP342 5.0 40.5 1.0

Cadmium binding site 2 out of 2 in 3a04

Go back to Cadmium Binding Sites List in 3a04
Cadmium binding site 2 out of 2 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd375

b:63.9
occ:1.00
O A:HOH653 2.0 52.8 1.0
NE2 A:HIS307 2.5 46.2 1.0
O A:HOH584 2.6 42.0 1.0
OE2 A:GLU13 3.1 0.3 1.0
CD2 A:HIS307 3.3 45.0 1.0
CE1 A:HIS307 3.5 49.4 1.0
CD A:GLU13 3.9 0.3 1.0
OE1 A:GLU13 4.0 0.6 1.0
O A:GLU301 4.4 45.8 1.0
CG A:HIS307 4.5 39.0 1.0
O A:HOH592 4.6 70.9 1.0
ND1 A:HIS307 4.6 48.1 1.0
NZ A:LYS247 4.8 63.3 1.0

Reference:

W.Tsuchiya, Z.Fujimoto, T.Hasegawa. Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 To Be Published.
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