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Iron 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:

Cadmium (Cd) 3 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 Complex with Tryptophan, PDB code: 3a05:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3a05

Go back to Iron Binding Sites List in 3a05
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe373

b:49.1
occ:1.00
 FE1 A:SF4373 0.0 49.1 1.0
SG A:CYS327 2.2 54.9 1.0
S3 A:SF4373 2.3 47.5 1.0
S2 A:SF4373 2.3 47.8 1.0
S4 A:SF4373 2.4 44.0 1.0
FE4 A:SF4373 2.7 48.0 1.0
FE2 A:SF4373 2.8 41.9 1.0
FE3 A:SF4373 2.8 43.1 1.0
CB A:CYS327 3.2 56.7 1.0
S1 A:SF4373 3.9 44.8 1.0
CA A:CYS327 4.2 57.4 1.0
CA A:GLY298 4.4 61.1 1.0
NE2 A:GLN293 4.7 79.2 1.0
SG A:CYS337 4.7 41.1 1.0
CG A:PRO300 4.7 47.2 1.0
SG A:CYS334 4.8 43.3 1.0
C A:GLY298 4.8 57.9 1.0
CD A:PRO300 4.9 48.7 1.0
N A:VAL299 4.9 54.1 1.0
C A:CYS327 5.0 58.5 1.0

Iron binding site 2 out of 4 in 3a05

Go back to Iron Binding Sites List in 3a05
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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:Fe373

b:41.9
occ:1.00
 FE2 A:SF4373 0.0 41.9 1.0
SG A:CYS337 2.2 41.1 1.0
S1 A:SF4373 2.3 44.8 1.0
S4 A:SF4373 2.3 44.0 1.0
S3 A:SF4373 2.3 47.5 1.0
FE3 A:SF4373 2.7 43.1 1.0
FE1 A:SF4373 2.8 49.1 1.0
FE4 A:SF4373 2.8 48.0 1.0
CB A:CYS337 3.0 38.5 1.0
S2 A:SF4373 3.9 47.8 1.0
CA A:CYS337 4.4 38.0 1.0
SG A:CYS327 4.7 54.9 1.0
SG A:CYS303 4.7 39.2 1.0
CG2 A:ILE323 4.7 40.7 1.0
CA A:CYS334 4.8 45.1 1.0
CB A:CYS327 4.8 56.7 1.0
CG1 A:VAL305 4.9 30.3 1.0
CB A:VAL305 4.9 32.4 1.0
C A:CYS337 5.0 35.6 1.0
SG A:CYS334 5.0 43.3 1.0

Iron binding site 3 out of 4 in 3a05

Go back to Iron Binding Sites List in 3a05
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe 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:Fe373

b:43.1
occ:1.00
 FE3 A:SF4373 0.0 43.1 1.0
S4 A:SF4373 2.2 44.0 1.0
S1 A:SF4373 2.3 44.8 1.0
S2 A:SF4373 2.4 47.8 1.0
SG A:CYS303 2.4 39.2 1.0
FE2 A:SF4373 2.7 41.9 1.0
FE1 A:SF4373 2.8 49.1 1.0
FE4 A:SF4373 2.9 48.0 1.0
CB A:CYS303 3.2 35.1 1.0
S3 A:SF4373 3.9 47.5 1.0
N A:GLY285 4.2 45.0 1.0
CB A:THR284 4.3 43.8 1.0
N A:TYR306 4.3 30.5 1.0
CB A:TYR306 4.4 30.4 1.0
CB A:VAL305 4.5 32.4 1.0
CA A:CYS303 4.6 35.9 1.0
CA A:THR284 4.6 43.0 1.0
SG A:CYS327 4.6 54.9 1.0
SG A:CYS337 4.7 41.1 1.0
CG2 A:THR284 4.8 38.6 1.0
SG A:CYS334 4.9 43.3 1.0
CA A:TYR306 4.9 31.2 1.0
C A:THR284 4.9 43.6 1.0

Iron binding site 4 out of 4 in 3a05

Go back to Iron Binding Sites List in 3a05
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe373

b:48.0
occ:1.00
 FE4 A:SF4373 0.0 48.0 1.0
S2 A:SF4373 2.3 47.8 1.0
S1 A:SF4373 2.3 44.8 1.0
S3 A:SF4373 2.3 47.5 1.0
SG A:CYS334 2.3 43.3 1.0
FE1 A:SF4373 2.7 49.1 1.0
FE2 A:SF4373 2.8 41.9 1.0
FE3 A:SF4373 2.9 43.1 1.0
CB A:CYS334 3.3 45.7 1.0
CA A:CYS334 3.4 45.1 1.0
N A:CYS334 3.9 45.8 1.0
S4 A:SF4373 4.0 44.0 1.0
CB A:THR284 4.1 43.8 1.0
CB A:CYS337 4.5 38.5 1.0
CG2 A:THR284 4.5 38.6 1.0
CA A:GLY286 4.5 52.4 1.0
N A:GLY286 4.5 50.1 1.0
OG1 A:THR284 4.6 44.4 1.0
C A:LEU333 4.7 47.0 1.0
SG A:CYS327 4.7 54.9 1.0
C A:CYS334 4.7 45.3 1.0
SG A:CYS337 4.7 41.1 1.0
OE1 A:GLN293 4.7 79.2 1.0
SG A:CYS303 4.8 39.2 1.0
O A:CYS334 4.9 45.4 1.0
N A:GLY285 4.9 45.0 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: Mon Aug 4 22:59:33 2025

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