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Iron 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:

Cadmium (Cd) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 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, PDB code: 3a04:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3a04

Go back to Iron Binding Sites List in 3a04
Iron binding site 1 out of 4 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe373

b:44.7
occ:1.00
 FE1 A:SF4373 0.0 44.7 1.0
S2 A:SF4373 2.2 44.9 1.0
SG A:CYS337 2.3 41.0 1.0
S3 A:SF4373 2.3 44.9 1.0
S4 A:SF4373 2.4 46.2 1.0
FE4 A:SF4373 2.6 42.4 1.0
FE3 A:SF4373 2.7 49.0 1.0
FE2 A:SF4373 2.7 49.3 1.0
CB A:CYS337 3.0 39.3 1.0
S1 A:SF4373 3.9 48.7 1.0
CA A:CYS337 4.4 39.0 1.0
CG2 A:ILE323 4.6 40.7 1.0
SG A:CYS303 4.7 38.5 1.0
SG A:CYS327 4.8 55.2 1.0
CA A:CYS334 4.8 45.3 1.0
CB A:CYS327 4.8 57.5 1.0
CG1 A:VAL305 4.8 36.0 1.0
SG A:CYS334 4.8 47.9 1.0
C A:CYS337 5.0 38.1 1.0

Iron binding site 2 out of 4 in 3a04

Go back to Iron Binding Sites List in 3a04
Iron binding site 2 out of 4 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe373

b:49.3
occ:1.00
 FE2 A:SF4373 0.0 49.3 1.0
SG A:CYS327 2.2 55.2 1.0
S1 A:SF4373 2.3 48.7 1.0
S4 A:SF4373 2.3 46.2 1.0
S3 A:SF4373 2.3 44.9 1.0
FE1 A:SF4373 2.7 44.7 1.0
FE3 A:SF4373 2.7 49.0 1.0
FE4 A:SF4373 2.8 42.4 1.0
CB A:CYS327 3.1 57.5 1.0
S2 A:SF4373 3.9 44.9 1.0
CA A:CYS327 4.3 57.9 1.0
NE2 A:GLN293 4.4 69.6 1.0
CG A:PRO300 4.5 48.7 1.0
CA A:GLY298 4.5 57.2 1.0
SG A:CYS337 4.8 41.0 1.0
SG A:CYS334 4.8 47.9 1.0
N A:VAL299 4.8 51.2 1.0
CD A:PRO300 4.9 50.2 1.0
C A:GLY298 4.9 54.7 1.0
N A:PRO300 4.9 49.7 1.0
CG2 A:ILE332 5.0 53.1 1.0

Iron binding site 3 out of 4 in 3a04

Go back to Iron Binding Sites List in 3a04
Iron binding site 3 out of 4 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe373

b:49.0
occ:1.00
 FE3 A:SF4373 0.0 49.0 1.0
SG A:CYS334 2.3 47.9 1.0
S1 A:SF4373 2.3 48.7 1.0
S2 A:SF4373 2.3 44.9 1.0
S4 A:SF4373 2.3 46.2 1.0
FE1 A:SF4373 2.7 44.7 1.0
FE4 A:SF4373 2.7 42.4 1.0
FE2 A:SF4373 2.7 49.3 1.0
CB A:CYS334 3.4 46.4 1.0
CA A:CYS334 3.6 45.3 1.0
S3 A:SF4373 3.9 44.9 1.0
N A:CYS334 4.0 45.5 1.0
CB A:THR284 4.1 44.1 1.0
CG2 A:THR284 4.5 42.8 1.0
NE2 A:GLN293 4.5 69.6 1.0
CB A:CYS337 4.5 39.3 1.0
OG1 A:THR284 4.6 47.0 1.0
N A:GLY286 4.6 52.1 1.0
CA A:GLY286 4.6 56.2 1.0
SG A:CYS303 4.7 38.5 1.0
C A:LEU333 4.7 46.3 1.0
SG A:CYS337 4.7 41.0 1.0
SG A:CYS327 4.7 55.2 1.0
C A:CYS334 4.9 45.5 1.0

Iron binding site 4 out of 4 in 3a04

Go back to Iron Binding Sites List in 3a04
Iron binding site 4 out of 4 in the Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe373

b:42.4
occ:1.00
 FE4 A:SF4373 0.0 42.4 1.0
S3 A:SF4373 2.2 44.9 1.0
S2 A:SF4373 2.3 44.9 1.0
SG A:CYS303 2.4 38.5 1.0
S1 A:SF4373 2.4 48.7 1.0
FE1 A:SF4373 2.6 44.7 1.0
FE3 A:SF4373 2.7 49.0 1.0
FE2 A:SF4373 2.8 49.3 1.0
CB A:CYS303 3.2 38.8 1.0
S4 A:SF4373 3.9 46.2 1.0
CB A:THR284 4.2 44.1 1.0
N A:GLY285 4.3 46.5 1.0
CB A:TYR306 4.4 34.0 1.0
N A:TYR306 4.4 35.0 1.0
CB A:VAL305 4.4 37.7 1.0
CA A:CYS303 4.6 38.5 1.0
CG2 A:THR284 4.6 42.8 1.0
SG A:CYS337 4.7 41.0 1.0
SG A:CYS334 4.7 47.9 1.0
CA A:THR284 4.7 44.6 1.0
SG A:CYS327 4.8 55.2 1.0
CA A:PRO300 5.0 49.0 1.0
CA A:TYR306 5.0 34.0 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: Sun Dec 13 14:59:36 2020

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