Iron in PDB 8tww: Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled

Protein crystallography data

The structure of Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled, PDB code: 8tww was solved by N.Ye, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.98 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.98, 88.131, 102.806, 90, 90, 90
R / Rfree (%) 19.5 / 21.8

Other elements in 8tww:

The structure of Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled (pdb code 8tww). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled, PDB code: 8tww:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 8tww

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Iron binding site 1 out of 5 in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled


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 Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:22.1
occ:1.00
 OE2 A:GLU176 2.0 33.4 1.0
O A:67I301 2.1 21.3 1.0
O A:HOH402 2.2 27.7 1.0
NE2 A:HIS172 2.2 19.6 1.0
ND1 A:HIS79 2.2 22.9 1.0
N A:67I301 2.2 24.4 1.0
C A:67I301 2.9 22.9 1.0
CE1 A:HIS172 3.0 27.7 1.0
CE1 A:HIS79 3.0 24.6 1.0
CA A:67I301 3.1 24.3 1.0
CD A:GLU176 3.2 45.1 1.0
CD2 A:HIS172 3.3 20.8 1.0
CG A:HIS79 3.3 23.4 1.0
CB A:HIS79 3.7 22.8 1.0
CB A:67I301 3.8 26.0 1.0
CG A:GLU176 3.9 43.9 1.0
OXT A:67I301 4.1 24.8 1.0
OE1 A:GLU176 4.1 53.5 1.0
NE2 A:HIS79 4.2 25.4 1.0
ND1 A:HIS172 4.2 25.2 1.0
CD2 A:HIS79 4.4 23.6 1.0
OD1 A:ASP76 4.4 40.8 1.0
CG A:HIS172 4.4 23.5 1.0
CE2 A:PHE48 5.0 24.4 1.0

Iron binding site 2 out of 5 in 8tww

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Iron binding site 2 out of 5 in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled


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 Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:36.0
occ:0.27
 OE1 A:GLU176 2.1 53.5 1.0
O A:HOH492 2.1 43.9 1.0
OE1 A:GLU140 2.1 39.4 0.5
OD1 A:ASP76 2.3 40.8 1.0
OD2 A:ASP76 2.5 35.3 1.0
CG A:ASP76 2.8 35.6 1.0
CD A:GLU140 2.9 38.9 0.5
CD A:GLU176 3.2 45.1 1.0
CE1 A:HIS72 3.6 44.9 1.0
OE2 A:GLU140 3.6 40.7 0.5
OE2 A:GLU176 3.6 33.4 1.0
O A:HOH402 3.8 27.7 1.0
CG A:GLU140 3.8 36.9 0.5
NE2 A:HIS72 4.0 44.1 1.0
CB A:ASP76 4.3 29.7 1.0
FE A:FE304 4.3 94.8 1.0
OE1 A:GLU140 4.3 43.9 0.5
CG A:GLU140 4.3 36.7 0.5
CD A:GLU140 4.4 42.6 0.5
CG A:GLU176 4.4 43.9 1.0
ND1 A:HIS72 4.5 43.4 1.0
CB A:GLU176 4.6 41.1 1.0
CB A:GLU140 4.6 30.7 0.5
O A:HOH409 4.6 38.3 1.0
CB A:GLU140 4.7 30.4 0.5
CA A:GLU176 4.7 41.6 1.0
O A:HOH508 4.8 66.8 1.0

Iron binding site 3 out of 5 in 8tww

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Iron binding site 3 out of 5 in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled


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 Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe304

b:94.8
occ:1.00
 OE1 A:GLU140 2.4 43.9 0.5
O A:HOH401 2.5 53.7 1.0
O A:HOH492 2.6 43.9 1.0
NE2 A:HIS72 2.7 44.1 1.0
OE2 A:GLU140 2.8 46.2 0.5
CD A:GLU140 2.8 42.6 0.5
O A:HOH508 2.9 66.8 1.0
CD2 A:HIS72 3.4 46.8 1.0
O A:GLU176 3.6 48.9 1.0
CE1 A:HIS72 3.8 44.9 1.0
CG A:GLU140 4.2 36.7 0.5
FE A:FE303 4.3 36.0 0.3
O A:GLY178 4.5 66.5 1.0
CG A:GLU140 4.5 36.9 0.5
CG A:HIS72 4.6 42.8 1.0
C A:GLU176 4.8 44.0 1.0
ND1 A:HIS72 4.8 43.4 1.0
CB A:GLU140 5.0 30.7 0.5
CB A:GLU140 5.0 30.4 0.5

Iron binding site 4 out of 5 in 8tww

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Iron binding site 4 out of 5 in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled


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 Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.7
occ:0.63
 OE1 B:GLU140 2.0 42.5 1.0
OD1 B:ASP76 2.1 36.4 1.0
OE1 B:GLU176 2.1 38.6 1.0
ND1 B:HIS179 2.5 48.8 1.0
O B:HOH433 2.6 39.7 1.0
OD2 B:ASP76 2.6 38.9 1.0
CG B:ASP76 2.7 36.0 1.0
CD B:GLU140 2.9 41.3 1.0
CD B:GLU176 3.0 35.3 1.0
OE2 B:GLU140 3.3 49.5 1.0
CE1 B:HIS179 3.3 48.5 1.0
OE2 B:GLU176 3.3 38.5 1.0
CG B:HIS179 3.6 49.6 1.0
CB B:HIS179 4.0 59.2 1.0
CE1 B:HIS72 4.0 40.3 1.0
CB B:ASP76 4.2 31.6 1.0
O B:HOH464 4.3 35.5 1.0
CG B:GLU140 4.3 40.4 1.0
CG B:GLU176 4.4 35.5 1.0
NE2 B:HIS72 4.5 45.4 1.0
NE2 B:HIS179 4.5 56.7 1.0
CA B:GLU176 4.6 44.7 1.0
CD2 B:HIS179 4.6 59.4 1.0
CE1 B:HIS79 4.7 29.0 1.0
CB B:GLU176 4.7 40.9 1.0
FE B:FE303 4.8 25.6 0.9
O B:HOH406 4.8 32.7 1.0
CA B:ASP76 4.9 28.5 1.0
CB B:GLU140 5.0 28.4 1.0
ND1 B:HIS72 5.0 44.8 1.0

Iron binding site 5 out of 5 in 8tww

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Iron binding site 5 out of 5 in the Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Nitrile Synthase Aetd with Substrate Bound and Cofactor Fully Assembled within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:25.6
occ:0.92
 OE2 B:GLU176 2.0 38.5 1.0
O B:67I301 2.1 26.3 1.0
ND1 B:HIS79 2.2 21.2 1.0
NE2 B:HIS172 2.2 27.5 1.0
N B:67I301 2.3 33.6 1.0
C B:67I301 2.9 30.1 1.0
CE1 B:HIS79 3.0 29.0 1.0
CA B:67I301 3.0 33.3 1.0
CE1 B:HIS172 3.1 24.1 1.0
CD B:GLU176 3.2 35.3 1.0
CG B:HIS79 3.2 26.1 1.0
CD2 B:HIS172 3.3 24.2 1.0
CB B:HIS79 3.6 23.4 1.0
CB B:67I301 3.6 35.1 1.0
CG B:GLU176 3.9 35.5 1.0
O B:HOH433 3.9 39.7 1.0
OXT B:67I301 4.1 29.6 1.0
OE1 B:GLU176 4.1 38.6 1.0
NE2 B:HIS79 4.2 24.9 1.0
ND1 B:HIS172 4.2 24.8 1.0
CD2 B:HIS79 4.3 25.6 1.0
OD1 B:ASP76 4.3 36.4 1.0
CG B:HIS172 4.4 24.9 1.0
FE B:FE302 4.8 27.7 0.6
CE2 B:PHE48 4.9 32.9 1.0

Reference:

S.Adak, N.Ye, L.A.Calderone, R.J.B.Schafer, A.L.Lukowski, M.-E.Pandelia, C.L.Drennan, B.S.Moore. Oxidative Rearrangement of Tryptophan to Indole Nitrile By A Single Diiron Enzyme To Be Published.
Page generated: Sat Sep 28 21:48:02 2024

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