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Iron in PDB 6qkm: Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase

Enzymatic activity of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase

All present enzymatic activity of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase:
1.13.11.55;

Protein crystallography data

The structure of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase, PDB code: 6qkm was solved by C.Frazao, A.Klezin, U.Poell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.90 / 2.10
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 162.012, 162.012, 153.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase (pdb code 6qkm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase, PDB code: 6qkm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 6qkm

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Iron binding site 1 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:44.0
occ:1.00
 OE2 A:GLU114 2.2 29.3 1.0
NE2 A:HIS90 2.3 46.3 1.0
NE2 A:HIS86 2.3 33.7 1.0
OE1 A:GLU114 2.4 33.4 1.0
CD A:GLU114 2.6 34.0 1.0
O A:HOH629 2.6 39.2 1.0
CE1 A:HIS90 3.1 39.6 1.0
O A:HOH637 3.1 50.1 1.0
CD2 A:HIS86 3.3 30.5 1.0
CE1 A:HIS86 3.3 34.7 1.0
CD2 A:HIS90 3.4 44.7 1.0
O A:HOH546 4.0 28.3 1.0
CG A:GLU114 4.1 28.0 1.0
ND1 A:HIS90 4.3 46.6 1.0
ND1 A:HIS86 4.4 32.2 1.0
CG A:HIS86 4.4 34.1 1.0
CG A:HIS90 4.4 39.8 1.0
CA A:GLY208 4.7 28.4 1.0
OG1 A:THR78 4.7 23.1 1.0
OD1 A:ASN9 4.8 39.8 1.0
CB A:ALA7 4.8 25.3 1.0
CE A:MET89 5.0 39.7 1.0

Iron binding site 2 out of 7 in 6qkm

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Iron binding site 2 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:43.0
occ:1.00
 NE2 B:HIS90 2.2 42.5 1.0
OE2 B:GLU114 2.2 37.1 1.0
NE2 B:HIS86 2.3 35.3 1.0
OE1 B:GLU114 2.5 36.7 1.0
O B:HOH620 2.5 45.7 1.0
CD B:GLU114 2.7 31.2 1.0
CE1 B:HIS90 3.0 43.3 1.0
CD2 B:HIS86 3.2 27.9 1.0
CE1 B:HIS86 3.3 35.0 1.0
CD2 B:HIS90 3.3 40.4 1.0
O B:HOH548 4.0 31.1 1.0
CG B:GLU114 4.2 29.6 1.0
ND1 B:HIS90 4.2 39.4 1.0
CG B:HIS86 4.3 35.9 1.0
ND1 B:HIS86 4.4 32.5 1.0
CG B:HIS90 4.4 39.5 1.0
CA B:GLY208 4.6 28.1 1.0
CB B:ALA7 4.9 19.8 1.0
OG1 B:THR78 4.9 26.6 1.0
CE B:MET89 4.9 37.6 1.0
OD1 B:ASN9 5.0 39.0 1.0

Iron binding site 3 out of 7 in 6qkm

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Iron binding site 3 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:44.4
occ:1.00
 NE2 C:HIS90 2.1 44.5 1.0
NE2 C:HIS86 2.3 31.7 1.0
OE1 C:GLU114 2.3 35.0 1.0
O C:HOH617 2.3 41.9 1.0
OE2 C:GLU114 2.3 37.0 1.0
O C:HOH611 2.4 41.3 1.0
CD C:GLU114 2.6 36.1 1.0
CE1 C:HIS90 3.0 40.4 1.0
CD2 C:HIS86 3.2 30.5 1.0
CD2 C:HIS90 3.2 40.3 1.0
CE1 C:HIS86 3.2 33.9 1.0
CG C:GLU114 4.1 30.6 1.0
O C:HOH554 4.1 30.9 1.0
ND1 C:HIS90 4.1 40.8 1.0
CG C:HIS90 4.3 38.9 1.0
CG C:HIS86 4.3 30.6 1.0
ND1 C:HIS86 4.3 34.5 1.0
CA C:GLY208 4.6 25.2 1.0
CE C:MET89 4.7 37.8 1.0
OG1 C:THR78 4.8 28.6 1.0
CB C:ALA7 4.8 23.9 1.0
OD1 C:ASN9 4.9 43.9 1.0
CB C:GLU114 5.0 26.3 1.0

Iron binding site 4 out of 7 in 6qkm

Go back to Iron Binding Sites List in 6qkm
Iron binding site 4 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:43.5
occ:1.00
 NE2 D:HIS86 2.2 39.1 1.0
NE2 D:HIS90 2.2 38.1 1.0
O D:HOH607 2.3 39.9 1.0
OE2 D:GLU114 2.4 36.7 1.0
OE1 D:GLU114 2.4 35.4 1.0
O D:HOH616 2.5 43.3 1.0
CD D:GLU114 2.7 33.7 1.0
CE1 D:HIS90 3.1 35.7 1.0
CD2 D:HIS86 3.1 31.3 1.0
CE1 D:HIS86 3.2 33.8 1.0
CD2 D:HIS90 3.3 37.9 1.0
O D:HOH534 4.2 28.8 1.0
CG D:GLU114 4.2 35.8 1.0
ND1 D:HIS90 4.3 44.4 1.0
CG D:HIS86 4.3 32.6 1.0
ND1 D:HIS86 4.3 31.8 1.0
CG D:HIS90 4.4 39.2 1.0
CA D:GLY208 4.6 25.7 1.0
CE D:MET89 4.8 37.8 1.0
CB D:ALA7 4.8 25.4 1.0
OG1 D:THR78 4.9 26.7 1.0

Iron binding site 5 out of 7 in 6qkm

Go back to Iron Binding Sites List in 6qkm
Iron binding site 5 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:44.5
occ:1.00
 NE2 E:HIS90 2.2 39.3 1.0
O E:HOH613 2.3 41.8 1.0
NE2 E:HIS86 2.3 29.4 1.0
O E:HOH618 2.3 36.3 1.0
OE2 E:GLU114 2.3 37.4 1.0
OE1 E:GLU114 2.4 35.3 1.0
CD E:GLU114 2.7 33.5 1.0
CE1 E:HIS90 3.1 40.3 1.0
CE1 E:HIS86 3.2 30.4 1.0
CD2 E:HIS86 3.3 29.5 1.0
CD2 E:HIS90 3.3 36.0 1.0
O E:HOH535 4.1 27.8 1.0
CG E:GLU114 4.2 28.2 1.0
ND1 E:HIS90 4.3 36.0 1.0
ND1 E:HIS86 4.3 31.7 1.0
CG E:HIS86 4.4 33.3 1.0
CG E:HIS90 4.4 34.9 1.0
CA E:GLY208 4.6 27.8 1.0
CE E:MET89 4.8 36.6 1.0
OG1 E:THR78 4.9 22.2 1.0
CB E:ALA7 4.9 25.2 1.0
OD1 E:ASN9 5.0 42.3 1.0

Iron binding site 6 out of 7 in 6qkm

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Iron binding site 6 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:43.1
occ:1.00
 NE2 F:HIS86 2.2 31.7 1.0
NE2 F:HIS90 2.2 41.4 1.0
OE2 F:GLU114 2.3 34.8 1.0
OE1 F:GLU114 2.4 29.6 1.0
O F:HOH624 2.5 37.6 1.0
O F:HOH629 2.6 39.8 1.0
CD F:GLU114 2.7 31.9 1.0
CD2 F:HIS86 3.2 30.7 1.0
CE1 F:HIS90 3.2 37.8 1.0
CE1 F:HIS86 3.2 36.5 1.0
CD2 F:HIS90 3.2 33.4 1.0
O F:HOH516 3.9 27.1 1.0
CG F:GLU114 4.2 29.2 1.0
ND1 F:HIS86 4.3 32.9 1.0
ND1 F:HIS90 4.3 40.9 1.0
CG F:HIS86 4.3 34.6 1.0
CG F:HIS90 4.4 37.3 1.0
CA F:GLY208 4.6 27.4 1.0
OD1 F:ASN9 4.8 41.6 1.0
OG1 F:THR78 4.9 24.3 1.0
CE F:MET89 4.9 38.7 1.0
CB F:ALA7 4.9 21.4 1.0

Iron binding site 7 out of 7 in 6qkm

Go back to Iron Binding Sites List in 6qkm
Iron binding site 7 out of 7 in the Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Diallyl Trisulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe402

b:56.3
occ:1.00
 OE1 F:GLU88 2.4 42.2 1.0
O F:HOH632 2.5 46.2 1.0
OE2 F:GLU88 3.1 52.0 1.0
CD F:GLU88 3.1 45.6 1.0
O F:HOH631 3.2 47.2 1.0
NE2 F:HIS37 3.9 37.4 1.0
CE1 F:HIS37 4.4 33.6 1.0
CG F:GLU88 4.5 43.4 1.0
NE2 F:GLN92 4.6 50.2 1.0
CD2 F:HIS37 4.9 36.4 1.0

Reference:

C.Frazao, A.Klezin. Multiple Sulfane Modifications in Active-Site Cysteine Thiols of Two Sulfur Oxygenase Reductases and Analysis of Substrate/Product Channels To Be Published.
Page generated: Wed Aug 7 07:59:44 2024

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