Iron in PDB 6qka: Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase

Enzymatic activity of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase

All present enzymatic activity of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase:
1.13.11.55;

Protein crystallography data

The structure of Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase, PDB code: 6qka 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) 76.95 / 2.10
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 161.913, 161.913, 153.901, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.3

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 6qka

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Iron binding site 1 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:0.9
occ:1.00
 OE2 A:GLU114 2.3 42.4 1.0
O A:HOH622 2.5 51.6 1.0
NE2 A:HIS90 2.7 63.3 1.0
O A:HOH618 2.9 76.4 1.0
CD A:GLU114 3.0 37.2 1.0
OE1 A:GLU114 3.1 42.7 1.0
NE2 A:HIS86 3.1 39.1 1.0
CE1 A:HIS90 3.3 62.2 1.0
O A:HOH527 3.9 31.1 1.0
CD2 A:HIS90 4.0 62.3 1.0
CD2 A:HIS86 4.0 36.9 1.0
CE1 A:HIS86 4.1 38.5 1.0
OD1 A:ASN9 4.4 49.2 1.0
CG A:GLU114 4.4 30.1 1.0
ND1 A:HIS90 4.5 63.5 1.0
OG1 A:THR78 4.7 26.0 1.0
CB A:ASN9 4.7 25.1 1.0
CG A:ASN9 4.9 39.3 1.0
CG A:HIS90 4.9 58.7 1.0
CA A:GLY208 5.0 23.6 1.0

Iron binding site 2 out of 6 in 6qka

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Iron binding site 2 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:0.5
occ:1.00
 OE2 B:GLU114 2.3 40.5 1.0
NE2 B:HIS90 2.6 46.5 1.0
NE2 B:HIS86 2.8 38.2 1.0
CD B:GLU114 3.0 39.5 1.0
OE1 B:GLU114 3.0 44.2 1.0
O B:HOH616 3.1 78.0 1.0
O B:HOH621 3.2 64.2 1.0
CE1 B:HIS90 3.4 47.1 1.0
CD2 B:HIS86 3.5 34.8 1.0
CD2 B:HIS90 3.6 46.0 1.0
O B:HOH552 3.7 28.8 1.0
CE1 B:HIS86 3.8 37.6 1.0
CG B:GLU114 4.5 34.1 1.0
OG1 B:THR78 4.6 25.9 1.0
ND1 B:HIS90 4.6 45.8 1.0
CG B:HIS86 4.7 36.1 1.0
CG B:HIS90 4.7 45.4 1.0
ND1 B:HIS86 4.8 34.4 1.0
CE B:MET89 4.9 45.1 1.0
CB B:ALA7 5.0 27.8 1.0

Iron binding site 3 out of 6 in 6qka

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Iron binding site 3 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:0.2
occ:1.00
 OE2 C:GLU114 2.3 47.1 1.0
NE2 C:HIS90 2.4 58.2 1.0
O C:HOH609 2.5 59.9 1.0
NE2 C:HIS86 2.6 37.7 1.0
O C:HOH590 2.6 73.5 1.0
OE1 C:GLU114 2.9 39.3 1.0
CD C:GLU114 2.9 40.8 1.0
CE1 C:HIS90 3.2 56.9 1.0
CD2 C:HIS86 3.4 37.6 1.0
CD2 C:HIS90 3.5 56.7 1.0
CE1 C:HIS86 3.6 37.5 1.0
O C:HOH551 4.0 33.2 1.0
ND1 C:HIS90 4.4 55.8 1.0
CG C:GLU114 4.4 28.6 1.0
CG C:HIS90 4.5 51.2 1.0
CG C:HIS86 4.6 40.0 1.0
ND1 C:HIS86 4.7 38.3 1.0
OG1 C:THR78 4.7 29.5 1.0
OD1 C:ASN9 4.7 48.7 1.0
CA C:GLY208 4.8 23.8 1.0
CE C:MET89 4.9 52.9 1.0
CB C:ALA7 5.0 21.2 1.0

Iron binding site 4 out of 6 in 6qka

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Iron binding site 4 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:0.3
occ:1.00
 O D:HOH612 2.3 66.5 1.0
OE2 D:GLU114 2.4 37.4 1.0
NE2 D:HIS90 2.6 60.4 1.0
O D:HOH615 2.7 68.0 1.0
NE2 D:HIS86 2.8 41.6 1.0
OE1 D:GLU114 3.0 41.3 1.0
CD D:GLU114 3.1 39.7 1.0
CE1 D:HIS90 3.4 62.1 1.0
CD2 D:HIS86 3.6 36.6 1.0
CD2 D:HIS90 3.6 59.4 1.0
CE1 D:HIS86 3.8 36.0 1.0
O D:HOH567 3.9 29.0 1.0
CG D:GLU114 4.6 35.6 1.0
ND1 D:HIS90 4.6 60.7 1.0
OG1 D:THR78 4.7 26.1 1.0
CG D:HIS90 4.7 54.8 1.0
CG D:HIS86 4.8 38.0 1.0
ND1 D:HIS86 4.9 37.8 1.0
CE D:MET89 4.9 47.7 1.0
OD1 D:ASN9 4.9 49.7 1.0

Iron binding site 5 out of 6 in 6qka

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Iron binding site 5 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:0.3
occ:1.00
 O E:HOH606 2.3 65.7 1.0
OE2 E:GLU114 2.5 48.2 1.0
O E:HOH615 2.6 62.0 1.0
NE2 E:HIS90 2.6 53.6 1.0
NE2 E:HIS86 3.0 30.9 1.0
OE1 E:GLU114 3.1 46.4 1.0
CD E:GLU114 3.1 43.3 1.0
CE1 E:HIS90 3.3 50.1 1.0
CD2 E:HIS90 3.8 50.5 1.0
CD2 E:HIS86 3.8 30.9 1.0
O E:HOH566 3.9 26.6 1.0
CE1 E:HIS86 4.0 26.6 1.0
ND1 E:HIS90 4.6 50.7 1.0
CG E:GLU114 4.6 31.2 1.0
OD1 E:ASN9 4.7 50.8 1.0
OG1 E:THR78 4.8 23.6 1.0
CE E:MET89 4.8 46.5 1.0
CG E:HIS90 4.8 46.8 1.0

Iron binding site 6 out of 6 in 6qka

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Iron binding site 6 out of 6 in the Di-Tert-Butyl Polysulfide 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 Di-Tert-Butyl Polysulfide Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:1.0
occ:1.00
 OE2 F:GLU114 2.3 46.0 1.0
O F:HOH598 2.4 45.5 1.0
CE1 F:HIS90 2.5 56.7 1.0
NE2 F:HIS86 2.6 38.4 1.0
O F:HOH621 2.8 73.7 1.0
OE1 F:GLU114 3.0 40.4 1.0
CD F:GLU114 3.0 38.1 1.0
NE2 F:HIS90 3.1 53.4 1.0
CD2 F:HIS86 3.4 35.4 1.0
CE1 F:HIS86 3.6 38.9 1.0
ND1 F:HIS90 3.7 51.6 1.0
O F:HOH525 3.7 26.7 1.0
CD2 F:HIS90 4.4 51.4 1.0
CG F:GLU114 4.5 34.8 1.0
OG1 F:THR78 4.6 25.4 1.0
CG F:HIS86 4.6 38.0 1.0
ND1 F:HIS86 4.6 37.6 1.0
CG F:HIS90 4.7 50.3 1.0
CE F:MET89 4.9 46.5 1.0
OD1 F:ASN9 4.9 53.9 1.0
CA F:GLY208 5.0 27.0 1.0
CB F:ALA7 5.0 21.7 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: Sun Dec 13 16:52:06 2020

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