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Iron in PDB 2yaw: Hg Inhibited Sulfur Oxygenase Reductase

Enzymatic activity of Hg Inhibited Sulfur Oxygenase Reductase

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

Protein crystallography data

The structure of Hg Inhibited Sulfur Oxygenase Reductase, PDB code: 2yaw was solved by A.Veith, T.Urich, K.Seyfarth, J.Protze, C.Frazao, A.Kletzin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.04 / 2.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 161.876, 161.876, 154.373, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.3

Other elements in 2yaw:

The structure of Hg Inhibited Sulfur Oxygenase Reductase also contains other interesting chemical elements:

Mercury (Hg) 12 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 1 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:38.0
occ:1.00
 NE2 A:HIS86 2.2 30.9 1.0
O A:HOH2017 2.2 54.0 1.0
NE2 A:HIS90 2.2 39.2 1.0
OE2 A:GLU114 2.2 29.1 1.0
O A:HOH2020 2.3 40.6 1.0
OE1 A:GLU114 2.4 27.7 1.0
CD A:GLU114 2.6 26.9 1.0
CE1 A:HIS86 3.1 27.1 1.0
CE1 A:HIS90 3.1 37.5 1.0
CD2 A:HIS86 3.2 27.9 1.0
CD2 A:HIS90 3.3 34.3 1.0
O A:HOH2022 4.0 24.9 1.0
CG A:GLU114 4.1 17.1 1.0
ND1 A:HIS86 4.2 29.4 1.0
ND1 A:HIS90 4.2 41.8 1.0
CG A:HIS86 4.3 28.4 1.0
CG A:HIS90 4.4 35.5 1.0
CA A:GLY208 4.7 15.9 1.0
ND2 A:ASN9 4.8 39.8 1.0
OG1 A:THR78 4.8 16.8 1.0
CB A:ALA7 4.8 19.4 1.0
CE A:MET89 4.9 17.4 1.0

Iron binding site 2 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 2 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:37.2
occ:1.00
 NE2 B:HIS86 2.1 31.1 1.0
OE2 B:GLU114 2.2 28.9 1.0
NE2 B:HIS90 2.2 37.5 1.0
O B:HOH2025 2.3 41.7 1.0
O B:HOH2026 2.3 37.0 1.0
OE1 B:GLU114 2.4 28.4 1.0
CD B:GLU114 2.6 26.1 1.0
CE1 B:HIS86 3.0 30.4 1.0
CE1 B:HIS90 3.1 35.4 1.0
CD2 B:HIS86 3.2 26.9 1.0
CD2 B:HIS90 3.3 35.7 1.0
O B:HOH2031 4.0 20.7 1.0
CG B:GLU114 4.1 22.3 1.0
ND1 B:HIS86 4.2 28.9 1.0
CG B:HIS86 4.3 28.4 1.0
ND1 B:HIS90 4.3 39.1 1.0
CG B:HIS90 4.4 34.0 1.0
CA B:GLY208 4.7 12.5 1.0
CB B:ALA7 4.7 15.4 1.0
ND2 B:ASN9 4.8 42.5 1.0
OG1 B:THR78 4.8 19.4 1.0
CE B:MET89 4.9 19.0 1.0
CB B:GLU114 5.0 15.9 1.0

Iron binding site 3 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 3 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:39.1
occ:1.00
 OE2 C:GLU114 2.2 32.4 1.0
NE2 C:HIS86 2.2 29.1 1.0
O C:HOH2021 2.2 39.9 1.0
NE2 C:HIS90 2.2 38.4 1.0
O C:HOH2028 2.2 46.7 1.0
OE1 C:GLU114 2.4 29.9 1.0
CD C:GLU114 2.6 26.8 1.0
CE1 C:HIS90 3.1 37.6 1.0
CE1 C:HIS86 3.1 26.8 1.0
CD2 C:HIS86 3.2 28.2 1.0
CD2 C:HIS90 3.3 36.1 1.0
CG C:GLU114 4.1 19.1 1.0
O C:HOH2020 4.1 20.4 1.0
ND1 C:HIS86 4.2 29.4 1.0
ND1 C:HIS90 4.2 42.0 1.0
CG C:HIS86 4.3 30.1 1.0
CG C:HIS90 4.4 35.0 1.0
CA C:GLY208 4.6 17.5 1.0
ND2 C:ASN9 4.7 40.7 1.0
CB C:ALA7 4.8 16.4 1.0
OG1 C:THR78 4.8 22.7 1.0
CE C:MET89 4.9 18.3 1.0
CB C:GLU114 5.0 15.8 1.0

Iron binding site 4 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 4 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:39.4
occ:1.00
 NE2 D:HIS86 2.1 28.3 1.0
NE2 D:HIS90 2.2 36.5 1.0
O D:HOH2023 2.2 38.4 1.0
OE2 D:GLU114 2.2 31.4 1.0
O D:HOH2024 2.2 36.7 1.0
OE1 D:GLU114 2.4 30.6 1.0
CD D:GLU114 2.7 25.5 1.0
CE1 D:HIS86 3.0 28.9 1.0
CD2 D:HIS86 3.1 24.1 1.0
CE1 D:HIS90 3.1 36.4 1.0
CD2 D:HIS90 3.2 33.2 1.0
O D:HOH2028 4.1 22.2 1.0
ND1 D:HIS86 4.1 29.9 1.0
CG D:GLU114 4.1 18.6 1.0
CG D:HIS86 4.2 28.4 1.0
ND1 D:HIS90 4.2 42.6 1.0
CG D:HIS90 4.3 36.2 1.0
OG1 D:THR78 4.7 19.3 1.0
CA D:GLY208 4.7 15.4 1.0
CB D:ALA7 4.8 18.3 1.0
CE D:MET89 4.9 16.2 1.0
ND2 D:ASN9 4.9 41.3 1.0

Iron binding site 5 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 5 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:39.0
occ:1.00
 O E:HOH2023 2.2 39.3 1.0
O E:HOH2020 2.2 36.3 1.0
NE2 E:HIS90 2.2 38.4 1.0
OE2 E:GLU114 2.2 33.9 1.0
NE2 E:HIS86 2.2 28.1 1.0
OE1 E:GLU114 2.4 31.8 1.0
CD E:GLU114 2.6 29.7 1.0
CE1 E:HIS90 3.1 36.4 1.0
CE1 E:HIS86 3.1 24.5 1.0
CD2 E:HIS86 3.2 24.8 1.0
CD2 E:HIS90 3.3 33.3 1.0
O E:HOH2019 4.0 22.7 1.0
CG E:GLU114 4.1 19.1 1.0
ND1 E:HIS90 4.2 39.0 1.0
ND1 E:HIS86 4.3 31.0 1.0
CG E:HIS86 4.3 27.3 1.0
CG E:HIS90 4.4 34.6 1.0
CA E:GLY208 4.7 10.6 1.0
ND2 E:ASN9 4.7 42.8 1.0
OG1 E:THR78 4.8 18.8 1.0
CB E:ALA7 4.9 17.4 1.0
CE E:MET89 4.9 17.6 1.0
CB E:GLU114 5.0 18.6 1.0

Iron binding site 6 out of 6 in 2yaw

Go back to Iron Binding Sites List in 2yaw
Iron binding site 6 out of 6 in the Hg 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 Hg Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:35.1
occ:1.00
 NE2 F:HIS86 2.1 30.6 1.0
OE2 F:GLU114 2.1 29.1 1.0
O F:HOH2030 2.2 44.8 1.0
O F:HOH2031 2.3 35.2 1.0
NE2 F:HIS90 2.3 38.6 1.0
OE1 F:GLU114 2.4 27.1 1.0
CD F:GLU114 2.6 26.3 1.0
CE1 F:HIS86 3.0 28.0 1.0
CD2 F:HIS86 3.1 25.9 1.0
CE1 F:HIS90 3.1 36.8 1.0
CD2 F:HIS90 3.3 34.9 1.0
O F:HOH2034 3.8 17.9 1.0
CG F:GLU114 4.1 19.0 1.0
ND1 F:HIS86 4.2 29.4 1.0
CG F:HIS86 4.2 27.3 1.0
ND1 F:HIS90 4.3 41.8 1.0
CG F:HIS90 4.4 34.5 1.0
CA F:GLY208 4.7 15.8 1.0
OG1 F:THR78 4.7 20.2 1.0
CB F:ALA7 4.7 18.0 1.0
ND2 F:ASN9 4.8 39.0 1.0
CE F:MET89 4.9 19.0 1.0
CB F:GLU114 5.0 17.7 1.0

Reference:

A.Veith, T.Urich, K.Seyfarth, J.Protze, C.Frazao, A.Kletzin. Substrate Pathways and Mechanisms of Inhibition in the Sulfur Oxygenase Reductase of Acidianus Ambivalens. Front.Microbiol. V. 2 37 2011.
ISSN: ESSN 1664-302X
PubMed: 21747782
DOI: 10.3389/FMICB.2011.00037
Page generated: Sun Aug 4 05:11:11 2024

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