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Iron in PDB 2yav: Zn Inhibited Sulfur Oxygenase Reductase

Enzymatic activity of Zn Inhibited Sulfur Oxygenase Reductase

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

Protein crystallography data

The structure of Zn Inhibited Sulfur Oxygenase Reductase, PDB code: 2yav 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) 38.20 / 1.70
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 162.074, 162.074, 154.237, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.3

Other elements in 2yav:

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

Zinc (Zn) 6 atoms
Chlorine (Cl) 6 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 2yav

Go back to Iron Binding Sites List in 2yav
Iron binding site 1 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:15.4
occ:1.00
 NE2 A:HIS86 2.0 18.6 1.0
O A:HOH2074 2.1 19.7 1.0
NE2 A:HIS90 2.1 23.0 1.0
OE2 A:GLU114 2.2 17.5 1.0
OE1 A:GLU114 2.3 17.3 1.0
O A:HOH2006 2.3 21.5 1.0
CD A:GLU114 2.5 14.5 1.0
CE1 A:HIS86 3.0 19.2 1.0
CD2 A:HIS86 3.1 18.6 1.0
CE1 A:HIS90 3.1 28.2 1.0
CD2 A:HIS90 3.2 22.4 1.0
O A:HOH2096 4.0 16.1 1.0
CG A:GLU114 4.1 15.1 1.0
ND1 A:HIS86 4.1 18.0 1.0
CG A:HIS86 4.2 16.4 1.0
ND1 A:HIS90 4.2 25.1 1.0
CG A:HIS90 4.3 22.2 1.0
ND2 A:ASN9 4.3 31.7 1.0
O A:HOH2004 4.6 41.4 1.0
OG1 A:THR78 4.7 13.2 1.0
CA A:GLY208 4.7 18.6 1.0
CB A:ALA7 4.7 15.4 1.0
CE A:MET89 4.7 24.9 1.0
CB A:GLU114 5.0 15.1 1.0

Iron binding site 2 out of 6 in 2yav

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Iron binding site 2 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:15.4
occ:1.00
 NE2 B:HIS86 2.1 13.2 1.0
NE2 B:HIS90 2.1 21.4 1.0
O B:HOH2063 2.1 22.4 1.0
OE2 B:GLU114 2.2 15.8 1.0
OE1 B:GLU114 2.2 17.8 1.0
O B:HOH2007 2.2 19.8 1.0
CD B:GLU114 2.5 17.8 1.0
CE1 B:HIS86 3.0 20.5 1.0
CE1 B:HIS90 3.1 25.0 1.0
CD2 B:HIS86 3.1 14.8 1.0
CD2 B:HIS90 3.2 18.0 1.0
O B:HOH2085 4.0 14.2 1.0
CG B:GLU114 4.0 14.5 1.0
ND1 B:HIS86 4.2 17.7 1.0
ND1 B:HIS90 4.2 22.6 1.0
CG B:HIS86 4.2 13.8 1.0
ND2 B:ASN9 4.3 39.7 1.0
CG B:HIS90 4.3 20.2 1.0
O B:HOH2005 4.6 45.5 1.0
CA B:GLY208 4.6 14.0 1.0
CB B:ALA7 4.7 14.2 1.0
OG1 B:THR78 4.7 13.8 1.0
CE B:MET89 4.8 24.5 1.0
CB B:GLU114 4.9 15.7 1.0

Iron binding site 3 out of 6 in 2yav

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Iron binding site 3 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:15.6
occ:1.00
 O C:HOH2063 2.1 19.9 1.0
NE2 C:HIS86 2.1 16.2 1.0
NE2 C:HIS90 2.1 24.7 1.0
OE2 C:GLU114 2.2 18.2 1.0
O C:HOH2005 2.2 22.5 1.0
OE1 C:GLU114 2.3 14.5 1.0
CD C:GLU114 2.6 14.0 1.0
CE1 C:HIS86 3.0 16.4 1.0
CE1 C:HIS90 3.0 21.3 1.0
CD2 C:HIS86 3.1 17.1 1.0
CD2 C:HIS90 3.1 23.9 1.0
O C:HOH2088 4.0 15.2 1.0
CG C:GLU114 4.1 12.1 1.0
ND1 C:HIS86 4.2 18.6 1.0
ND1 C:HIS90 4.2 23.5 1.0
CG C:HIS86 4.2 13.2 1.0
ND2 C:ASN9 4.3 34.0 1.0
CG C:HIS90 4.3 23.4 1.0
O C:HOH2003 4.6 47.0 1.0
CA C:GLY208 4.7 16.4 1.0
OG1 C:THR78 4.7 15.6 1.0
CE C:MET89 4.7 26.9 1.0
CB C:ALA7 4.8 13.3 1.0
CB C:GLU114 5.0 14.6 1.0

Iron binding site 4 out of 6 in 2yav

Go back to Iron Binding Sites List in 2yav
Iron binding site 4 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:15.7
occ:1.00
 O D:HOH2070 2.0 19.2 1.0
NE2 D:HIS86 2.1 14.0 1.0
NE2 D:HIS90 2.2 23.8 1.0
OE2 D:GLU114 2.2 15.5 1.0
O D:HOH2007 2.2 20.5 1.0
OE1 D:GLU114 2.3 16.5 1.0
CD D:GLU114 2.6 13.7 1.0
CE1 D:HIS86 3.1 18.0 1.0
CD2 D:HIS86 3.1 15.8 1.0
CE1 D:HIS90 3.1 26.0 1.0
CD2 D:HIS90 3.2 21.2 1.0
O D:HOH2015 3.9 42.5 1.0
O D:HOH2092 3.9 17.6 1.0
CG D:GLU114 4.1 14.9 1.0
ND1 D:HIS86 4.2 16.0 1.0
CG D:HIS86 4.2 17.0 1.0
ND1 D:HIS90 4.2 24.9 1.0
ND2 D:ASN9 4.3 36.0 1.0
CG D:HIS90 4.3 19.8 1.0
O D:HOH2005 4.4 44.7 1.0
OG1 D:THR78 4.7 14.2 1.0
CE D:MET89 4.7 25.5 1.0
CA D:GLY208 4.7 15.6 1.0
CB D:ALA7 4.7 14.0 1.0
CB D:GLU114 5.0 14.7 1.0

Iron binding site 5 out of 6 in 2yav

Go back to Iron Binding Sites List in 2yav
Iron binding site 5 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe402

b:14.8
occ:1.00
 NE2 E:HIS86 2.1 14.9 1.0
OE2 E:GLU114 2.1 13.7 1.0
NE2 E:HIS90 2.2 23.3 1.0
O E:HOH2003 2.2 18.9 1.0
O E:HOH2056 2.2 18.9 1.0
OE1 E:GLU114 2.3 15.0 1.0
CD E:GLU114 2.5 13.1 1.0
CE1 E:HIS86 3.0 17.6 1.0
CD2 E:HIS86 3.1 16.7 1.0
CE1 E:HIS90 3.1 24.1 1.0
CD2 E:HIS90 3.2 21.2 1.0
O E:HOH2077 3.9 14.2 1.0
CG E:GLU114 4.0 14.9 1.0
O E:HOH2013 4.1 37.8 1.0
ND1 E:HIS86 4.2 16.3 1.0
CG E:HIS86 4.2 14.8 1.0
ND2 E:ASN9 4.3 34.0 1.0
ND1 E:HIS90 4.3 20.5 1.0
CG E:HIS90 4.3 20.5 1.0
O E:HOH2002 4.4 40.2 1.0
CA E:GLY208 4.6 17.2 1.0
CB E:ALA7 4.7 12.9 1.0
OG1 E:THR78 4.7 15.0 1.0
CE E:MET89 4.8 24.8 1.0
CB E:GLU114 4.9 12.7 1.0
O E:HOH2006 4.9 46.0 1.0

Iron binding site 6 out of 6 in 2yav

Go back to Iron Binding Sites List in 2yav
Iron binding site 6 out of 6 in the Zn 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 Zn Inhibited Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe402

b:15.1
occ:1.00
 NE2 F:HIS90 2.1 19.6 1.0
O F:HOH2009 2.1 20.2 1.0
NE2 F:HIS86 2.2 15.9 1.0
OE2 F:GLU114 2.2 16.2 1.0
OE1 F:GLU114 2.2 14.2 1.0
O F:HOH2080 2.3 20.6 1.0
CD F:GLU114 2.5 13.3 1.0
CE1 F:HIS90 3.0 24.3 1.0
CE1 F:HIS86 3.1 15.8 1.0
CD2 F:HIS86 3.2 16.1 1.0
CD2 F:HIS90 3.2 20.0 1.0
CG F:GLU114 4.0 12.7 1.0
O F:HOH2106 4.1 14.1 1.0
ND1 F:HIS90 4.2 23.1 1.0
ND1 F:HIS86 4.2 15.7 1.0
ND2 F:ASN9 4.2 36.8 1.0
CG F:HIS90 4.3 22.5 1.0
CG F:HIS86 4.3 13.6 1.0
O F:HOH2007 4.4 42.0 1.0
CA F:GLY208 4.6 17.8 1.0
CE F:MET89 4.8 28.8 1.0
CB F:ALA7 4.8 12.1 1.0
OG1 F:THR78 4.8 12.8 1.0
CB F:GLU114 4.9 14.8 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 05:11:12 2024

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