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Iron in PDB 6qpa: Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase

Enzymatic activity of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase

All present enzymatic activity of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase:
1.13.11.55;

Protein crystallography data

The structure of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase, PDB code: 6qpa was solved by C.Frazao, A.Klezin, U.Poell, A.Veith, P.Ruehl, R.Coelho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.70 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 200.840, 212.450, 215.980, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase (pdb code 6qpa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase, PDB code: 6qpa:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 6qpa

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Iron binding site 1 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:40.5
occ:0.40
 O A:HOH564 2.1 52.3 1.0
OE2 A:GLU116 2.1 50.2 1.0
NE2 A:HIS88 2.2 41.1 1.0
O A:HOH659 2.3 50.9 1.0
NE2 A:HIS92 2.5 57.7 1.0
CD A:GLU116 2.8 36.1 1.0
OE1 A:GLU116 2.8 41.3 1.0
CE1 A:HIS88 2.9 40.5 1.0
CD2 A:HIS92 3.4 52.2 1.0
CD2 A:HIS88 3.4 38.9 1.0
CE1 A:HIS92 3.5 57.7 1.0
O A:HOH518 3.8 39.8 1.0
O A:HOH675 4.0 58.1 1.0
ND1 A:HIS88 4.2 40.8 1.0
CG A:GLU116 4.2 33.1 1.0
OG1 A:THR80 4.3 28.3 1.0
CG A:HIS88 4.4 36.1 1.0
CG A:HIS92 4.5 47.6 1.0
ND1 A:HIS92 4.6 52.0 1.0
CA A:GLY208 4.7 31.6 1.0
ND2 A:ASN11 4.7 51.6 1.0
CE A:MET91 4.9 44.1 1.0
CB A:ALA9 5.0 25.7 1.0

Iron binding site 2 out of 24 in 6qpa

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Iron binding site 2 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:37.4
occ:0.40
 O B:HOH609 2.1 46.1 1.0
NE2 B:HIS88 2.2 38.5 1.0
NE2 B:HIS92 2.2 54.0 1.0
OE2 B:GLU116 2.3 49.5 1.0
O B:HOH633 2.3 50.5 1.0
OE1 B:GLU116 2.6 41.1 1.0
CD B:GLU116 2.7 40.1 1.0
CE1 B:HIS88 2.8 32.2 1.0
CE1 B:HIS92 3.1 54.0 1.0
CD2 B:HIS92 3.3 56.0 1.0
CD2 B:HIS88 3.4 32.9 1.0
O B:HOH515 3.9 32.8 1.0
ND1 B:HIS88 4.1 37.6 1.0
CG B:GLU116 4.2 34.9 1.0
ND1 B:HIS92 4.2 50.4 1.0
CG B:HIS88 4.3 36.9 1.0
CG B:HIS92 4.4 47.5 1.0
OG1 B:THR80 4.4 31.1 1.0
CA B:GLY208 4.5 32.8 1.0
CE B:MET91 4.8 41.1 1.0
ND2 B:ASN11 4.8 55.8 1.0
CB B:ALA9 5.0 26.4 1.0

Iron binding site 3 out of 24 in 6qpa

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Iron binding site 3 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:44.1
occ:0.40
 NE2 C:HIS92 2.1 62.3 1.0
NE2 C:HIS88 2.2 45.8 1.0
OE2 C:GLU116 2.4 53.9 1.0
O C:HOH608 2.4 68.1 1.0
OE1 C:GLU116 2.6 36.4 1.0
CD C:GLU116 2.8 46.2 1.0
CE1 C:HIS88 2.8 43.3 1.0
CE1 C:HIS92 3.0 58.1 1.0
CD2 C:HIS92 3.2 58.8 1.0
CD2 C:HIS88 3.4 44.2 1.0
O C:HOH503 3.9 42.2 1.0
ND1 C:HIS88 4.1 46.9 1.0
ND1 C:HIS92 4.2 55.4 1.0
CG C:HIS92 4.3 56.0 1.0
CG C:GLU116 4.3 40.6 1.0
CG C:HIS88 4.4 44.0 1.0
CA C:GLY208 4.5 34.7 1.0
OG1 C:THR80 4.6 35.0 1.0
ND2 C:ASN11 4.8 57.0 1.0
CE C:MET91 4.8 53.3 1.0

Iron binding site 4 out of 24 in 6qpa

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Iron binding site 4 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:61.1
occ:0.40
 NE2 D:HIS92 2.2 70.1 1.0
OE2 D:GLU116 2.4 59.1 1.0
NE2 D:HIS88 2.5 61.7 1.0
OE1 D:GLU116 2.8 58.1 1.0
O D:HOH598 2.8 61.0 1.0
CD D:GLU116 2.9 55.7 1.0
CE1 D:HIS92 3.2 68.0 1.0
CD2 D:HIS92 3.2 72.9 1.0
CE1 D:HIS88 3.3 58.2 1.0
CD2 D:HIS88 3.7 57.5 1.0
O D:HOH518 4.1 44.3 1.0
ND1 D:HIS92 4.3 70.7 1.0
CG D:HIS92 4.4 70.0 1.0
CG D:GLU116 4.4 47.9 1.0
ND1 D:HIS88 4.5 60.2 1.0
OG1 D:THR80 4.5 43.4 1.0
CA D:GLY208 4.6 48.3 1.0
CG D:HIS88 4.7 57.8 1.0
CE D:MET91 4.8 69.7 1.0
ND2 D:ASN11 4.8 70.4 1.0

Iron binding site 5 out of 24 in 6qpa

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Iron binding site 5 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:50.0
occ:0.40
 NE2 E:HIS92 2.1 65.6 1.0
O E:HOH623 2.3 57.1 1.0
OE2 E:GLU116 2.3 45.6 1.0
NE2 E:HIS88 2.6 50.5 1.0
OE1 E:GLU116 2.8 45.4 1.0
CE1 E:HIS92 2.9 66.2 1.0
CD E:GLU116 2.9 43.5 1.0
CD2 E:HIS92 3.2 65.2 1.0
CE1 E:HIS88 3.2 49.6 1.0
CD2 E:HIS88 3.7 46.7 1.0
O E:HOH525 4.1 37.8 1.0
ND1 E:HIS92 4.1 64.5 1.0
CG E:HIS92 4.3 60.2 1.0
CG E:GLU116 4.4 35.4 1.0
ND1 E:HIS88 4.4 52.9 1.0
CA E:GLY208 4.5 39.8 1.0
ND2 E:ASN11 4.5 65.8 1.0
O E:HOH618 4.6 61.7 1.0
OG1 E:THR80 4.7 40.5 1.0
CG E:HIS88 4.7 48.6 1.0
CE E:MET91 4.8 55.6 1.0

Iron binding site 6 out of 24 in 6qpa

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Iron binding site 6 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:50.1
occ:0.40
 OE2 F:GLU116 2.2 61.3 1.0
NE2 F:HIS92 2.4 66.6 1.0
NE2 F:HIS88 2.4 50.8 1.0
O F:HOH600 2.4 65.5 1.0
O F:HOH598 2.6 76.2 1.0
OE1 F:GLU116 2.6 44.9 1.0
CD F:GLU116 2.7 52.2 1.0
CE1 F:HIS88 3.0 50.3 1.0
CE1 F:HIS92 3.3 63.0 1.0
CD2 F:HIS92 3.4 64.6 1.0
CD2 F:HIS88 3.6 51.0 1.0
O F:HOH511 3.8 43.1 1.0
CG F:GLU116 4.2 46.6 1.0
ND1 F:HIS88 4.3 53.4 1.0
ND1 F:HIS92 4.4 63.7 1.0
CG F:HIS92 4.5 62.3 1.0
CA F:GLY208 4.5 43.8 1.0
ND2 F:ASN11 4.5 58.8 1.0
CG F:HIS88 4.6 53.1 1.0
OG1 F:THR80 4.6 48.0 1.0
CE F:MET91 5.0 74.1 1.0

Iron binding site 7 out of 24 in 6qpa

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Iron binding site 7 out of 24 in the Halothiobacillus Neapolitanus 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 Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe401

b:38.5
occ:0.40
 OE2 G:GLU116 2.2 42.8 1.0
NE2 G:HIS92 2.2 54.8 1.0
NE2 G:HIS88 2.3 38.2 1.0
O G:HOH663 2.3 52.7 1.0
O G:HOH683 2.4 48.9 1.0
OE1 G:GLU116 2.7 38.8 1.0
CD G:GLU116 2.8 35.9 1.0
CE1 G:HIS88 2.9 36.5 1.0
CE1 G:HIS92 3.1 56.7 1.0
CD2 G:HIS92 3.3 51.7 1.0
CD2 G:HIS88 3.5 35.1 1.0
O G:HOH551 4.0 26.5 1.0
ND1 G:HIS88 4.2 42.0 1.0
ND1 G:HIS92 4.3 49.8 1.0
CG G:GLU116 4.3 27.1 1.0
O G:HOH668 4.3 55.6 1.0
CG G:HIS92 4.4 46.5 1.0
OG1 G:THR80 4.4 28.8 1.0
CG G:HIS88 4.5 34.6 1.0
CA G:GLY208 4.5 24.7 1.0
CE G:MET91 4.7 42.0 1.0
ND2 G:ASN11 4.8 45.3 1.0

Iron binding site 8 out of 24 in 6qpa

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Iron binding site 8 out of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe401

b:40.5
occ:0.40
 NE2 H:HIS88 2.2 42.8 1.0
O H:HOH637 2.2 55.7 1.0
NE2 H:HIS92 2.3 57.9 1.0
OE2 H:GLU116 2.3 46.0 1.0
OE1 H:GLU116 2.7 42.0 1.0
CD H:GLU116 2.8 38.1 1.0
CE1 H:HIS88 2.9 39.4 1.0
CD2 H:HIS92 3.2 56.9 1.0
CE1 H:HIS92 3.3 57.5 1.0
CD2 H:HIS88 3.4 40.1 1.0
O H:HOH502 3.8 32.0 1.0
O H:HOH670 4.0 46.0 1.0
ND1 H:HIS88 4.1 40.5 1.0
OG1 H:THR80 4.3 30.0 1.0
CG H:GLU116 4.3 29.8 1.0
ND1 H:HIS92 4.4 53.2 1.0
CG H:HIS88 4.4 38.6 1.0
CG H:HIS92 4.4 50.3 1.0
CA H:GLY208 4.7 33.9 1.0
CE H:MET91 4.8 40.4 1.0
ND2 H:ASN11 4.9 53.4 1.0
CB H:ALA9 5.0 31.1 1.0

Iron binding site 9 out of 24 in 6qpa

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Iron binding site 9 out of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe401

b:34.3
occ:0.40
 NE2 I:HIS88 2.2 34.9 1.0
O I:HOH621 2.2 53.9 1.0
OE2 I:GLU116 2.3 40.6 1.0
NE2 I:HIS92 2.4 52.3 1.0
O I:HOH680 2.4 54.5 1.0
OE1 I:GLU116 2.6 38.3 1.0
CD I:GLU116 2.8 32.9 1.0
CE1 I:HIS88 2.9 35.2 1.0
CD2 I:HIS92 3.3 52.3 1.0
CD2 I:HIS88 3.3 32.3 1.0
CE1 I:HIS92 3.4 54.4 1.0
O I:HOH522 4.0 29.4 1.0
ND1 I:HIS88 4.1 39.0 1.0
O I:HOH698 4.2 56.5 1.0
CG I:GLU116 4.3 28.4 1.0
CG I:HIS88 4.3 35.0 1.0
OG1 I:THR80 4.4 25.7 1.0
CG I:HIS92 4.4 46.7 1.0
ND1 I:HIS92 4.4 52.4 1.0
CA I:GLY208 4.5 34.4 1.0
CE I:MET91 4.8 43.6 1.0
ND2 I:ASN11 4.8 50.4 1.0
CB I:ALA9 4.9 26.5 1.0

Iron binding site 10 out of 24 in 6qpa

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Iron binding site 10 out of 24 in the Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Halothiobacillus Neapolitanus Sulfur Oxygenase Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe401

b:47.8
occ:0.40
 O J:HOH646 2.0 50.9 1.0
OE2 J:GLU116 2.2 51.5 1.0
NE2 J:HIS88 2.4 46.4 1.0
NE2 J:HIS92 2.4 55.3 1.0
O J:HOH687 2.8 69.7 1.0
OE1 J:GLU116 2.8 48.9 1.0
CD J:GLU116 2.8 42.5 1.0
CE1 J:HIS88 3.1 42.5 1.0
CE1 J:HIS92 3.3 57.8 1.0
CD2 J:HIS92 3.5 55.5 1.0
CD2 J:HIS88 3.6 42.1 1.0
O J:HOH513 3.7 36.3 1.0
ND1 J:HIS88 4.3 47.3 1.0
CG J:GLU116 4.3 39.2 1.0
OG1 J:THR80 4.4 34.4 1.0
ND1 J:HIS92 4.5 53.7 1.0
CG J:HIS92 4.6 47.5 1.0
CG J:HIS88 4.6 45.2 1.0
CA J:GLY208 4.6 33.1 1.0
ND2 J:ASN11 4.7 54.1 1.0
CE J:MET91 4.9 55.0 1.0

Reference:

C.Frazao, A.Klezin, U.Poell, A.Veith, P.Ruehl, R.Coelho. 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 16:57:48 2020

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