Atomistry » Iron » PDB 6ll1-6m54 » 6m35
Atomistry »
  Iron »
    PDB 6ll1-6m54 »
      6m35 »

Iron in PDB 6m35: Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii

Enzymatic activity of Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii

All present enzymatic activity of Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii:
1.13.11.55;

Protein crystallography data

The structure of Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii, PDB code: 6m35 was solved by Y.Sato, T.Yabuki, T.Arakawa, C.Yamada, S.Fushinobu, T.Wakagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 1.73
Space group I 2 3 1
Cell size a, b, c (Å), α, β, γ (°) 299.806, 299.806, 299.806, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 17.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii (pdb code 6m35). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii, PDB code: 6m35:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 1 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.5
occ:1.00
 NE2 A:HIS86 2.1 25.4 1.0
O A:HOH638 2.2 33.3 1.0
OE2 A:GLU114 2.2 24.7 1.0
NE2 A:HIS90 2.2 31.7 1.0
O A:HOH635 2.2 29.3 1.0
OE1 A:GLU114 2.3 27.0 1.0
CD A:GLU114 2.5 25.6 1.0
CE1 A:HIS86 3.0 28.0 1.0
CD2 A:HIS90 3.2 35.5 1.0
CE1 A:HIS90 3.2 34.4 1.0
CD2 A:HIS86 3.2 27.8 1.0
O A:HOH523 3.9 28.5 1.0
CG A:GLU114 4.0 23.6 1.0
ND1 A:HIS86 4.2 24.2 1.0
O A:HOH592 4.2 39.4 1.0
ND1 A:HIS90 4.3 31.1 1.0
CG A:HIS86 4.3 24.0 1.0
CG A:HIS90 4.3 29.4 1.0
O A:HOH506 4.3 38.9 1.0
CA A:GLY208 4.5 25.7 1.0
OG1 A:THR78 4.7 21.8 1.0
CB A:ALA7 4.7 23.6 1.0
O A:HOH645 4.8 38.3 1.0
CE A:MET89 4.8 32.5 1.0
CB A:GLU114 4.9 22.9 1.0

Iron binding site 2 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 2 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.5
occ:1.00
 OE2 B:GLU114 2.2 25.7 1.0
NE2 B:HIS86 2.2 22.4 1.0
NE2 B:HIS90 2.2 32.8 1.0
O B:HOH639 2.2 29.5 1.0
O B:HOH635 2.3 30.6 1.0
OE1 B:GLU114 2.3 28.6 1.0
CD B:GLU114 2.5 23.7 1.0
CE1 B:HIS86 3.0 25.7 1.0
CE1 B:HIS90 3.2 36.4 1.0
CD2 B:HIS90 3.2 37.7 1.0
CD2 B:HIS86 3.2 23.4 1.0
O B:HOH536 3.9 28.3 1.0
CG B:GLU114 4.0 22.9 1.0
O B:HOH576 4.1 42.1 1.0
ND1 B:HIS86 4.2 25.1 1.0
ND1 B:HIS90 4.3 30.6 1.0
CG B:HIS86 4.3 21.2 1.0
CG B:HIS90 4.3 31.4 1.0
O B:HOH504 4.4 39.5 1.0
CA B:GLY208 4.5 25.2 1.0
OG1 B:THR78 4.7 22.2 1.0
CB B:ALA7 4.7 20.9 1.0
O B:HOH643 4.8 39.9 1.0
CE B:MET89 4.8 32.9 1.0
CB B:GLU114 5.0 21.9 1.0

Iron binding site 3 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 3 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.5
occ:1.00
 O C:HOH637 2.1 31.2 1.0
NE2 C:HIS90 2.2 31.1 1.0
NE2 C:HIS86 2.2 24.7 1.0
OE2 C:GLU114 2.2 26.6 1.0
O C:HOH630 2.3 31.4 1.0
OE1 C:GLU114 2.3 26.1 1.0
CD C:GLU114 2.5 27.1 1.0
CE1 C:HIS86 3.0 26.7 1.0
CD2 C:HIS90 3.1 36.9 1.0
CE1 C:HIS90 3.1 33.2 1.0
CD2 C:HIS86 3.2 27.4 1.0
O C:HOH548 4.0 23.2 1.0
CG C:GLU114 4.0 24.4 1.0
O C:HOH611 4.1 42.3 1.0
ND1 C:HIS86 4.2 22.2 1.0
ND1 C:HIS90 4.2 30.2 1.0
CG C:HIS90 4.3 29.6 1.0
CG C:HIS86 4.3 24.4 1.0
O C:HOH513 4.3 40.6 1.0
CA C:GLY208 4.5 23.9 1.0
OG1 C:THR78 4.7 21.8 1.0
CB C:ALA7 4.7 21.9 1.0
CE C:MET89 4.8 30.3 1.0
O C:HOH644 4.8 39.2 1.0
CB C:GLU114 5.0 22.0 1.0

Iron binding site 4 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 4 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.8
occ:1.00
 OE2 D:GLU114 2.2 24.6 1.0
O D:HOH641 2.2 33.0 1.0
NE2 D:HIS86 2.2 23.0 1.0
NE2 D:HIS90 2.2 31.4 1.0
O D:HOH635 2.2 30.6 1.0
OE1 D:GLU114 2.3 26.3 1.0
CD D:GLU114 2.5 23.2 1.0
CE1 D:HIS86 3.0 26.2 1.0
CD2 D:HIS90 3.2 35.1 1.0
CE1 D:HIS90 3.2 32.5 1.0
CD2 D:HIS86 3.2 25.8 1.0
O D:HOH554 4.0 24.7 1.0
CG D:GLU114 4.0 23.2 1.0
O D:HOH597 4.1 43.5 1.0
ND1 D:HIS86 4.2 24.3 1.0
ND1 D:HIS90 4.3 32.5 1.0
CG D:HIS86 4.3 22.7 1.0
CG D:HIS90 4.3 31.0 1.0
O D:HOH505 4.3 40.1 1.0
CA D:GLY208 4.5 23.9 1.0
OG1 D:THR78 4.7 21.2 1.0
CB D:ALA7 4.7 21.2 1.0
CE D:MET89 4.8 31.6 1.0
O D:HOH646 4.9 39.2 1.0
CB D:GLU114 5.0 21.3 1.0

Iron binding site 5 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 5 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.6
occ:1.00
 O E:HOH629 2.2 30.6 1.0
OE2 E:GLU114 2.2 24.5 1.0
NE2 E:HIS86 2.2 24.6 1.0
NE2 E:HIS90 2.2 36.6 1.0
O E:HOH619 2.2 36.1 1.0
OE1 E:GLU114 2.3 26.8 1.0
CD E:GLU114 2.6 23.4 1.0
CE1 E:HIS86 3.1 26.2 1.0
CE1 E:HIS90 3.2 35.9 1.0
CD2 E:HIS90 3.2 36.5 1.0
CD2 E:HIS86 3.2 26.2 1.0
O E:HOH521 3.9 24.2 1.0
CG E:GLU114 4.1 22.9 1.0
ND1 E:HIS86 4.2 25.5 1.0
O E:HOH555 4.2 40.5 1.0
ND1 E:HIS90 4.3 32.0 1.0
CG E:HIS86 4.3 24.6 1.0
CG E:HIS90 4.3 31.2 1.0
O E:HOH505 4.4 38.6 1.0
CA E:GLY208 4.6 24.6 1.0
OG1 E:THR78 4.6 21.6 1.0
CB E:ALA7 4.7 21.9 1.0
CE E:MET89 4.8 30.8 1.0
O E:HOH633 4.9 37.8 1.0
CB E:GLU114 5.0 21.4 1.0

Iron binding site 6 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 6 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.6
occ:1.00
 NE2 F:HIS86 2.2 24.9 1.0
O F:HOH632 2.2 32.4 1.0
OE2 F:GLU114 2.2 25.6 1.0
NE2 F:HIS90 2.2 32.6 1.0
O F:HOH631 2.2 31.4 1.0
OE1 F:GLU114 2.3 28.9 1.0
CD F:GLU114 2.5 24.0 1.0
CE1 F:HIS86 3.0 27.8 1.0
CE1 F:HIS90 3.2 36.2 1.0
CD2 F:HIS90 3.2 37.5 1.0
CD2 F:HIS86 3.2 27.2 1.0
O F:HOH527 4.0 25.2 1.0
CG F:GLU114 4.0 21.4 1.0
ND1 F:HIS86 4.2 26.5 1.0
O F:HOH517 4.2 39.5 1.0
ND1 F:HIS90 4.3 29.9 1.0
CG F:HIS86 4.3 22.9 1.0
CG F:HIS90 4.3 29.6 1.0
CA F:GLY208 4.5 24.9 1.0
OG1 F:THR78 4.7 22.0 1.0
CB F:ALA7 4.7 20.8 1.0
O F:HOH637 4.8 37.4 1.0
CE F:MET89 4.8 29.5 1.0
CB F:GLU114 5.0 21.4 1.0

Iron binding site 7 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 7 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe401

b:35.4
occ:1.00
 NE2 G:HIS86 2.1 23.9 1.0
O G:HOH633 2.2 32.4 1.0
OE2 G:GLU114 2.2 26.0 1.0
NE2 G:HIS90 2.2 34.6 1.0
O G:HOH632 2.2 30.2 1.0
OE1 G:GLU114 2.3 27.8 1.0
CD G:GLU114 2.5 26.1 1.0
CE1 G:HIS86 3.0 27.1 1.0
CD2 G:HIS90 3.2 34.7 1.0
CE1 G:HIS90 3.2 35.5 1.0
CD2 G:HIS86 3.2 27.6 1.0
O G:HOH515 3.9 24.6 1.0
O G:HOH645 4.0 48.6 1.0
CG G:GLU114 4.0 22.7 1.0
O G:HOH610 4.1 42.7 1.0
ND1 G:HIS86 4.2 25.0 1.0
CG G:HIS86 4.3 24.3 1.0
ND1 G:HIS90 4.3 29.4 1.0
CG G:HIS90 4.3 30.1 1.0
O G:HOH508 4.3 49.1 1.0
CA G:GLY208 4.5 24.4 1.0
OG1 G:THR78 4.7 22.5 1.0
CB G:ALA7 4.7 23.8 1.0
CE G:MET89 4.8 31.5 1.0
O G:HOH638 4.9 34.8 1.0
CB G:GLU114 4.9 22.3 1.0

Iron binding site 8 out of 8 in 6m35

Go back to Iron Binding Sites List in 6m35
Iron binding site 8 out of 8 in the Crystal Structure of Sulfur Oxygenase Reductase From Sulfurisphaera Tokodaii


Mono view


Stereo pair view

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

b:35.3
occ:1.00
 O H:HOH648 2.2 31.4 1.0
OE2 H:GLU114 2.2 23.9 1.0
NE2 H:HIS90 2.2 31.3 1.0
NE2 H:HIS86 2.2 22.7 1.0
O H:HOH641 2.3 27.1 1.0
OE1 H:GLU114 2.3 27.8 1.0
CD H:GLU114 2.5 24.9 1.0
CE1 H:HIS86 3.1 26.4 1.0
CE1 H:HIS90 3.2 32.9 1.0
CD2 H:HIS90 3.2 32.9 1.0
CD2 H:HIS86 3.2 23.9 1.0
O H:HOH539 3.9 22.8 1.0
CG H:GLU114 4.0 22.8 1.0
O H:HOH608 4.1 41.9 1.0
ND1 H:HIS86 4.2 23.2 1.0
ND1 H:HIS90 4.3 31.4 1.0
CG H:HIS90 4.3 29.6 1.0
CG H:HIS86 4.3 24.3 1.0
O H:HOH510 4.4 39.0 1.0
CA H:GLY208 4.5 23.9 1.0
OG1 H:THR78 4.7 22.4 1.0
CB H:ALA7 4.7 22.6 1.0
CE H:MET89 4.8 29.0 1.0
O H:HOH650 4.9 37.5 1.0
CB H:GLU114 5.0 22.5 1.0

Reference:

Y.Sato, T.Yabuki, N.Adachi, T.Moriya, T.Arakawa, M.Kawasaki, C.Yamada, T.Senda, S.Fushinobu, T.Wakagi. Crystallographic and Cryogenic Electron Microscopic Structures and Enzymatic Characterization of Sulfur Oxygenase Reductase Fromsulfurisphaera Tokodaii. J Struct Biol X V. 4 00030 2020.
ISSN: ESSN 2590-1524
PubMed: 32775998
DOI: 10.1016/J.YJSBX.2020.100030
Page generated: Wed Aug 7 01:53:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy