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Iron in PDB 5wqq: High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State

Protein crystallography data

The structure of High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State, PDB code: 5wqq was solved by H.Ohno, K.Takeda, S.Niwa, T.Tsujinaka, Y.Hanazono, Y.Hirano, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.97 / 0.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.336, 58.813, 23.438, 90.00, 90.00, 90.00
R / Rfree (%) 11.6 / 12.9

Iron Binding Sites:

The binding sites of Iron atom in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State (pdb code 5wqq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State, PDB code: 5wqq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5wqq

Go back to Iron Binding Sites List in 5wqq
Iron binding site 1 out of 4 in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:1.8
occ:1.00
 FE1 A:SF4101 0.0 1.8 1.0
SG A:CYS43 2.2 2.0 1.0
S2 A:SF4101 2.2 2.0 1.0
S4 A:SF4101 2.3 1.9 1.0
S3 A:SF4101 2.3 1.9 1.0
FE3 A:SF4101 2.7 1.8 1.0
FE4 A:SF4101 2.7 1.8 1.0
FE2 A:SF4101 2.8 1.8 1.0
HA A:CYS43 3.0 2.2 1.0
CB A:CYS43 3.2 1.9 1.0
HB3 A:CYS43 3.2 2.3 1.0
CA A:CYS43 3.6 1.8 1.0
HG12 A:ILE69 3.6 3.2 1.0
S1 A:SF4101 3.9 2.1 1.0
HA A:TRP74 4.0 2.1 1.0
HB2 A:CYS43 4.1 2.3 1.0
HE1 A:TYR19 4.2 3.1 1.0
HD12 A:ILE69 4.2 4.2 1.0
HB3 A:CYS46 4.3 2.2 1.0
HD1 A:TYR19 4.4 2.7 1.0
HG22 A:ILE69 4.4 5.0 1.0
N A:CYS43 4.4 1.8 1.0
CG1 A:ILE69 4.4 2.7 1.0
HB A:ILE69 4.5 2.9 1.0
HB2 A:CYS61 4.5 3.2 1.0
H A:CYS43 4.5 2.2 1.0
N A:CYS75 4.5 1.8 1.0
HB2 A:CYS46 4.6 2.2 1.0
H A:CYS75 4.6 2.1 1.0
CA A:TRP74 4.6 1.8 1.0
CD1 A:ILE69 4.7 2.8 1.0
HB3 A:CYS75 4.7 2.6 1.0
C A:TRP74 4.7 1.7 1.0
HD11 A:ILE69 4.7 4.2 1.0
CB A:CYS46 4.8 1.8 1.0
SG A:CYS46 4.8 2.0 1.0
N A:TRP74 4.8 1.8 1.0
SG A:CYS75 4.8 1.9 1.0
SG A:CYS61 4.8 2.3 1.0
HD1 A:TRP78 4.8 2.3 1.0
C A:CYS43 4.8 1.9 1.0
HB2 A:MET49 4.9 3.2 0.6
CE1 A:TYR19 4.9 2.6 1.0
CB A:ILE69 4.9 2.4 1.0
C A:GLY73 5.0 1.8 1.0
O A:CYS43 5.0 2.2 1.0
O A:GLY73 5.0 2.0 1.0
CD1 A:TYR19 5.0 2.2 1.0

Iron binding site 2 out of 4 in 5wqq

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Iron binding site 2 out of 4 in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:1.8
occ:1.00
 FE2 A:SF4101 0.0 1.8 1.0
S1 A:SF4101 2.2 2.1 1.0
SG A:CYS46 2.2 2.0 1.0
S3 A:SF4101 2.3 1.9 1.0
S4 A:SF4101 2.3 1.9 1.0
FE3 A:SF4101 2.7 1.8 1.0
FE4 A:SF4101 2.7 1.8 1.0
FE1 A:SF4101 2.8 1.8 1.0
HB3 A:CYS46 3.0 2.2 1.0
CB A:CYS46 3.1 1.8 1.0
HB2 A:CYS46 3.2 2.2 1.0
HB2 A:PHE48 3.3 2.7 1.0
HA A:TRP78 3.3 2.2 1.0
HA A:CYS43 3.8 2.2 1.0
HD2 A:PHE48 3.8 4.3 1.0
S2 A:SF4101 3.9 2.0 1.0
H A:PHE48 4.1 2.7 1.0
HD1 A:TRP78 4.1 2.3 1.0
CB A:PHE48 4.3 2.2 1.0
CA A:TRP78 4.3 1.9 1.0
H A:THR79 4.3 2.4 1.0
CA A:CYS46 4.5 2.2 1.0
H A:MET49 4.6 3.1 1.0
SG A:CYS61 4.6 2.3 1.0
N A:TRP78 4.6 2.1 1.0
CD2 A:PHE48 4.6 3.6 1.0
CA A:CYS43 4.7 1.8 1.0
CD1 A:TRP78 4.7 1.9 1.0
HB3 A:PHE48 4.7 2.7 1.0
N A:PHE48 4.7 2.3 1.0
SG A:CYS75 4.7 1.9 1.0
HB2 A:MET49 4.7 3.2 0.6
SG A:CYS43 4.7 2.0 1.0
HB2 A:TRP78 4.8 2.4 1.0
HB2 A:MET49 4.8 2.6 0.4
HB3 A:CYS43 4.8 2.3 1.0
N A:MET49 4.8 2.6 1.0
O A:SER77 4.8 2.6 1.0
CA A:PHE48 4.9 2.1 1.0
HA A:CYS46 4.9 2.6 1.0
C A:SER77 4.9 2.1 1.0
C A:CYS46 5.0 1.9 1.0
CB A:TRP78 5.0 2.0 1.0
C A:PHE48 5.0 2.1 1.0
CB A:CYS43 5.0 1.9 1.0
CG A:PHE48 5.0 2.8 1.0
O A:CYS43 5.0 2.2 1.0

Iron binding site 3 out of 4 in 5wqq

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Iron binding site 3 out of 4 in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:1.8
occ:1.00
 FE3 A:SF4101 0.0 1.8 1.0
SG A:CYS61 2.2 2.3 1.0
S4 A:SF4101 2.2 1.9 1.0
S1 A:SF4101 2.3 2.1 1.0
S2 A:SF4101 2.3 2.0 1.0
FE2 A:SF4101 2.7 1.8 1.0
FE1 A:SF4101 2.7 1.8 1.0
FE4 A:SF4101 2.7 1.8 1.0
HB2 A:CYS61 3.0 3.2 1.0
CB A:CYS61 3.2 2.7 1.0
HB2 A:PHE48 3.5 2.7 1.0
HG12 A:ILE69 3.7 3.2 1.0
HB3 A:CYS61 3.8 3.2 1.0
S3 A:SF4101 3.9 1.9 1.0
HD2 A:PHE64 4.0 3.2 1.0
HG22 A:ILE69 4.0 5.0 1.0
HE2 A:PHE64 4.0 3.3 1.0
HG A:LEU63 4.2 3.1 1.0
HB3 A:PHE48 4.2 2.7 1.0
HA A:CYS61 4.2 2.8 1.0
HD11 A:LEU63 4.3 4.7 1.0
CB A:PHE48 4.3 2.2 1.0
CA A:CYS61 4.3 2.3 1.0
HB2 A:LEU63 4.5 2.8 1.0
SG A:CYS75 4.5 1.9 1.0
CG1 A:ILE69 4.6 2.7 1.0
CD2 A:PHE64 4.7 2.7 1.0
SG A:CYS43 4.7 2.0 1.0
SG A:CYS46 4.7 2.0 1.0
H A:LEU63 4.7 2.6 1.0
CE2 A:PHE64 4.7 2.8 1.0
HA A:MET49 4.9 2.9 0.6
C A:PHE48 4.9 2.1 1.0
HA A:MET49 4.9 3.0 0.4
CD1 A:LEU63 4.9 3.1 1.0
CG A:LEU63 4.9 2.6 1.0
HD2 A:PHE48 4.9 4.3 1.0
CG2 A:ILE69 4.9 3.3 1.0
HG13 A:ILE69 4.9 3.2 1.0
O A:PHE48 4.9 2.9 1.0
HD12 A:LEU63 5.0 4.7 1.0
HB3 A:CYS43 5.0 2.3 1.0

Iron binding site 4 out of 4 in 5wqq

Go back to Iron Binding Sites List in 5wqq
Iron binding site 4 out of 4 in the High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High Resolution Structure of High-Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:1.8
occ:1.00
 FE4 A:SF4101 0.0 1.8 1.0
SG A:CYS75 2.2 1.9 1.0
S3 A:SF4101 2.3 1.9 1.0
S1 A:SF4101 2.3 2.1 1.0
S2 A:SF4101 2.3 2.0 1.0
FE1 A:SF4101 2.7 1.8 1.0
FE2 A:SF4101 2.7 1.8 1.0
FE3 A:SF4101 2.7 1.8 1.0
HB3 A:CYS75 3.2 2.6 1.0
CB A:CYS75 3.2 2.2 1.0
N A:CYS75 3.6 1.8 1.0
H A:CYS75 3.6 2.1 1.0
S4 A:SF4101 3.8 1.9 1.0
CA A:CYS75 3.9 1.9 1.0
HB2 A:SER77 4.0 3.7 1.0
HB2 A:CYS75 4.1 2.6 1.0
HE2 A:PHE64 4.1 3.3 1.0
O A:CYS75 4.2 2.0 1.0
HA A:TRP78 4.2 2.2 1.0
C A:CYS75 4.2 1.9 1.0
HD11 A:LEU63 4.2 4.7 1.0
HD1 A:TYR19 4.3 2.7 1.0
H A:SER77 4.3 2.5 1.0
H A:TRP78 4.4 2.5 1.0
N A:TRP78 4.4 2.1 1.0
C A:TRP74 4.4 1.7 1.0
HA A:TRP74 4.6 2.1 1.0
SG A:CYS61 4.6 2.3 1.0
C A:SER77 4.7 2.1 1.0
HB2 A:TRP78 4.7 2.4 1.0
SG A:CYS43 4.7 2.0 1.0
SG A:CYS46 4.8 2.0 1.0
HA A:CYS75 4.8 2.3 1.0
CA A:TRP78 4.8 1.9 1.0
CB A:SER77 4.8 3.1 1.0
N A:SER77 4.9 2.1 1.0
HD12 A:LEU63 5.0 4.7 1.0

Reference:

H.Ohno, K.Takeda, S.Niwa, T.Tsujinaka, Y.Hanazono, Y.Hirano, K.Miki. Crystallographic Characterization of the High-Potential Iron-Sulfur Protein in the Oxidized State at 0.8 Angstrom Resolution Plos One V. 12 78183 2017.
ISSN: ESSN 1932-6203
PubMed: 28542634
DOI: 10.1371/JOURNAL.PONE.0178183
Page generated: Wed Aug 6 02:33:37 2025

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