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Iron in PDB 8hdd: Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase

Enzymatic activity of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase

All present enzymatic activity of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase:
1.1.5.9;

Protein crystallography data

The structure of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase, PDB code: 8hdd was solved by H.Yoshida, K.Sode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 3.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 204.015, 71.797, 114.221, 90, 90, 90
R / Rfree (%) 27.5 / 32.3

Iron Binding Sites:

The binding sites of Iron atom in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase (pdb code 8hdd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase, PDB code: 8hdd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8hdd

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Iron binding site 1 out of 4 in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:73.0
occ:1.00
 FE1 A:F3S702 0.0 73.0 1.0
S3 A:F3S702 2.2 57.3 1.0
S1 A:F3S702 2.2 68.4 1.0
S2 A:F3S702 2.2 69.6 1.0
SG A:CYS212 2.3 65.2 1.0
FE3 A:F3S702 3.0 69.2 1.0
FE4 A:F3S702 3.1 63.9 1.0
CB A:CYS212 3.4 59.4 1.0
CA A:CYS212 3.9 60.5 1.0
CG A:PRO339 3.9 56.9 1.0
N A:GLY214 4.0 63.9 1.0
N A:ASN215 4.1 67.0 1.0
S4 A:F3S702 4.2 64.5 1.0
N A:CYS213 4.2 66.7 1.0
CA A:GLY214 4.3 64.5 1.0
CD A:PRO339 4.5 58.0 1.0
C A:CYS212 4.5 66.1 1.0
CB A:PRO339 4.5 60.1 1.0
CA A:PRO339 4.6 61.5 1.0
SG A:CYS222 4.7 85.9 1.0
N A:PRO339 4.7 62.4 1.0
SG A:CYS218 4.7 56.8 1.0
C A:GLY214 4.7 64.8 1.0
N A:ASN216 4.7 53.2 1.0
CB A:ASN215 4.9 62.0 1.0
C A:CYS213 4.9 63.2 1.0
NE A:ARG201 4.9 74.0 1.0

Iron binding site 2 out of 4 in 8hdd

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Iron binding site 2 out of 4 in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:69.2
occ:1.00
 FE3 A:F3S702 0.0 69.2 1.0
S3 A:F3S702 2.2 57.3 1.0
S1 A:F3S702 2.2 68.4 1.0
S4 A:F3S702 2.2 64.5 1.0
SG A:CYS222 2.3 85.9 1.0
FE1 A:F3S702 3.0 73.0 1.0
FE4 A:F3S702 3.1 63.9 1.0
CB A:ASN215 3.6 62.0 1.0
CB A:CYS222 3.8 85.7 1.0
CD1 A:ILE224 3.9 78.1 1.0
CA A:CYS222 4.0 78.9 1.0
OD1 A:ASN215 4.1 64.3 1.0
S2 A:F3S702 4.1 69.6 1.0
CG A:ASN215 4.3 64.2 1.0
CB A:ALA226 4.3 91.2 1.0
CG1 A:ILE224 4.4 80.6 1.0
N A:ASN215 4.5 67.0 1.0
CD A:PRO223 4.5 68.1 1.0
CA A:ASN215 4.6 61.5 1.0
C A:CYS222 5.0 75.0 1.0

Iron binding site 3 out of 4 in 8hdd

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Iron binding site 3 out of 4 in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:63.9
occ:1.00
 FE4 A:F3S702 0.0 63.9 1.0
S3 A:F3S702 2.2 57.3 1.0
S4 A:F3S702 2.2 64.5 1.0
S2 A:F3S702 2.2 69.6 1.0
SG A:CYS218 2.3 56.8 1.0
N A:CYS218 3.0 62.9 1.0
FE3 A:F3S702 3.1 69.2 1.0
FE1 A:F3S702 3.1 73.0 1.0
CA A:CYS218 3.3 62.5 1.0
CB A:CYS218 3.4 60.8 1.0
N A:ASN217 3.7 57.0 1.0
SG A:CYS222 4.0 85.9 1.0
C A:ASN217 4.0 61.4 1.0
N A:ASN216 4.1 53.2 1.0
S1 A:F3S702 4.3 68.4 1.0
CA A:ASN216 4.4 50.5 1.0
C A:ASN216 4.4 53.1 1.0
CA A:ASN217 4.5 60.1 1.0
NE A:ARG201 4.5 74.0 1.0
CA A:PRO339 4.6 61.5 1.0
CB A:ASN215 4.7 62.0 1.0
SD A:MET227 4.7 83.8 1.0
C A:ASN215 4.7 56.0 1.0
NH2 A:ARG201 4.8 75.0 1.0
C A:CYS218 4.8 62.8 1.0
CB A:PRO339 4.8 60.1 1.0

Iron binding site 4 out of 4 in 8hdd

Go back to Iron Binding Sites List in 8hdd
Iron binding site 4 out of 4 in the Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex Structure of Catalytic, Small, and A Partial Electron Transfer Subunits From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:80.6
occ:1.00
 FE B:HEM501 0.0 80.6 1.0
ND B:HEM501 1.9 76.7 1.0
NA B:HEM501 2.0 79.0 1.0
NC B:HEM501 2.1 73.1 1.0
NB B:HEM501 2.1 77.3 1.0
NE2 B:HIS338 2.4 73.6 1.0
SD B:MET386 2.5 83.8 1.0
C4D B:HEM501 2.9 78.5 1.0
C1D B:HEM501 2.9 73.7 1.0
C1A B:HEM501 3.0 79.0 1.0
C4C B:HEM501 3.0 72.3 1.0
C4A B:HEM501 3.1 81.0 1.0
C1B B:HEM501 3.1 78.7 1.0
C4B B:HEM501 3.1 76.3 1.0
C1C B:HEM501 3.1 72.2 1.0
CE1 B:HIS338 3.2 76.7 1.0
CG B:MET386 3.3 84.9 1.0
CHA B:HEM501 3.3 79.0 1.0
CHD B:HEM501 3.4 73.1 1.0
CHB B:HEM501 3.5 80.7 1.0
CD2 B:HIS338 3.5 73.9 1.0
CHC B:HEM501 3.5 73.8 1.0
CB B:MET386 3.7 88.5 1.0
CE B:MET386 4.1 86.6 1.0
C3D B:HEM501 4.1 76.8 1.0
C2D B:HEM501 4.1 73.3 1.0
C2A B:HEM501 4.2 78.5 1.0
C3A B:HEM501 4.2 79.2 1.0
C3C B:HEM501 4.3 69.9 1.0
C2C B:HEM501 4.3 70.0 1.0
C2B B:HEM501 4.3 77.3 1.0
ND1 B:HIS338 4.4 76.3 1.0
C3B B:HEM501 4.4 77.7 1.0
CG B:HIS338 4.6 74.7 1.0
CA B:MET386 5.0 88.2 1.0

Reference:

J.Okuda-Shimazaki, H.Yoshida, I.Lee, K.Kojima, N.Suzuki, W.Tsugawa, M.Yamada, K.Inaka, H.Tanaka, K.Sode. Microgravity Environment Grown Crystal Structure Information Based Engineering of Direct Electron Transfer Type Glucose Dehydrogenase Commun Biol V. 5 1334 2022.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-022-04286-9
Page generated: Thu Aug 7 17:45:28 2025

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