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Iron in PDB 6a2u: Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase

Enzymatic activity of Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase

All present enzymatic activity of Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase:
1.1.5.9;

Protein crystallography data

The structure of Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase, PDB code: 6a2u was solved by H.Yoshida, K.Kojima, K.Yoshimatsu, M.Shiota, T.Yamazaki, S.Ferri, W.Tsugawa, S.Kamitori, K.Sode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.74 / 2.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 110.521, 110.521, 524.877, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase (pdb code 6a2u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase, PDB code: 6a2u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6a2u

Go back to Iron Binding Sites List in 6a2u
Iron binding site 1 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:32.4
occ:1.00
 FE1 B:F3S702 0.0 32.4 1.0
S3 B:F3S702 2.2 34.1 1.0
S2 B:F3S702 2.2 36.2 1.0
S1 B:F3S702 2.2 31.7 1.0
SG B:CYS212 2.3 29.9 1.0
FE4 B:F3S702 3.0 38.3 1.0
FE3 B:F3S702 3.0 36.3 1.0
CB B:CYS212 3.5 28.5 1.0
N B:GLY214 3.6 21.9 1.0
N B:CYS213 3.8 29.9 1.0
CA B:CYS212 4.0 29.5 1.0
CA B:GLY214 4.0 26.6 1.0
S4 B:F3S702 4.1 32.4 1.0
N B:ASN215 4.2 37.9 1.0
C B:CYS212 4.3 29.1 1.0
CD B:ARG201 4.5 33.7 1.0
NE B:ARG201 4.6 33.8 1.0
C B:GLY214 4.6 34.4 1.0
C B:CYS213 4.7 27.5 1.0
CG B:PRO339 4.7 22.7 1.0
CA B:CYS213 4.9 29.3 1.0
SG B:CYS218 4.9 32.3 1.0
CB B:ALA226 4.9 35.1 1.0
SG B:CYS222 5.0 28.9 1.0
OD1 B:ASN215 5.0 41.5 1.0
N B:ASN216 5.0 32.5 1.0

Iron binding site 2 out of 6 in 6a2u

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Iron binding site 2 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:36.3
occ:1.00
 FE3 B:F3S702 0.0 36.3 1.0
S3 B:F3S702 2.2 34.1 1.0
S4 B:F3S702 2.2 32.4 1.0
S1 B:F3S702 2.2 31.7 1.0
SG B:CYS222 2.3 28.9 1.0
FE4 B:F3S702 3.0 38.3 1.0
FE1 B:F3S702 3.0 32.4 1.0
CB B:CYS222 3.1 27.2 1.0
CA B:CYS222 3.7 29.2 1.0
OD1 B:ASN215 3.7 41.5 1.0
CB B:ASN215 4.1 35.9 1.0
S2 B:F3S702 4.1 36.2 1.0
CG B:ASN215 4.4 37.9 1.0
CD B:PRO223 4.4 33.4 1.0
CB B:ALA226 4.6 35.1 1.0
CG1 B:ILE224 4.7 31.6 1.0
C B:CYS222 4.7 26.9 1.0
CG B:MET227 4.7 34.8 1.0
N B:ASN215 4.8 37.9 1.0
N B:CYS222 4.8 31.8 1.0
N B:PRO223 4.9 32.3 1.0
SD B:MET227 4.9 33.1 1.0

Iron binding site 3 out of 6 in 6a2u

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Iron binding site 3 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:38.3
occ:1.00
 FE4 B:F3S702 0.0 38.3 1.0
S3 B:F3S702 2.2 34.1 1.0
S4 B:F3S702 2.2 32.4 1.0
S2 B:F3S702 2.2 36.2 1.0
SG B:CYS218 2.3 32.3 1.0
FE3 B:F3S702 3.0 36.3 1.0
FE1 B:F3S702 3.0 32.4 1.0
CB B:CYS218 3.4 36.9 1.0
N B:CYS218 3.5 36.6 1.0
CA B:CYS218 3.5 35.0 1.0
N B:ASN217 3.9 35.1 1.0
S1 B:F3S702 4.2 31.7 1.0
N B:ASN216 4.2 32.5 1.0
C B:ASN217 4.3 37.8 1.0
SD B:MET227 4.4 33.1 1.0
NE B:ARG201 4.5 33.8 1.0
CA B:ASN216 4.5 34.5 1.0
CA B:PRO339 4.5 23.4 1.0
C B:ASN216 4.7 32.5 1.0
CA B:ASN217 4.7 36.2 1.0
NH2 B:ARG201 4.8 29.7 1.0
CB B:PRO339 4.8 22.6 1.0
CB B:ASN215 4.9 35.9 1.0
C B:ASN215 4.9 34.2 1.0
N B:ASN215 4.9 37.9 1.0
CB B:CYS222 4.9 27.2 1.0
SG B:CYS222 4.9 28.9 1.0
SG B:CYS212 5.0 29.9 1.0
CZ B:ARG201 5.0 34.4 1.0

Iron binding site 4 out of 6 in 6a2u

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Iron binding site 4 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe702

b:27.9
occ:1.00
 FE1 D:F3S702 0.0 27.9 1.0
S3 D:F3S702 2.2 28.3 1.0
S2 D:F3S702 2.2 28.1 1.0
S1 D:F3S702 2.2 35.9 1.0
SG D:CYS212 2.3 24.8 1.0
FE4 D:F3S702 3.0 29.1 1.0
FE3 D:F3S702 3.0 35.3 1.0
CB D:CYS212 3.4 22.1 1.0
N D:GLY214 3.7 22.8 1.0
N D:CYS213 3.8 24.3 1.0
CA D:CYS212 3.8 22.0 1.0
N D:ASN215 4.1 29.9 1.0
S4 D:F3S702 4.1 35.4 1.0
C D:CYS212 4.2 22.3 1.0
CA D:GLY214 4.2 26.2 1.0
CB D:ALA226 4.6 26.8 1.0
NE D:ARG201 4.6 26.8 1.0
CD D:ARG201 4.6 22.5 1.0
C D:GLY214 4.7 26.8 1.0
C D:CYS213 4.7 23.9 1.0
CG D:PRO339 4.8 24.6 1.0
CA D:CYS213 4.8 29.6 1.0
CB D:ASN215 4.9 24.4 1.0
SG D:CYS218 4.9 26.9 1.0
OD1 D:ASN215 5.0 39.3 1.0

Iron binding site 5 out of 6 in 6a2u

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Iron binding site 5 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 5 of Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe702

b:35.3
occ:1.00
 FE3 D:F3S702 0.0 35.3 1.0
S3 D:F3S702 2.2 28.3 1.0
S4 D:F3S702 2.2 35.4 1.0
S1 D:F3S702 2.2 35.9 1.0
SG D:CYS222 2.3 27.5 1.0
FE1 D:F3S702 3.0 27.9 1.0
FE4 D:F3S702 3.0 29.1 1.0
CB D:CYS222 3.2 24.6 1.0
CA D:CYS222 3.9 23.7 1.0
OD1 D:ASN215 4.0 39.3 1.0
CD D:PRO223 4.0 32.6 1.0
CB D:ASN215 4.1 24.4 1.0
S2 D:F3S702 4.1 28.1 1.0
CB D:ALA226 4.5 26.8 1.0
CG D:ASN215 4.5 27.7 1.0
C D:CYS222 4.6 27.2 1.0
N D:PRO223 4.6 31.3 1.0
CG1 D:ILE224 4.7 27.1 1.0
CG D:MET227 4.7 27.9 1.0
SD D:MET227 4.9 31.1 1.0
N D:ALA226 4.9 25.3 1.0
N D:ASN215 4.9 29.9 1.0

Iron binding site 6 out of 6 in 6a2u

Go back to Iron Binding Sites List in 6a2u
Iron binding site 6 out of 6 in the Crystal Structure of Gamma-Alpha Subunit Complex 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 6 of Crystal Structure of Gamma-Alpha Subunit Complex From Burkholderia Cepacia Fad Glucose Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe702

b:29.1
occ:1.00
 FE4 D:F3S702 0.0 29.1 1.0
S3 D:F3S702 2.2 28.3 1.0
S4 D:F3S702 2.2 35.4 1.0
S2 D:F3S702 2.2 28.1 1.0
SG D:CYS218 2.3 26.9 1.0
FE1 D:F3S702 3.0 27.9 1.0
FE3 D:F3S702 3.0 35.3 1.0
N D:CYS218 3.5 25.2 1.0
CB D:CYS218 3.5 28.9 1.0
CA D:CYS218 3.6 29.5 1.0
N D:ASN217 3.9 28.8 1.0
S1 D:F3S702 4.2 35.9 1.0
N D:ASN216 4.2 27.3 1.0
C D:ASN217 4.3 27.4 1.0
NE D:ARG201 4.4 26.8 1.0
CA D:PRO339 4.5 23.0 1.0
CA D:ASN216 4.5 25.2 1.0
SD D:MET227 4.5 31.1 1.0
NH2 D:ARG201 4.6 24.0 1.0
C D:ASN216 4.6 25.3 1.0
CA D:ASN217 4.7 26.2 1.0
CB D:ASN215 4.7 24.4 1.0
CB D:PRO339 4.8 25.2 1.0
CZ D:ARG201 4.8 21.8 1.0
SG D:CYS212 4.8 24.8 1.0
N D:ASN215 4.9 29.9 1.0
C D:ASN215 4.9 27.8 1.0
SG D:CYS222 4.9 27.5 1.0
CB D:CYS222 4.9 24.6 1.0

Reference:

H.Yoshida, K.Kojima, M.Shiota, K.Yoshimatsu, T.Yamazaki, S.Ferri, W.Tsugawa, S.Kamitori, K.Sode. X-Ray Structure of the Direct Electron Transfer-Type Fad Glucose Dehydrogenase Catalytic Subunit Complexed with A Hitchhiker Protein. Acta Crystallogr D Struct V. 75 841 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31478907
DOI: 10.1107/S2059798319010878
Page generated: Tue Aug 6 13:25:24 2024

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