Iron in PDB 8k6j: Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
All present enzymatic activity of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A:
1.1.99.11;
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
(pdb code 8k6j). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A, PDB code: 8k6j:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8k6j
Go back to
Iron Binding Sites List in 8k6j
Iron binding site 1 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:177.9
occ:1.00
|
FE1
|
A:F3S602
|
0.0
|
177.9
|
1.0
|
S1
|
A:F3S602
|
2.2
|
165.2
|
1.0
|
S2
|
A:F3S602
|
2.2
|
164.0
|
1.0
|
SG
|
A:CYS216
|
2.3
|
139.4
|
1.0
|
S3
|
A:F3S602
|
2.3
|
159.5
|
1.0
|
SG
|
A:CYS226
|
2.3
|
104.5
|
1.0
|
FE4
|
A:F3S602
|
2.4
|
181.3
|
1.0
|
FE3
|
A:F3S602
|
2.6
|
159.7
|
1.0
|
CB
|
A:CYS216
|
3.4
|
114.9
|
1.0
|
S4
|
A:F3S602
|
3.5
|
155.7
|
1.0
|
CB
|
A:ALA230
|
3.6
|
89.2
|
1.0
|
CB
|
A:CYS226
|
4.0
|
93.9
|
1.0
|
CD
|
A:ARG205
|
4.2
|
108.9
|
1.0
|
CA
|
A:CYS216
|
4.2
|
120.9
|
1.0
|
CG
|
A:ARG205
|
4.3
|
105.8
|
1.0
|
C
|
A:ALA230
|
4.3
|
103.6
|
1.0
|
CA
|
A:ALA230
|
4.3
|
91.0
|
1.0
|
N
|
A:MET231
|
4.4
|
110.9
|
1.0
|
N
|
A:ALA230
|
4.5
|
107.3
|
1.0
|
NH1
|
A:ARG205
|
4.5
|
102.3
|
1.0
|
O
|
A:ALA230
|
4.7
|
111.9
|
1.0
|
SG
|
A:CYS222
|
4.8
|
124.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 8k6j
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Iron Binding Sites List in 8k6j
Iron binding site 2 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:159.7
occ:1.00
|
FE3
|
A:F3S602
|
0.0
|
159.7
|
1.0
|
S4
|
A:F3S602
|
2.2
|
155.7
|
1.0
|
S3
|
A:F3S602
|
2.2
|
159.5
|
1.0
|
S1
|
A:F3S602
|
2.2
|
165.2
|
1.0
|
SG
|
A:CYS222
|
2.3
|
124.3
|
1.0
|
FE1
|
A:F3S602
|
2.6
|
177.9
|
1.0
|
FE4
|
A:F3S602
|
2.7
|
181.3
|
1.0
|
SG
|
A:CYS216
|
3.4
|
139.4
|
1.0
|
CB
|
A:CYS222
|
3.5
|
104.4
|
1.0
|
SG
|
A:CYS226
|
3.7
|
104.5
|
1.0
|
NH1
|
A:ARG205
|
3.7
|
102.3
|
1.0
|
N
|
A:CYS222
|
3.8
|
115.9
|
1.0
|
CA
|
A:CYS222
|
3.8
|
103.3
|
1.0
|
OG
|
A:SER343
|
3.8
|
129.9
|
1.0
|
S2
|
A:F3S602
|
4.0
|
164.0
|
1.0
|
CD
|
A:ARG205
|
4.0
|
108.9
|
1.0
|
CZ
|
A:ARG205
|
4.4
|
105.7
|
1.0
|
NE
|
A:ARG205
|
4.5
|
103.7
|
1.0
|
N
|
A:ASN220
|
4.5
|
111.1
|
1.0
|
N
|
A:ASN221
|
4.5
|
110.5
|
1.0
|
CA
|
A:SER343
|
4.5
|
114.9
|
1.0
|
CB
|
A:SER343
|
4.6
|
118.6
|
1.0
|
C
|
A:ASN221
|
4.6
|
112.4
|
1.0
|
CB
|
A:CYS226
|
4.7
|
93.9
|
1.0
|
CG
|
A:ARG205
|
4.9
|
105.8
|
1.0
|
CA
|
A:ASN220
|
4.9
|
101.8
|
1.0
|
CB
|
A:CYS216
|
5.0
|
114.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 8k6j
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Iron Binding Sites List in 8k6j
Iron binding site 3 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:181.3
occ:1.00
|
FE4
|
A:F3S602
|
0.0
|
181.3
|
1.0
|
S3
|
A:F3S602
|
2.2
|
159.5
|
1.0
|
S2
|
A:F3S602
|
2.2
|
164.0
|
1.0
|
S4
|
A:F3S602
|
2.3
|
155.7
|
1.0
|
SG
|
A:CYS216
|
2.3
|
139.4
|
1.0
|
FE1
|
A:F3S602
|
2.4
|
177.9
|
1.0
|
FE3
|
A:F3S602
|
2.7
|
159.7
|
1.0
|
N
|
A:ASN219
|
3.0
|
99.2
|
1.0
|
SG
|
A:CYS226
|
3.3
|
104.5
|
1.0
|
CB
|
A:ASN219
|
3.4
|
92.3
|
1.0
|
ND2
|
A:ASN219
|
3.6
|
106.8
|
1.0
|
CA
|
A:ASN219
|
3.6
|
94.3
|
1.0
|
CG
|
A:ASN219
|
3.8
|
103.0
|
1.0
|
N
|
A:ASN220
|
3.9
|
111.1
|
1.0
|
S1
|
A:F3S602
|
3.9
|
165.2
|
1.0
|
C
|
A:GLY218
|
3.9
|
106.8
|
1.0
|
N
|
A:GLY218
|
3.9
|
111.1
|
1.0
|
CA
|
A:GLY218
|
4.0
|
114.4
|
1.0
|
CB
|
A:CYS216
|
4.1
|
114.9
|
1.0
|
C
|
A:ASN219
|
4.2
|
105.3
|
1.0
|
N
|
A:CYS217
|
4.6
|
117.5
|
1.0
|
CA
|
A:CYS216
|
4.7
|
120.9
|
1.0
|
SG
|
A:CYS222
|
4.8
|
124.3
|
1.0
|
C
|
A:CYS217
|
4.8
|
106.5
|
1.0
|
OD1
|
A:ASN219
|
4.8
|
118.0
|
1.0
|
N
|
A:ASN221
|
4.9
|
110.5
|
1.0
|
CB
|
A:CYS226
|
4.9
|
93.9
|
1.0
|
C
|
A:CYS216
|
4.9
|
123.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 8k6j
Go back to
Iron Binding Sites List in 8k6j
Iron binding site 4 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:133.1
occ:1.00
|
FE
|
C:HEC501
|
0.0
|
133.1
|
1.0
|
NE2
|
C:HIS347
|
2.0
|
112.8
|
1.0
|
NC
|
C:HEC501
|
2.0
|
116.6
|
1.0
|
NA
|
C:HEC501
|
2.0
|
117.1
|
1.0
|
NB
|
C:HEC501
|
2.0
|
116.9
|
1.0
|
ND
|
C:HEC501
|
2.0
|
116.8
|
1.0
|
CE1
|
C:HIS347
|
2.6
|
109.5
|
1.0
|
SD
|
C:MET395
|
2.8
|
100.1
|
1.0
|
C1D
|
C:HEC501
|
3.0
|
113.9
|
1.0
|
C1B
|
C:HEC501
|
3.0
|
114.2
|
1.0
|
C4A
|
C:HEC501
|
3.0
|
113.2
|
1.0
|
C4B
|
C:HEC501
|
3.0
|
116.7
|
1.0
|
C1C
|
C:HEC501
|
3.0
|
114.6
|
1.0
|
C4C
|
C:HEC501
|
3.0
|
115.8
|
1.0
|
C1A
|
C:HEC501
|
3.0
|
115.8
|
1.0
|
C4D
|
C:HEC501
|
3.1
|
117.5
|
1.0
|
CD2
|
C:HIS347
|
3.2
|
107.3
|
1.0
|
CHD
|
C:HEC501
|
3.4
|
115.4
|
1.0
|
CHB
|
C:HEC501
|
3.4
|
115.1
|
1.0
|
CHA
|
C:HEC501
|
3.4
|
116.0
|
1.0
|
CHC
|
C:HEC501
|
3.4
|
115.9
|
1.0
|
CE
|
C:MET395
|
3.7
|
102.6
|
1.0
|
ND1
|
C:HIS347
|
3.8
|
110.0
|
1.0
|
CG
|
C:HIS347
|
4.2
|
105.6
|
1.0
|
C2D
|
C:HEC501
|
4.2
|
110.8
|
1.0
|
C3B
|
C:HEC501
|
4.2
|
114.7
|
1.0
|
C2B
|
C:HEC501
|
4.2
|
114.4
|
1.0
|
C3C
|
C:HEC501
|
4.2
|
112.5
|
1.0
|
C3A
|
C:HEC501
|
4.2
|
110.1
|
1.0
|
C2A
|
C:HEC501
|
4.3
|
114.7
|
1.0
|
C2C
|
C:HEC501
|
4.3
|
111.5
|
1.0
|
C3D
|
C:HEC501
|
4.3
|
114.5
|
1.0
|
CG
|
C:MET395
|
4.5
|
114.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 8k6j
Go back to
Iron Binding Sites List in 8k6j
Iron binding site 5 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:147.2
occ:1.00
|
FE
|
C:HEC502
|
0.0
|
147.2
|
1.0
|
NE2
|
C:HIS205
|
1.9
|
120.0
|
1.0
|
NC
|
C:HEC502
|
2.0
|
120.1
|
1.0
|
NB
|
C:HEC502
|
2.0
|
121.6
|
1.0
|
NA
|
C:HEC502
|
2.0
|
122.3
|
1.0
|
ND
|
C:HEC502
|
2.0
|
121.5
|
1.0
|
CD2
|
C:HIS205
|
2.7
|
115.5
|
1.0
|
SD
|
C:MET267
|
2.8
|
113.4
|
1.0
|
C1D
|
C:HEC502
|
3.0
|
121.7
|
1.0
|
C1B
|
C:HEC502
|
3.0
|
118.3
|
1.0
|
C4A
|
C:HEC502
|
3.0
|
121.5
|
1.0
|
C4C
|
C:HEC502
|
3.0
|
118.3
|
1.0
|
C4B
|
C:HEC502
|
3.0
|
117.4
|
1.0
|
C1C
|
C:HEC502
|
3.0
|
117.7
|
1.0
|
C4D
|
C:HEC502
|
3.0
|
116.2
|
1.0
|
C1A
|
C:HEC502
|
3.0
|
115.3
|
1.0
|
CE1
|
C:HIS205
|
3.1
|
117.7
|
1.0
|
CHD
|
C:HEC502
|
3.4
|
122.5
|
1.0
|
CHB
|
C:HEC502
|
3.4
|
120.3
|
1.0
|
CHA
|
C:HEC502
|
3.4
|
114.6
|
1.0
|
CHC
|
C:HEC502
|
3.5
|
117.3
|
1.0
|
CE
|
C:MET267
|
3.5
|
105.2
|
1.0
|
CG
|
C:HIS205
|
3.9
|
110.9
|
1.0
|
ND1
|
C:HIS205
|
4.1
|
117.3
|
1.0
|
C3C
|
C:HEC502
|
4.2
|
109.7
|
1.0
|
C3B
|
C:HEC502
|
4.2
|
113.6
|
1.0
|
C2B
|
C:HEC502
|
4.2
|
116.6
|
1.0
|
C2D
|
C:HEC502
|
4.2
|
118.3
|
1.0
|
C3A
|
C:HEC502
|
4.3
|
119.7
|
1.0
|
C2A
|
C:HEC502
|
4.3
|
114.7
|
1.0
|
C3D
|
C:HEC502
|
4.3
|
113.9
|
1.0
|
C2C
|
C:HEC502
|
4.3
|
113.0
|
1.0
|
CG
|
C:MET267
|
4.5
|
112.5
|
1.0
|
|
Iron binding site 6 out
of 6 in 8k6j
Go back to
Iron Binding Sites List in 8k6j
Iron binding site 6 out
of 6 in the Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cryo-Em Structure of Membrane-Bound Fructose Dehydrogenase From Gluconobacter Japonicus Variant-H1147A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe503
b:153.8
occ:1.00
|
FE
|
C:HEC503
|
0.0
|
153.8
|
1.0
|
NC
|
C:HEC503
|
2.0
|
137.1
|
1.0
|
NA
|
C:HEC503
|
2.0
|
138.6
|
1.0
|
NB
|
C:HEC503
|
2.0
|
140.6
|
1.0
|
ND
|
C:HEC503
|
2.0
|
136.1
|
1.0
|
NE2
|
C:HIS56
|
2.1
|
137.0
|
1.0
|
CE1
|
C:HIS56
|
2.6
|
135.4
|
1.0
|
SD
|
C:MET118
|
2.9
|
139.9
|
1.0
|
C1D
|
C:HEC503
|
3.0
|
135.5
|
1.0
|
C1B
|
C:HEC503
|
3.0
|
136.5
|
1.0
|
C4A
|
C:HEC503
|
3.0
|
139.0
|
1.0
|
C4C
|
C:HEC503
|
3.0
|
134.9
|
1.0
|
C4B
|
C:HEC503
|
3.0
|
136.8
|
1.0
|
C4D
|
C:HEC503
|
3.0
|
138.8
|
1.0
|
C1A
|
C:HEC503
|
3.0
|
137.7
|
1.0
|
C1C
|
C:HEC503
|
3.0
|
135.9
|
1.0
|
CD2
|
C:HIS56
|
3.3
|
134.9
|
1.0
|
CHD
|
C:HEC503
|
3.4
|
137.0
|
1.0
|
CHB
|
C:HEC503
|
3.4
|
138.5
|
1.0
|
CG
|
C:MET118
|
3.4
|
131.6
|
1.0
|
CHA
|
C:HEC503
|
3.4
|
140.3
|
1.0
|
CHC
|
C:HEC503
|
3.5
|
135.3
|
1.0
|
ND1
|
C:HIS56
|
3.8
|
133.7
|
1.0
|
CG
|
C:HIS56
|
4.2
|
130.5
|
1.0
|
CE
|
C:MET118
|
4.2
|
135.6
|
1.0
|
C2D
|
C:HEC503
|
4.2
|
135.2
|
1.0
|
C3C
|
C:HEC503
|
4.2
|
130.4
|
1.0
|
C3B
|
C:HEC503
|
4.2
|
133.7
|
1.0
|
C2B
|
C:HEC503
|
4.2
|
133.8
|
1.0
|
C3A
|
C:HEC503
|
4.3
|
136.7
|
1.0
|
C2A
|
C:HEC503
|
4.3
|
135.2
|
1.0
|
C3D
|
C:HEC503
|
4.3
|
134.8
|
1.0
|
C2C
|
C:HEC503
|
4.3
|
130.8
|
1.0
|
CB
|
C:MET118
|
4.8
|
128.3
|
1.0
|
CD1
|
C:ILE83
|
4.8
|
157.8
|
1.0
|
|
Reference:
E.Fukawa,
Y.Suzuki,
T.Adachi,
T.Miyata,
F.Makino,
H.Tanaka,
K.Namba,
K.Sowa,
Y.Kitazumi,
O.Shirai.
Structural and Electrochemical Elucidation of Biocatalytic Mechanisms in Direct Electron Transfer-Type D-Fructose Dehydrogenase. Electrochim Acta V. 490 2024.
DOI: 10.1016/J.ELECTACTA.2024.144271
Page generated: Sat Aug 10 07:26:48 2024
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