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Iron in PDB 8gy3: Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans

Enzymatic activity of Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans

All present enzymatic activity of Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans:
1.2.99.7;

Other elements in 8gy3:

The structure of Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans (pdb code 8gy3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans, PDB code: 8gy3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 8gy3

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Iron binding site 1 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:126.8
occ:1.00
 FE A:HEC501 0.0 126.8 1.0
NC A:HEC501 2.0 99.2 1.0
ND A:HEC501 2.0 101.8 1.0
NB A:HEC501 2.0 106.0 1.0
NA A:HEC501 2.0 104.2 1.0
NE2 A:HIS61 2.3 103.3 1.0
C1D A:HEC501 3.0 104.4 1.0
C1B A:HEC501 3.0 104.3 1.0
C4B A:HEC501 3.0 99.3 1.0
C4A A:HEC501 3.0 103.2 1.0
C1C A:HEC501 3.0 100.8 1.0
C4D A:HEC501 3.0 101.6 1.0
C4C A:HEC501 3.0 97.5 1.0
C1A A:HEC501 3.1 103.4 1.0
CD1 A:PHE125 3.1 102.4 1.0
CE1 A:HIS61 3.1 103.0 1.0
CD2 A:HIS61 3.4 102.7 1.0
CHD A:HEC501 3.4 100.8 1.0
CHB A:HEC501 3.4 104.1 1.0
CHA A:HEC501 3.4 103.0 1.0
CHC A:HEC501 3.4 99.9 1.0
CE1 A:PHE125 3.5 103.7 1.0
CG A:PHE125 4.0 98.3 1.0
C3B A:HEC501 4.2 101.8 1.0
C2B A:HEC501 4.2 103.2 1.0
C2D A:HEC501 4.2 103.5 1.0
C3C A:HEC501 4.2 102.0 1.0
C3D A:HEC501 4.3 102.2 1.0
C3A A:HEC501 4.3 103.9 1.0
C2C A:HEC501 4.3 103.3 1.0
C2A A:HEC501 4.3 102.8 1.0
ND1 A:HIS61 4.3 102.6 1.0
CB A:PHE125 4.4 100.7 1.0
CG A:HIS61 4.5 98.2 1.0
CZ A:PHE125 4.6 102.9 1.0
CA A:PHE125 5.0 98.8 1.0
CD2 A:PHE125 5.0 97.7 1.0

Iron binding site 2 out of 7 in 8gy3

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Iron binding site 2 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:119.2
occ:1.00
 FE A:HEC502 0.0 119.2 1.0
NC A:HEC502 2.0 82.8 1.0
NB A:HEC502 2.0 85.0 1.0
NA A:HEC502 2.0 90.1 1.0
ND A:HEC502 2.0 91.2 1.0
NE2 A:HIS211 2.0 87.3 1.0
CD2 A:HIS211 2.6 79.1 1.0
SD A:MET273 2.8 80.9 1.0
C1D A:HEC502 3.0 86.5 1.0
C1B A:HEC502 3.0 80.9 1.0
C4B A:HEC502 3.0 82.3 1.0
C4D A:HEC502 3.0 82.3 1.0
C4A A:HEC502 3.0 86.4 1.0
C1C A:HEC502 3.0 79.5 1.0
C4C A:HEC502 3.0 83.2 1.0
C1A A:HEC502 3.0 84.7 1.0
CE1 A:HIS211 3.3 80.3 1.0
CHD A:HEC502 3.4 81.5 1.0
CHB A:HEC502 3.4 81.7 1.0
CHA A:HEC502 3.4 81.9 1.0
CHC A:HEC502 3.4 84.6 1.0
CE A:MET273 3.6 81.2 1.0
CG A:HIS211 3.9 74.1 1.0
ND1 A:HIS211 4.2 81.2 1.0
C3B A:HEC502 4.2 78.4 1.0
C2D A:HEC502 4.2 79.6 1.0
C2B A:HEC502 4.2 78.3 1.0
C3C A:HEC502 4.2 89.6 1.0
C3A A:HEC502 4.3 80.4 1.0
C3D A:HEC502 4.3 78.1 1.0
C2A A:HEC502 4.3 77.9 1.0
C2C A:HEC502 4.3 84.7 1.0
CG A:MET273 4.4 80.2 1.0
CB A:MET273 5.0 74.6 1.0

Iron binding site 3 out of 7 in 8gy3

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Iron binding site 3 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:119.0
occ:1.00
 FE A:HEC503 0.0 119.0 1.0
NB A:HEC503 2.0 84.5 1.0
NC A:HEC503 2.0 82.3 1.0
NA A:HEC503 2.0 88.8 1.0
ND A:HEC503 2.0 88.0 1.0
NE2 A:HIS345 2.0 83.5 1.0
SD A:MET392 2.7 93.9 1.0
CD2 A:HIS345 2.8 71.4 1.0
C1B A:HEC503 3.0 83.6 1.0
C4B A:HEC503 3.0 79.8 1.0
C1D A:HEC503 3.0 86.0 1.0
C4A A:HEC503 3.0 80.6 1.0
C1C A:HEC503 3.0 81.1 1.0
C1A A:HEC503 3.0 80.2 1.0
C4C A:HEC503 3.0 82.9 1.0
C4D A:HEC503 3.0 77.4 1.0
CE1 A:HIS345 3.1 72.6 1.0
CHD A:HEC503 3.4 84.6 1.0
CHB A:HEC503 3.4 75.6 1.0
CHA A:HEC503 3.4 73.8 1.0
CHC A:HEC503 3.4 80.8 1.0
CE A:MET392 3.6 71.1 1.0
CG A:HIS345 4.0 61.9 1.0
ND1 A:HIS345 4.1 68.3 1.0
C3B A:HEC503 4.2 81.0 1.0
C2B A:HEC503 4.2 83.3 1.0
C3C A:HEC503 4.2 82.4 1.0
C2D A:HEC503 4.2 80.6 1.0
C3A A:HEC503 4.3 79.7 1.0
C2A A:HEC503 4.3 83.0 1.0
C3D A:HEC503 4.3 81.7 1.0
C2C A:HEC503 4.3 83.9 1.0
CG A:MET392 4.4 90.4 1.0
CB A:MET392 4.8 82.5 1.0

Iron binding site 4 out of 7 in 8gy3

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Iron binding site 4 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:118.1
occ:1.00
 FE1 B:FES201 0.0 118.1 1.0
S2 B:FES201 2.2 89.5 1.0
S1 B:FES201 2.2 100.0 1.0
SG B:CYS44 2.3 96.3 1.0
SG B:CYS39 2.3 98.4 1.0
N B:CYS39 3.1 86.5 1.0
FE2 B:FES201 3.1 108.5 1.0
CB B:CYS44 3.4 75.7 1.0
CB B:CYS39 3.5 78.5 1.0
N B:GLY40 3.5 84.0 1.0
N B:CYS44 3.5 80.0 1.0
CA B:CYS39 3.7 80.9 1.0
CA B:CYS44 3.8 74.3 1.0
N B:GLY45 3.8 77.3 1.0
C B:GLY38 4.0 78.3 1.0
C B:CYS39 4.1 82.9 1.0
CA B:GLY38 4.2 73.0 1.0
N B:GLU43 4.2 86.0 1.0
C B:CYS44 4.2 77.3 1.0
N B:ALA46 4.3 62.0 1.0
N B:GLY38 4.4 81.0 1.0
N B:GLY42 4.4 81.7 1.0
CA B:GLY40 4.5 81.6 1.0
SG B:CYS59 4.6 95.6 1.0
C B:GLU43 4.6 86.2 1.0
N B:ILE41 4.7 85.1 1.0
CA B:GLY42 4.7 81.7 1.0
CA B:GLY45 4.9 76.6 1.0
C B:GLY42 4.9 81.9 1.0
CB B:ALA46 4.9 65.3 1.0
CA B:GLU43 5.0 80.2 1.0
SG B:CYS47 5.0 96.5 1.0

Iron binding site 5 out of 7 in 8gy3

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Iron binding site 5 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:108.5
occ:1.00
 FE2 B:FES201 0.0 108.5 1.0
S2 B:FES201 2.2 89.5 1.0
S1 B:FES201 2.2 100.0 1.0
SG B:CYS47 2.3 96.5 1.0
SG B:CYS59 2.3 95.6 1.0
CB B:CYS59 2.7 73.9 1.0
FE1 B:FES201 3.1 118.1 1.0
CB B:CYS47 3.5 79.2 1.0
N B:CYS59 3.8 77.4 1.0
CA B:CYS59 3.9 75.8 1.0
N B:GLY42 4.1 81.7 1.0
CA B:GLY42 4.2 81.7 1.0
N B:CYS47 4.3 86.9 1.0
CB B:ARG57 4.3 73.6 1.0
CA B:CYS47 4.5 78.5 1.0
N B:GLY40 4.5 84.0 1.0
CA B:GLY40 4.6 81.6 1.0
SG B:CYS39 4.7 98.4 1.0
C B:CYS59 4.8 83.1 1.0
CD B:ARG57 4.9 75.8 1.0
C B:GLY40 4.9 84.7 1.0
CA B:ARG57 4.9 77.7 1.0
SG B:CYS44 5.0 96.3 1.0
N B:SER58 5.0 65.0 1.0
N B:ILE41 5.0 85.1 1.0

Iron binding site 6 out of 7 in 8gy3

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Iron binding site 6 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


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 Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:121.2
occ:1.00
 FE1 B:FES202 0.0 121.2 1.0
S1 B:FES202 2.2 103.5 1.0
S2 B:FES202 2.2 100.7 1.0
SG B:CYS97 2.3 94.7 1.0
SG B:CYS134 2.3 90.9 1.0
CB B:CYS97 3.0 78.2 1.0
FE2 B:FES202 3.1 117.0 1.0
CB B:CYS134 3.2 78.4 1.0
N B:CYS97 3.6 75.1 1.0
CA B:CYS97 3.8 74.2 1.0
N B:CYS134 3.9 75.2 1.0
N B:GLY98 4.1 78.7 1.0
CA B:CYS134 4.1 69.9 1.0
C B:CYS97 4.2 81.2 1.0
SG B:CYS132 4.5 94.8 1.0
N B:TYR99 4.6 65.2 1.0
C B:GLN96 4.8 73.1 1.0
CB B:GLN96 4.8 68.6 1.0
C B:ARG133 5.0 83.8 1.0
N B:ARG133 5.0 75.2 1.0

Iron binding site 7 out of 7 in 8gy3

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Iron binding site 7 out of 7 in the Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Membrane-Bound Aldehyde Dehydrogenase From Gluconobacter Oxydans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:117.0
occ:1.00
 FE2 B:FES202 0.0 117.0 1.0
S2 B:FES202 2.2 100.7 1.0
S1 B:FES202 2.2 103.5 1.0
SG B:CYS100 2.3 84.4 1.0
SG B:CYS132 2.3 94.8 1.0
FE1 B:FES202 3.1 121.2 1.0
CB B:CYS132 3.2 84.2 1.0
CB B:CYS100 3.5 73.6 1.0
CA B:CYS132 3.6 80.6 1.0
NE2 B:GLN101 3.7 77.1 1.0
N B:ARG133 4.1 75.2 1.0
C B:CYS132 4.2 83.9 1.0
N B:CYS100 4.3 78.6 1.0
N B:CYS134 4.3 75.2 1.0
CB B:CYS134 4.4 78.4 1.0
CA B:CYS100 4.4 75.8 1.0
CD B:GLN101 4.6 74.6 1.0
CG2 B:THR136 4.7 71.0 1.0
OG1 B:THR136 4.7 84.8 1.0
SG B:CYS134 4.8 90.9 1.0
CG B:GLN101 4.8 72.8 1.0
SG B:CYS97 4.8 94.7 1.0
N B:CYS132 4.9 82.3 1.0
CA B:CYS134 4.9 69.9 1.0
N B:GLN101 5.0 71.9 1.0
C B:CYS100 5.0 81.2 1.0

Reference:

T.Adachi, T.Miyata, F.Makino, H.Tanaka, K.Namba, K.Kano, K.Sowa, Y.Kitazumi, O.Shirai. Experimental and Theoretical Insights Into Bienzymatic Cascade For Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases Acs Catalysis V. 13 7955 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C01962
Page generated: Sat Aug 10 05:03:51 2024

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