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Zinc in PDB 7bkb: Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)

Enzymatic activity of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)

All present enzymatic activity of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure):
1.17.1.9; 1.2.7.12; 1.2.99.5;

Other elements in 7bkb:

The structure of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) also contains other interesting chemical elements:

Iron (Fe) 212 atoms
Molybdenum (Mo) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) (pdb code 7bkb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure), PDB code: 7bkb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7bkb

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Zinc binding site 1 out of 4 in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn601

b:82.3
occ:1.00
 NE2 G:HIS60 2.0 51.0 1.0
OQ2 G:KCX184 2.0 50.8 1.0
OD1 G:ASP390 2.0 52.5 1.0
NE2 G:HIS58 2.0 51.8 1.0
CG G:ASP390 2.8 52.5 1.0
CX G:KCX184 2.9 50.8 1.0
CE1 G:HIS60 2.9 51.0 1.0
CD2 G:HIS60 2.9 51.0 1.0
CE1 G:HIS58 3.0 51.8 1.0
CD2 G:HIS58 3.0 51.8 1.0
OD2 G:ASP390 3.0 52.5 1.0
NZ G:KCX184 3.6 50.8 1.0
OQ1 G:KCX184 3.7 50.8 1.0
ND1 G:HIS60 3.9 51.0 1.0
CG G:HIS60 4.0 51.0 1.0
ND2 G:ASN393 4.0 49.3 1.0
ZN G:ZN602 4.0 96.7 1.0
ND1 G:HIS58 4.1 51.8 1.0
CG G:HIS58 4.1 51.8 1.0
CB G:ASP390 4.2 52.5 1.0
CD2 G:HIS276 4.4 52.2 1.0
CA G:ASP390 4.7 52.5 1.0
CE G:KCX184 4.7 50.8 1.0
CB G:ALA121 4.7 48.8 1.0
NE2 G:HIS276 4.7 52.2 1.0

Zinc binding site 2 out of 4 in 7bkb

Go back to Zinc Binding Sites List in 7bkb
Zinc binding site 2 out of 4 in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn602

b:96.7
occ:1.00
 NE2 G:HIS237 1.8 54.7 1.0
NE2 G:HIS276 2.0 52.2 1.0
OQ1 G:KCX184 2.1 50.8 1.0
CE1 G:HIS237 2.4 54.7 1.0
CD2 G:HIS237 2.6 54.7 1.0
CX G:KCX184 2.8 50.8 1.0
OQ2 G:KCX184 2.8 50.8 1.0
CE1 G:HIS276 2.9 52.2 1.0
ND1 G:HIS237 3.0 54.7 1.0
CD2 G:HIS276 3.0 52.2 1.0
CG G:HIS237 3.2 54.7 1.0
OD2 G:ASP390 3.9 52.5 1.0
ND1 G:HIS276 4.0 52.2 1.0
NZ G:KCX184 4.0 50.8 1.0
ZN G:ZN601 4.0 82.3 1.0
CG G:HIS276 4.1 52.2 1.0
CG2 G:THR323 4.4 54.1 1.0
CB G:HIS237 4.4 54.7 1.0
CG2 G:THR275 4.6 50.4 1.0
CB G:THR323 4.7 54.1 1.0
CE G:KCX184 4.8 50.8 1.0
CA G:HIS237 4.8 54.7 1.0
CG G:ASP390 4.8 52.5 1.0
NE2 G:HIS58 4.9 51.8 1.0

Zinc binding site 3 out of 4 in 7bkb

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Zinc binding site 3 out of 4 in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
g:Zn601

b:82.3
occ:1.00
 NE2 g:HIS60 2.0 51.0 1.0
OQ1 g:KCX184 2.0 50.8 1.0
OD1 g:ASP390 2.0 52.5 1.0
NE2 g:HIS58 2.0 51.8 1.0
CG g:ASP390 2.8 52.5 1.0
CX g:KCX184 2.9 50.8 1.0
CE1 g:HIS60 2.9 51.0 1.0
CD2 g:HIS60 2.9 51.0 1.0
CE1 g:HIS58 3.0 51.8 1.0
CD2 g:HIS58 3.0 51.8 1.0
OD2 g:ASP390 3.0 52.5 1.0
NZ g:KCX184 3.6 50.8 1.0
OQ2 g:KCX184 3.7 50.8 1.0
ND1 g:HIS60 3.9 51.0 1.0
CG g:HIS60 4.0 51.0 1.0
ND2 g:ASN393 4.0 49.3 1.0
ZN g:ZN602 4.0 96.7 1.0
ND1 g:HIS58 4.1 51.8 1.0
CG g:HIS58 4.1 51.8 1.0
CB g:ASP390 4.2 52.5 1.0
CD2 g:HIS276 4.4 52.2 1.0
CA g:ASP390 4.7 52.5 1.0
CE g:KCX184 4.7 50.8 1.0
CB g:ALA121 4.7 48.8 1.0
NE2 g:HIS276 4.7 52.2 1.0

Zinc binding site 4 out of 4 in 7bkb

Go back to Zinc Binding Sites List in 7bkb
Zinc binding site 4 out of 4 in the Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Formate Dehydrogenase - Heterodisulfide Reductase - Formylmethanofuran Dehydrogenase Complex From Methanospirillum Hungatei (Hexameric, Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
g:Zn602

b:96.7
occ:1.00
 NE2 g:HIS237 1.8 54.7 1.0
NE2 g:HIS276 2.0 52.2 1.0
OQ2 g:KCX184 2.1 50.8 1.0
CE1 g:HIS237 2.4 54.7 1.0
CD2 g:HIS237 2.6 54.7 1.0
CX g:KCX184 2.8 50.8 1.0
OQ1 g:KCX184 2.8 50.8 1.0
CE1 g:HIS276 2.9 52.2 1.0
ND1 g:HIS237 3.0 54.7 1.0
CD2 g:HIS276 3.0 52.2 1.0
CG g:HIS237 3.2 54.7 1.0
OD2 g:ASP390 3.9 52.5 1.0
ND1 g:HIS276 4.0 52.2 1.0
NZ g:KCX184 4.0 50.8 1.0
ZN g:ZN601 4.0 82.3 1.0
CG g:HIS276 4.1 52.2 1.0
CG2 g:THR323 4.4 54.1 1.0
CB g:HIS237 4.4 54.7 1.0
CG2 g:THR275 4.6 50.4 1.0
CB g:THR323 4.7 54.1 1.0
CE g:KCX184 4.8 50.8 1.0
CA g:HIS237 4.8 54.7 1.0
CG g:ASP390 4.8 52.5 1.0
NE2 g:HIS58 4.9 51.8 1.0

Reference:

T.Watanabe, O.Pfeil-Gardiner, J.Kahnt, J.Koch, S.Shima, B.J.Murphy. Three-Megadalton Complex of Methanogenic Electron-Bifurcating and Co 2 -Fixing Enzymes. Science V. 373 1151 2021.
ISSN: ESSN 1095-9203
PubMed: 34516836
DOI: 10.1126/SCIENCE.ABG5550
Page generated: Tue Oct 29 17:37:39 2024

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