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Iron in PDB 7xk6: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42

Enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42

All present enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42:
7.2.1.1;

Other elements in 7xk6:

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 (pdb code 7xk6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42, PDB code: 7xk6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7xk6

Go back to Iron Binding Sites List in 7xk6
Iron binding site 1 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42


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 Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:72.7
occ:1.00
 FE1 E:FES301 0.0 72.7 1.0
S1 E:FES301 2.2 72.7 1.0
S2 E:FES301 2.2 72.7 1.0
O D:THR110 2.6 55.2 1.0
SG E:CYS120 3.0 56.8 1.0
FE2 E:FES301 3.1 72.7 1.0
SG D:CYS112 3.1 55.3 1.0
CB E:CYS120 3.6 56.8 1.0
C D:THR110 3.7 55.2 1.0
N E:CYS120 3.9 56.8 1.0
N D:CYS112 4.3 55.3 1.0
CA E:CYS120 4.3 56.8 1.0
CA D:ASN111 4.4 54.3 1.0
N D:ASN111 4.4 54.3 1.0
CB D:CYS112 4.5 55.3 1.0
OD1 E:ASN119 4.5 60.4 1.0
C D:ASN111 4.6 54.3 1.0
CB D:THR110 4.6 55.2 1.0
OG1 D:THR110 4.7 55.2 1.0
SG D:CYS29 4.7 50.2 1.0
CA D:THR110 4.7 55.2 1.0
CA D:CYS112 4.8 55.3 1.0
C E:ASN119 4.9 60.4 1.0
SG E:CYS26 4.9 51.1 1.0

Iron binding site 2 out of 4 in 7xk6

Go back to Iron Binding Sites List in 7xk6
Iron binding site 2 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42


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 Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:72.7
occ:1.00
 FE2 E:FES301 0.0 72.7 1.0
S2 E:FES301 2.2 72.7 1.0
S1 E:FES301 2.2 72.7 1.0
SG E:CYS26 2.9 51.1 1.0
SG D:CYS29 2.9 50.2 1.0
FE1 E:FES301 3.1 72.7 1.0
N E:CYS26 3.4 51.1 1.0
N E:MET25 3.5 49.2 1.0
CB E:CYS26 3.7 51.1 1.0
CB D:CYS29 4.0 50.2 1.0
C E:GLY24 4.1 50.3 1.0
CA E:GLY24 4.1 50.3 1.0
CA E:CYS26 4.1 51.1 1.0
SG D:CYS112 4.2 55.3 1.0
N D:CYS29 4.2 50.2 1.0
C E:MET25 4.3 49.2 1.0
CA E:MET25 4.4 49.2 1.0
N E:GLY24 4.4 50.3 1.0
N D:VAL28 4.5 49.2 1.0
CB E:MET25 4.7 49.2 1.0
CA D:CYS29 4.7 50.2 1.0
SG E:CYS120 4.7 56.8 1.0
CB E:CYS120 4.8 56.8 1.0
N D:GLY27 5.0 50.7 1.0

Iron binding site 3 out of 4 in 7xk6

Go back to Iron Binding Sites List in 7xk6
Iron binding site 3 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42


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 Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:131.5
occ:1.00
 FE1 F:FES501 0.0 131.5 1.0
S1 F:FES501 2.2 131.5 1.0
S2 F:FES501 2.2 131.5 1.0
N F:SER75 2.9 127.6 1.0
FE2 F:FES501 3.1 131.5 1.0
N F:CYS76 3.2 124.5 1.0
SG F:CYS76 3.2 124.5 1.0
CA F:GLY74 3.3 128.7 1.0
N F:GLY74 3.3 128.7 1.0
C F:GLY74 3.4 128.7 1.0
SG F:CYS70 3.6 115.9 1.0
CA F:SER75 3.8 127.6 1.0
N F:GLY77 3.9 121.8 1.0
C F:SER75 3.9 127.6 1.0
CA F:CYS76 4.1 124.5 1.0
CB F:CYS76 4.1 124.5 1.0
CB F:SER75 4.3 127.6 1.0
O F:GLY74 4.4 128.7 1.0
C F:CYS76 4.5 124.5 1.0
C F:GLY73 4.6 127.3 1.0
N F:GLY73 4.7 127.3 1.0
N F:CYS70 4.8 115.9 1.0
CA F:GLY77 4.9 121.8 1.0
C F:GLY72 4.9 121.4 1.0
N F:ALA69 4.9 109.2 1.0
O F:SER75 5.0 127.6 1.0
CA F:GLY72 5.0 121.4 1.0

Iron binding site 4 out of 4 in 7xk6

Go back to Iron Binding Sites List in 7xk6
Iron binding site 4 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42


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 Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Aurachin D-42 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:131.5
occ:1.00
 FE2 F:FES501 0.0 131.5 1.0
S2 F:FES501 2.2 131.5 1.0
S1 F:FES501 2.2 131.5 1.0
SG F:CYS111 3.0 116.0 1.0
FE1 F:FES501 3.1 131.5 1.0
OG F:SER68 3.9 104.0 1.0
CA F:GLY72 3.9 121.4 1.0
SG F:CYS79 4.0 112.1 1.0
CB F:SER68 4.0 104.0 1.0
CA F:SER68 4.3 104.0 1.0
N F:GLY72 4.3 121.4 1.0
CB F:CYS79 4.5 112.1 1.0
N F:GLY73 4.5 127.3 1.0
SG F:CYS76 4.5 124.5 1.0
C F:GLY72 4.6 121.4 1.0
N F:GLY74 4.6 128.7 1.0
CB F:CYS111 4.7 116.0 1.0
O F:SER67 4.8 99.5 1.0
N F:ALA69 4.8 109.2 1.0
CD1 F:LEU56 4.9 112.4 1.0

Reference:

J.I.Kishikawa, M.Ishikawa, T.Masuya, M.Murai, Y.Kitazumi, N.L.Butler, T.Kato, B.Barquera, H.Miyoshi. Cryo-Em Structures of Na + -Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae. Nat Commun V. 13 4082 2022.
ISSN: ESSN 2041-1723
PubMed: 35882843
DOI: 10.1038/S41467-022-31718-1
Page generated: Fri Aug 9 11:02:44 2024

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