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Iron in PDB 7xk7: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin

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

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

Other elements in 7xk7:

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin 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 Korormicin (pdb code 7xk7). 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 Korormicin, PDB code: 7xk7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7xk7

Go back to Iron Binding Sites List in 7xk7
Iron binding site 1 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin


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 Korormicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:56.3
occ:1.00
 FE1 D:FES301 0.0 56.3 1.0
S2 D:FES301 2.2 56.3 1.0
S1 D:FES301 2.2 56.3 1.0
SG D:CYS112 2.9 45.3 1.0
SG E:CYS26 3.0 41.9 1.0
FE2 D:FES301 3.1 56.3 1.0
CB D:CYS112 3.4 45.3 1.0
N D:GLY27 3.5 43.2 1.0
N D:CYS112 3.6 45.3 1.0
CA D:GLY27 4.0 43.2 1.0
CA D:CYS112 4.1 45.3 1.0
CB E:CYS26 4.1 41.9 1.0
O D:THR110 4.4 42.7 1.0
N D:VAL28 4.5 42.5 1.0
C D:ASN111 4.5 43.2 1.0
SG E:CYS120 4.5 45.6 1.0
CA D:ASN111 4.6 43.2 1.0
C D:LEU26 4.6 45.1 1.0
C D:GLY27 4.7 43.2 1.0
CA D:LEU26 4.7 45.1 1.0
OD1 D:ASN111 4.7 43.2 1.0
N E:CYS26 5.0 41.9 1.0

Iron binding site 2 out of 4 in 7xk7

Go back to Iron Binding Sites List in 7xk7
Iron binding site 2 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin


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 Korormicin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:56.3
occ:1.00
 FE2 D:FES301 0.0 56.3 1.0
S1 D:FES301 2.2 56.3 1.0
S2 D:FES301 2.2 56.3 1.0
SG D:CYS29 2.9 44.2 1.0
SG E:CYS120 3.0 45.6 1.0
CB E:CYS120 3.0 45.6 1.0
FE1 D:FES301 3.1 56.3 1.0
N E:GLY24 3.6 40.4 1.0
CA E:GLY24 3.8 40.4 1.0
CB D:CYS29 3.9 44.2 1.0
N E:MET25 3.9 41.0 1.0
CA E:CYS120 4.3 45.6 1.0
C E:GLY24 4.3 40.4 1.0
N E:CYS120 4.3 45.6 1.0
SG E:CYS26 4.7 41.9 1.0
C E:LEU23 4.8 40.8 1.0
N E:CYS26 4.8 41.9 1.0
N D:CYS29 4.8 44.2 1.0
ND2 E:ASN119 4.8 49.0 1.0
O D:THR110 4.9 42.7 1.0
CA D:CYS29 5.0 44.2 1.0

Iron binding site 3 out of 4 in 7xk7

Go back to Iron Binding Sites List in 7xk7
Iron binding site 3 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin


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 Korormicin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:108.1
occ:1.00
 FE1 F:FES501 0.0 108.1 1.0
S2 F:FES501 2.2 108.1 1.0
S1 F:FES501 2.2 108.1 1.0
N F:GLY77 2.8 90.7 1.0
N F:SER75 2.8 94.9 1.0
N F:CYS76 3.0 93.8 1.0
FE2 F:FES501 3.1 108.1 1.0
C F:GLY74 3.1 93.1 1.0
CA F:GLY74 3.2 93.1 1.0
C F:SER75 3.4 94.9 1.0
CA F:GLY77 3.5 90.7 1.0
CA F:SER75 3.6 94.9 1.0
C F:CYS76 3.6 93.8 1.0
SG F:CYS76 3.7 93.8 1.0
N F:GLY74 3.8 93.1 1.0
CA F:CYS76 3.8 93.8 1.0
CD1 F:LEU109 3.8 90.2 1.0
O F:GLY74 4.1 93.1 1.0
O F:SER75 4.1 94.9 1.0
CB F:CYS76 4.2 93.8 1.0
C F:GLY77 4.5 90.7 1.0
N F:GLN78 4.6 87.7 1.0
O F:CYS76 4.7 93.8 1.0
CB F:SER75 4.8 94.9 1.0
C F:GLY73 4.9 94.3 1.0
CE1 F:HIS97 4.9 93.2 1.0
CG F:LEU109 5.0 90.2 1.0

Iron binding site 4 out of 4 in 7xk7

Go back to Iron Binding Sites List in 7xk7
Iron binding site 4 out of 4 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, with Korormicin


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 Korormicin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:108.1
occ:1.00
 FE2 F:FES501 0.0 108.1 1.0
S1 F:FES501 2.2 108.1 1.0
S2 F:FES501 2.2 108.1 1.0
SG F:CYS111 3.0 88.9 1.0
SG F:CYS79 3.1 90.0 1.0
CA F:GLY72 3.1 95.7 1.0
FE1 F:FES501 3.1 108.1 1.0
C F:GLY72 3.5 95.7 1.0
CB F:CYS79 3.9 90.0 1.0
N F:GLY74 3.9 93.1 1.0
N F:GLY72 3.9 95.7 1.0
SG F:CYS76 3.9 93.8 1.0
O F:GLY72 4.0 95.7 1.0
N F:GLY73 4.0 94.3 1.0
CB F:CYS111 4.1 88.9 1.0
O F:ALA69 4.2 93.2 1.0
CA F:GLY74 4.4 93.1 1.0
N F:SER75 4.6 94.9 1.0
N F:CYS76 4.8 93.8 1.0
C F:GLY73 4.9 94.3 1.0
N F:CYS79 4.9 90.0 1.0
N F:GLY77 4.9 90.7 1.0
CB F:CYS76 5.0 93.8 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 11:02:43 2024

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