Iron in PDB 6q9k: Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh

Enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh

All present enzymatic activity of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh:
1.6.5.11;

Protein crystallography data

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh, PDB code: 6q9k was solved by D.Wohlwend, S.Gerhardt, E.Gnandt, T.Friedrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.26 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.380, 115.940, 189.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.9

Other elements in 6q9k:

The structure of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh (pdb code 6q9k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh, PDB code: 6q9k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6q9k

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Iron binding site 1 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:14.2
occ:1.00
 FE1 A:FES201 0.0 14.2 1.0
S2 A:FES201 2.2 14.9 1.0
S1 A:FES201 2.2 14.6 1.0
SG A:CYS86 2.3 17.9 1.0
SG A:CYS91 2.3 17.1 1.0
FE2 A:FES201 2.7 15.0 1.0
CB A:CYS86 3.2 17.1 1.0
CB A:CYS91 3.3 17.1 1.0
N A:CYS91 3.8 17.2 1.0
CA A:CYS91 4.1 17.3 1.0
CA A:CYS127 4.2 18.5 1.0
N A:LEU128 4.3 16.4 1.0
SG A:CYS127 4.5 19.6 1.0
CA A:CYS86 4.6 17.2 1.0
SG A:CYS131 4.7 19.3 1.0
CG2 A:VAL136 4.7 16.2 1.0
CB A:CYS127 4.7 19.4 1.0
CB A:SER88 4.7 18.1 1.0
CB A:VAL136 4.8 15.9 1.0
CA A:CYS131 4.8 17.8 1.0
C A:CYS127 4.9 17.5 1.0
C A:VAL90 4.9 17.5 1.0
O A:SER88 4.9 17.5 1.0
C A:CYS86 5.0 17.3 1.0
N A:SER88 5.0 17.8 1.0
CB A:CYS131 5.0 18.7 1.0

Iron binding site 2 out of 12 in 6q9k

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Iron binding site 2 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:15.0
occ:1.00
 FE2 A:FES201 0.0 15.0 1.0
S1 A:FES201 2.2 14.6 1.0
S2 A:FES201 2.2 14.9 1.0
SG A:CYS131 2.3 19.3 1.0
SG A:CYS127 2.3 19.6 1.0
FE1 A:FES201 2.7 14.2 1.0
CB A:CYS127 3.3 19.4 1.0
CB A:CYS131 3.4 18.7 1.0
CA A:CYS127 3.7 18.5 1.0
CA A:CYS131 3.8 17.8 1.0
N A:LEU128 4.0 16.4 1.0
N A:CYS131 4.0 17.2 1.0
N A:GLY129 4.0 16.2 1.0
C A:CYS127 4.2 17.5 1.0
N B:GLY99 4.2 15.2 1.0
SG A:CYS86 4.3 17.9 1.0
N A:ALA130 4.4 16.2 1.0
CA A:GLY129 4.6 16.6 1.0
SG A:CYS91 4.6 17.1 1.0
CG2 A:VAL90 4.8 17.9 1.0
CB A:VAL90 4.8 17.3 1.0
C A:ALA130 4.8 16.6 1.0
CA B:GLY99 4.9 15.1 1.0
C A:LEU128 5.0 15.9 1.0
C A:GLY129 5.0 16.4 1.0

Iron binding site 3 out of 12 in 6q9k

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Iron binding site 3 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.9
occ:1.00
 FE1 B:SF4501 0.0 13.9 1.0
SG B:CYS347 2.3 21.2 1.0
S4 B:SF4501 2.3 13.1 1.0
S2 B:SF4501 2.3 13.1 1.0
S3 B:SF4501 2.3 13.6 1.0
FE4 B:SF4501 2.7 12.9 1.0
FE3 B:SF4501 2.7 12.7 1.0
FE2 B:SF4501 2.7 12.6 1.0
CB B:CYS347 3.5 21.0 1.0
N B:CYS347 3.7 18.8 1.0
S1 B:SF4501 3.9 12.5 1.0
N B:GLY348 3.9 19.1 1.0
CA B:CYS347 4.0 20.1 1.0
N B:GLN349 4.2 19.7 1.0
C B:CYS347 4.3 20.1 1.0
CB B:GLN349 4.4 20.7 1.0
CD B:PRO199 4.4 19.2 1.0
OG1 B:THR346 4.5 16.7 1.0
NE2 B:GLN349 4.5 21.7 1.0
CG B:PRO199 4.5 18.8 1.0
SG B:CYS350 4.7 18.7 1.0
SG B:CYS393 4.8 18.4 1.0
C B:THR346 4.8 18.2 1.0
N B:CYS350 4.8 18.6 1.0
SG B:CYS353 4.8 15.8 1.0
CA B:GLN349 4.9 20.4 1.0
CG B:GLN349 4.9 21.9 1.0
CD1 B:ILE181 4.9 16.3 1.0
CA B:GLY348 5.0 19.2 1.0
CG1 B:ILE181 5.0 16.6 1.0
C B:GLY348 5.0 19.6 1.0

Iron binding site 4 out of 12 in 6q9k

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Iron binding site 4 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:12.6
occ:1.00
 FE2 B:SF4501 0.0 12.6 1.0
S1 B:SF4501 2.3 12.5 1.0
S4 B:SF4501 2.3 13.1 1.0
SG B:CYS353 2.3 15.8 1.0
S3 B:SF4501 2.3 13.6 1.0
FE4 B:SF4501 2.7 12.9 1.0
FE3 B:SF4501 2.7 12.7 1.0
FE1 B:SF4501 2.7 13.9 1.0
CB B:CYS353 3.1 15.8 1.0
OG1 B:THR346 3.5 16.7 1.0
S2 B:SF4501 3.9 13.1 1.0
N B:GLY396 4.0 15.8 1.0
CA B:GLY396 4.3 15.6 1.0
CD2 B:LEU395 4.3 15.8 1.0
CB B:THR346 4.4 16.6 1.0
CB B:LEU395 4.6 16.4 1.0
CA B:CYS353 4.6 15.5 1.0
N B:CYS347 4.6 18.8 1.0
CA B:THR346 4.7 17.1 1.0
SG B:CYS393 4.7 18.4 1.0
SG B:CYS350 4.7 18.7 1.0
SG B:CYS347 4.9 21.2 1.0
CB B:CYS350 4.9 17.9 1.0
C B:LEU395 4.9 15.6 1.0
CG B:LEU395 4.9 16.1 1.0

Iron binding site 5 out of 12 in 6q9k

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Iron binding site 5 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:12.7
occ:1.00
 FE3 B:SF4501 0.0 12.7 1.0
S4 B:SF4501 2.3 13.1 1.0
SG B:CYS393 2.3 18.4 1.0
S1 B:SF4501 2.3 12.5 1.0
S2 B:SF4501 2.3 13.1 1.0
FE1 B:SF4501 2.7 13.9 1.0
FE2 B:SF4501 2.7 12.6 1.0
FE4 B:SF4501 2.8 12.9 1.0
CB B:CYS393 3.4 19.1 1.0
S3 B:SF4501 3.9 13.6 1.0
N B:CYS393 3.9 18.6 1.0
CA B:CYS393 4.0 18.7 1.0
CG B:PRO199 4.1 18.8 1.0
CB B:LEU395 4.3 16.4 1.0
CD1 B:ILE181 4.3 16.3 1.0
O B:CYS393 4.3 17.1 1.0
C B:CYS393 4.3 17.8 1.0
N B:GLY396 4.4 15.8 1.0
SG B:CYS347 4.7 21.2 1.0
CB B:PRO199 4.7 19.0 1.0
N B:LEU395 4.7 16.5 1.0
C B:ILE392 4.8 19.5 1.0
SG B:CYS350 4.9 18.7 1.0
CD B:PRO199 4.9 19.2 1.0
SG B:CYS353 4.9 15.8 1.0
CA B:LEU395 5.0 16.0 1.0
N B:ILE392 5.0 18.4 1.0

Iron binding site 6 out of 12 in 6q9k

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Iron binding site 6 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:12.9
occ:1.00
 FE4 B:SF4501 0.0 12.9 1.0
S3 B:SF4501 2.3 13.6 1.0
SG B:CYS350 2.3 18.7 1.0
S2 B:SF4501 2.3 13.1 1.0
S1 B:SF4501 2.3 12.5 1.0
FE2 B:SF4501 2.7 12.6 1.0
FE1 B:SF4501 2.7 13.9 1.0
FE3 B:SF4501 2.8 12.7 1.0
CB B:CYS350 3.2 17.9 1.0
N B:CYS350 3.8 18.6 1.0
S4 B:SF4501 3.9 13.1 1.0
N B:ILE392 4.1 18.4 1.0
CG1 B:ILE392 4.1 20.4 1.0
CA B:CYS350 4.1 18.3 1.0
CB B:CYS353 4.4 15.8 1.0
CB B:GLN349 4.5 20.7 1.0
SG B:CYS353 4.6 15.8 1.0
CA B:SER391 4.6 17.3 0.5
SG B:CYS347 4.6 21.2 1.0
CA B:SER391 4.7 17.6 0.5
N B:CYS393 4.7 18.6 1.0
C B:GLN349 4.7 19.8 1.0
N B:GLN349 4.8 19.7 1.0
C B:SER391 4.9 18.2 0.5
SG B:CYS393 4.9 18.4 1.0
CB B:SER391 4.9 16.4 0.5
C B:SER391 4.9 18.4 0.5
CD1 B:ILE392 4.9 21.5 1.0
CA B:GLN349 5.0 20.4 1.0
CA B:ILE392 5.0 19.7 1.0

Iron binding site 7 out of 12 in 6q9k

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Iron binding site 7 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:13.9
occ:1.00
 FE1 C:FES201 0.0 13.9 1.0
S1 C:FES201 2.2 14.8 1.0
S2 C:FES201 2.2 14.1 1.0
SG C:CYS91 2.3 20.4 1.0
SG C:CYS86 2.3 19.7 1.0
FE2 C:FES201 2.7 13.9 1.0
CB C:CYS86 3.3 18.9 1.0
CB C:CYS91 3.3 20.6 1.0
N C:CYS91 3.9 21.2 1.0
CA C:CYS91 4.2 21.3 1.0
CA C:CYS127 4.2 19.5 1.0
N C:LEU128 4.3 17.6 1.0
SG C:CYS127 4.5 19.6 1.0
CB C:SER88 4.6 17.9 1.0
CA C:CYS86 4.6 19.2 1.0
SG C:CYS131 4.7 19.3 1.0
CB C:VAL136 4.8 17.3 1.0
CB C:CYS127 4.8 20.0 1.0
C C:CYS127 4.8 18.5 1.0
CG2 C:VAL136 4.9 17.3 1.0
CA C:CYS131 4.9 18.1 1.0
N C:SER88 4.9 18.4 1.0
C C:CYS86 4.9 19.2 1.0
O C:SER88 4.9 17.8 1.0
C C:VAL90 5.0 17.1 1.0
CB C:VAL90 5.0 16.6 1.0

Iron binding site 8 out of 12 in 6q9k

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Iron binding site 8 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:13.9
occ:1.00
 FE2 C:FES201 0.0 13.9 1.0
S2 C:FES201 2.2 14.1 1.0
S1 C:FES201 2.2 14.8 1.0
SG C:CYS131 2.3 19.3 1.0
SG C:CYS127 2.3 19.6 1.0
FE1 C:FES201 2.7 13.9 1.0
CB C:CYS131 3.4 18.8 1.0
CB C:CYS127 3.5 20.0 1.0
CA C:CYS127 3.7 19.5 1.0
CA C:CYS131 3.8 18.1 1.0
N C:LEU128 4.0 17.6 1.0
N C:CYS131 4.0 17.4 1.0
N C:GLY129 4.1 16.7 1.0
N D:GLY99 4.2 16.5 1.0
C C:CYS127 4.2 18.5 1.0
SG C:CYS86 4.3 19.7 1.0
N C:ALA130 4.4 16.4 1.0
SG C:CYS91 4.6 20.4 1.0
CA C:GLY129 4.7 16.6 1.0
CB C:VAL90 4.7 16.6 1.0
CG2 C:VAL90 4.7 16.8 1.0
C C:ALA130 4.8 16.9 1.0
CA D:GLY99 4.8 16.6 1.0
C C:LEU128 5.0 16.6 1.0

Iron binding site 9 out of 12 in 6q9k

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Iron binding site 9 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:13.4
occ:1.00
 FE1 D:SF4501 0.0 13.4 1.0
S4 D:SF4501 2.3 12.8 1.0
SG D:CYS347 2.3 20.5 1.0
S3 D:SF4501 2.3 12.9 1.0
S2 D:SF4501 2.3 12.9 1.0
FE3 D:SF4501 2.7 12.2 1.0
FE4 D:SF4501 2.7 12.9 1.0
FE2 D:SF4501 2.7 12.2 1.0
CB D:CYS347 3.5 19.7 1.0
N D:CYS347 3.7 18.2 1.0
S1 D:SF4501 3.9 12.6 1.0
N D:GLY348 3.9 18.5 1.0
CA D:CYS347 4.0 19.0 1.0
N D:GLN349 4.2 19.2 1.0
C D:CYS347 4.2 19.1 1.0
CB D:GLN349 4.4 20.3 1.0
CD D:PRO199 4.4 19.2 1.0
OG1 D:THR346 4.6 17.4 1.0
NE2 D:GLN349 4.6 20.8 1.0
CG D:PRO199 4.6 18.6 1.0
SG D:CYS350 4.7 20.1 1.0
SG D:CYS393 4.7 18.5 1.0
C D:THR346 4.8 17.9 1.0
SG D:CYS353 4.8 17.0 1.0
N D:CYS350 4.8 19.2 1.0
CA D:GLN349 4.9 20.0 1.0
CG D:GLN349 4.9 21.0 1.0
CD1 D:ILE181 4.9 17.4 1.0
CA D:GLY348 4.9 18.7 1.0
CG1 D:ILE181 5.0 17.5 1.0
C D:GLY348 5.0 19.1 1.0

Iron binding site 10 out of 12 in 6q9k

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Iron binding site 10 out of 12 in the Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Reduced Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M Bound to Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:12.2
occ:1.00
 FE2 D:SF4501 0.0 12.2 1.0
S1 D:SF4501 2.3 12.6 1.0
SG D:CYS353 2.3 17.0 1.0
S4 D:SF4501 2.3 12.8 1.0
S3 D:SF4501 2.3 12.9 1.0
FE4 D:SF4501 2.7 12.9 1.0
FE3 D:SF4501 2.7 12.2 1.0
FE1 D:SF4501 2.7 13.4 1.0
CB D:CYS353 3.1 17.0 1.0
OG1 D:THR346 3.6 17.4 1.0
S2 D:SF4501 3.9 12.9 1.0
N D:GLY396 4.1 15.9 1.0
CD2 D:LEU395 4.2 15.0 1.0
CA D:GLY396 4.4 16.1 1.0
CA D:CYS353 4.5 16.7 1.0
CB D:THR346 4.5 17.2 1.0
CB D:LEU395 4.6 15.3 1.0
N D:CYS347 4.6 18.2 1.0
CA D:THR346 4.7 17.3 1.0
SG D:CYS393 4.7 18.5 1.0
SG D:CYS350 4.7 20.1 1.0
CB D:CYS350 4.8 19.3 1.0
SG D:CYS347 4.9 20.5 1.0
CG D:LEU395 5.0 14.9 1.0
C D:CYS353 5.0 16.5 1.0
C D:LEU395 5.0 15.5 1.0
N D:GLY348 5.0 18.5 1.0

Reference:

M.Schulte, K.Frick, E.Gnandt, S.Jurkovic, S.Burschel, R.Labatzke, K.Aierstock, D.Fiegen, D.Wohlwend, S.Gerhardt, O.Einsle, T.Friedrich. A Mechanism to Prevent Production of Reactive Oxygen Species By Escherichia Coli Respiratory Complex I. Nat Commun V. 10 2551 2019.
ISSN: ESSN 2041-1723
PubMed: 31186428
DOI: 10.1038/S41467-019-10429-0
Page generated: Wed Aug 7 07:53:12 2024

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