Iron in PDB 8qhk: Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide

Protein crystallography data

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qhk was solved by D.Wohlwend, T.Friedrich, S.Bucka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.413, 116.013, 189.741, 90, 90, 90
R / Rfree (%) 16.7 / 20

Other elements in 8qhk:

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide also contains other interesting chemical elements:

Sodium (Na) 2 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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (pdb code 8qhk). 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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qhk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 8qhk

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Iron binding site 1 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:27.3
occ:1.00
 FE1 A:FES201 0.0 27.3 1.0
S1 A:FES201 2.2 24.9 1.0
S2 A:FES201 2.2 26.4 1.0
SG A:CYS86 2.3 26.4 1.0
SG A:CYS91 2.3 27.4 1.0
FE2 A:FES201 2.7 26.6 1.0
CB A:CYS86 3.3 26.1 1.0
CB A:CYS91 3.3 28.0 1.0
N A:CYS91 3.9 27.1 1.0
CA A:CYS127 4.2 25.1 1.0
CA A:CYS91 4.2 28.2 1.0
N A:LEU128 4.3 24.7 1.0
SG A:CYS127 4.5 25.2 1.0
CG2 A:VAL136 4.6 26.3 1.0
CA A:CYS86 4.7 26.3 1.0
CB A:CYS127 4.7 25.2 1.0
CB A:VAL136 4.7 26.0 1.0
CB A:SER88 4.7 27.1 1.0
SG A:CYS131 4.8 26.0 1.0
C A:CYS127 4.8 24.8 1.0
O A:SER88 4.9 26.4 1.0
CA A:CYS131 4.9 25.0 1.0
C A:CYS86 4.9 26.9 1.0
N A:SER88 4.9 27.4 1.0
C A:VAL90 5.0 27.1 1.0

Iron binding site 2 out of 12 in 8qhk

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Iron binding site 2 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:26.6
occ:1.00
 FE2 A:FES201 0.0 26.6 1.0
S1 A:FES201 2.2 24.9 1.0
S2 A:FES201 2.2 26.4 1.0
SG A:CYS131 2.3 26.0 1.0
SG A:CYS127 2.4 25.2 1.0
FE1 A:FES201 2.7 27.3 1.0
CB A:CYS131 3.4 25.2 1.0
CB A:CYS127 3.4 25.2 1.0
CA A:CYS127 3.8 25.1 1.0
CA A:CYS131 3.8 25.0 1.0
N A:LEU128 4.0 24.7 1.0
N A:CYS131 4.1 24.0 1.0
N A:GLY129 4.1 24.0 1.0
N B:GLY99 4.2 24.0 1.0
C A:CYS127 4.2 24.8 1.0
SG A:CYS86 4.4 26.4 1.0
N A:ALA130 4.4 25.0 1.0
CA A:GLY129 4.6 24.0 1.0
SG A:CYS91 4.7 27.4 1.0
CB A:VAL90 4.7 26.2 1.0
CG2 A:VAL90 4.8 26.0 1.0
CA B:GLY99 4.8 24.4 1.0
C A:ALA130 4.9 24.6 1.0
C A:LEU128 5.0 23.9 1.0

Iron binding site 3 out of 12 in 8qhk

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Iron binding site 3 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:32.9
occ:1.00
 FE1 B:SF4501 0.0 32.9 1.0
SG B:CYS347 2.3 35.0 1.0
S4 B:SF4501 2.3 32.0 1.0
S3 B:SF4501 2.3 33.6 1.0
S2 B:SF4501 2.3 31.8 1.0
FE2 B:SF4501 2.8 31.5 1.0
FE3 B:SF4501 2.8 31.5 1.0
FE4 B:SF4501 2.8 32.5 1.0
CB B:CYS347 3.4 34.6 1.0
N B:CYS347 3.7 35.8 1.0
N B:GLY348 3.9 37.0 1.0
CA B:CYS347 3.9 35.8 1.0
S1 B:SF4501 4.0 32.4 1.0
N B:GLN349 4.1 37.6 1.0
C B:CYS347 4.1 37.8 1.0
CB B:GLN349 4.3 39.6 1.0
CD B:PRO199 4.4 29.1 1.0
NE2 B:GLN349 4.5 36.1 1.0
CG B:PRO199 4.5 28.8 1.0
OG1 B:THR346 4.6 36.9 1.0
SG B:CYS350 4.7 33.5 1.0
CG B:GLN349 4.7 40.9 1.0
SG B:CYS393 4.8 30.4 1.0
CA B:GLN349 4.8 38.9 1.0
N B:CYS350 4.8 36.1 1.0
C B:THR346 4.8 35.5 1.0
SG B:CYS353 4.8 31.6 1.0
CA B:GLY348 4.9 38.5 1.0
CD1 B:ILE181 5.0 27.2 1.0
CG1 B:ILE181 5.0 27.4 1.0
C B:GLY348 5.0 38.8 1.0

Iron binding site 4 out of 12 in 8qhk

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Iron binding site 4 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:31.5
occ:1.00
 FE2 B:SF4501 0.0 31.5 1.0
SG B:CYS353 2.3 31.6 1.0
S4 B:SF4501 2.3 32.0 1.0
S3 B:SF4501 2.3 33.6 1.0
S1 B:SF4501 2.3 32.4 1.0
FE4 B:SF4501 2.7 32.5 1.0
FE3 B:SF4501 2.8 31.5 1.0
FE1 B:SF4501 2.8 32.9 1.0
CB B:CYS353 3.1 33.0 1.0
OG1 B:THR346 3.7 36.9 1.0
S2 B:SF4501 3.9 31.8 1.0
N B:GLY396 4.1 34.6 1.0
CD2 B:LEU395 4.3 35.7 1.0
CA B:GLY396 4.4 35.6 1.0
CB B:THR346 4.6 35.8 1.0
CA B:CYS353 4.6 34.3 1.0
N B:CYS347 4.6 35.8 1.0
SG B:CYS350 4.6 33.5 1.0
CB B:LEU395 4.7 33.6 1.0
SG B:CYS393 4.7 30.4 1.0
CA B:THR346 4.8 35.0 1.0
N B:GLY348 4.9 37.0 1.0
CB B:CYS350 4.9 34.6 1.0
SG B:CYS347 4.9 35.0 1.0
C B:CYS353 5.0 34.8 1.0
CG B:LEU395 5.0 34.5 1.0

Iron binding site 5 out of 12 in 8qhk

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Iron binding site 5 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:31.5
occ:1.00
 FE3 B:SF4501 0.0 31.5 1.0
SG B:CYS393 2.3 30.4 1.0
S1 B:SF4501 2.3 32.4 1.0
S2 B:SF4501 2.3 31.8 1.0
S4 B:SF4501 2.4 32.0 1.0
FE2 B:SF4501 2.8 31.5 1.0
FE4 B:SF4501 2.8 32.5 1.0
FE1 B:SF4501 2.8 32.9 1.0
CB B:CYS393 3.3 31.5 1.0
N B:CYS393 3.9 34.4 1.0
S3 B:SF4501 4.0 33.6 1.0
CA B:CYS393 4.0 32.8 1.0
CG B:PRO199 4.2 28.8 1.0
C B:CYS393 4.2 32.5 1.0
O B:CYS393 4.3 33.5 1.0
CB B:LEU395 4.3 33.6 1.0
CD1 B:ILE181 4.4 27.2 1.0
N B:GLY396 4.4 34.6 1.0
CB B:PRO199 4.7 28.8 1.0
N B:LEU395 4.7 33.9 1.0
SG B:CYS347 4.8 35.0 1.0
C B:ILE392 4.8 36.0 1.0
SG B:CYS350 4.8 33.5 1.0
SG B:CYS353 4.9 31.6 1.0
CD B:PRO199 4.9 29.1 1.0
N B:ILE392 5.0 37.2 1.0
CA B:LEU395 5.0 33.5 1.0

Iron binding site 6 out of 12 in 8qhk

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Iron binding site 6 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:32.5
occ:1.00
 FE4 B:SF4501 0.0 32.5 1.0
SG B:CYS350 2.2 33.5 1.0
S2 B:SF4501 2.3 31.8 1.0
S1 B:SF4501 2.3 32.4 1.0
S3 B:SF4501 2.3 33.6 1.0
FE2 B:SF4501 2.7 31.5 1.0
FE3 B:SF4501 2.8 31.5 1.0
FE1 B:SF4501 2.8 32.9 1.0
CB B:CYS350 3.3 34.6 1.0
N B:CYS350 3.8 36.1 1.0
S4 B:SF4501 3.9 32.0 1.0
N B:ILE392 4.0 37.2 1.0
CG1 B:ILE392 4.1 40.1 1.0
CA B:CYS350 4.2 36.1 1.0
CB B:GLN349 4.4 39.6 1.0
CB B:CYS353 4.4 33.0 1.0
CA B:SER391 4.6 36.8 1.0
SG B:CYS353 4.6 31.6 1.0
N B:CYS393 4.7 34.4 1.0
SG B:CYS347 4.7 35.0 1.0
CB B:SER391 4.8 36.6 1.0
C B:GLN349 4.8 38.2 1.0
CD1 B:ILE392 4.8 42.0 1.0
C B:SER391 4.8 37.1 1.0
N B:GLN349 4.9 37.6 1.0
SG B:CYS393 4.9 30.4 1.0
CA B:ILE392 4.9 37.7 1.0
CA B:GLN349 5.0 38.9 1.0
NE2 B:GLN349 5.0 36.1 1.0

Iron binding site 7 out of 12 in 8qhk

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Iron binding site 7 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:27.2
occ:1.00
 FE1 C:FES201 0.0 27.2 1.0
S2 C:FES201 2.2 27.6 1.0
S1 C:FES201 2.2 25.8 1.0
SG C:CYS131 2.3 28.3 1.0
SG C:CYS127 2.4 26.3 1.0
FE2 C:FES201 2.7 29.2 1.0
CB C:CYS131 3.3 27.1 1.0
CB C:CYS127 3.5 27.5 1.0
CA C:CYS131 3.8 26.9 1.0
CA C:CYS127 3.8 27.1 1.0
N C:LEU128 4.0 25.6 1.0
N C:CYS131 4.0 25.7 1.0
N C:GLY129 4.1 24.6 1.0
C C:CYS127 4.3 26.2 1.0
N D:GLY99 4.3 26.3 1.0
N C:ALA130 4.4 25.0 1.0
SG C:CYS86 4.4 29.3 1.0
SG C:CYS91 4.6 30.0 1.0
CB C:VAL90 4.7 27.8 1.0
CA C:GLY129 4.7 24.4 1.0
C C:ALA130 4.7 25.6 1.0
CG2 C:VAL90 4.8 27.9 1.0
CA D:GLY99 4.9 26.5 1.0
C C:LEU128 5.0 25.1 1.0

Iron binding site 8 out of 12 in 8qhk

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Iron binding site 8 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:29.2
occ:1.00
 FE2 C:FES201 0.0 29.2 1.0
S1 C:FES201 2.2 25.8 1.0
S2 C:FES201 2.2 27.6 1.0
SG C:CYS91 2.3 30.0 1.0
SG C:CYS86 2.3 29.3 1.0
FE1 C:FES201 2.7 27.2 1.0
CB C:CYS86 3.3 28.9 1.0
CB C:CYS91 3.3 29.9 1.0
N C:CYS91 3.9 29.2 1.0
CA C:CYS91 4.2 30.2 1.0
CA C:CYS127 4.2 27.1 1.0
N C:LEU128 4.3 25.6 1.0
SG C:CYS127 4.5 26.3 1.0
CA C:CYS86 4.7 29.7 1.0
CB C:CYS127 4.7 27.5 1.0
SG C:CYS131 4.7 28.3 1.0
CB C:SER88 4.7 29.4 1.0
CG2 C:VAL136 4.7 28.7 1.0
CB C:VAL136 4.8 28.2 1.0
C C:CYS127 4.9 26.2 1.0
O C:SER88 4.9 31.1 1.0
N C:SER88 4.9 30.2 1.0
CA C:CYS131 4.9 26.9 1.0
C C:CYS86 4.9 30.7 1.0
C C:VAL90 5.0 29.1 1.0

Iron binding site 9 out of 12 in 8qhk

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Iron binding site 9 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:33.8
occ:1.00
 FE1 D:SF4501 0.0 33.8 1.0
SG D:CYS347 2.3 35.1 1.0
S3 D:SF4501 2.3 35.6 1.0
S4 D:SF4501 2.3 31.4 1.0
S2 D:SF4501 2.3 32.6 1.0
FE4 D:SF4501 2.8 34.7 1.0
FE3 D:SF4501 2.8 31.8 1.0
FE2 D:SF4501 2.8 33.5 1.0
CB D:CYS347 3.4 34.5 1.0
N D:CYS347 3.7 35.2 1.0
N D:GLY348 3.9 35.9 1.0
CA D:CYS347 3.9 35.2 1.0
S1 D:SF4501 4.0 32.5 1.0
N D:GLN349 4.1 36.5 1.0
C D:CYS347 4.2 37.0 1.0
CB D:GLN349 4.3 37.9 1.0
CD D:PRO199 4.3 31.5 1.0
NE2 D:GLN349 4.5 35.7 1.0
CG D:PRO199 4.5 30.9 1.0
OG1 D:THR346 4.6 36.3 1.0
SG D:CYS350 4.7 36.1 1.0
CA D:GLN349 4.8 38.0 1.0
SG D:CYS393 4.8 32.5 1.0
C D:THR346 4.8 36.0 1.0
CG D:GLN349 4.8 39.0 1.0
N D:CYS350 4.9 36.8 1.0
SG D:CYS353 4.9 32.1 1.0
CA D:GLY348 4.9 37.8 1.0
CG1 D:ILE181 5.0 28.1 1.0
C D:GLY348 5.0 38.1 1.0

Iron binding site 10 out of 12 in 8qhk

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Iron binding site 10 out of 12 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:33.5
occ:1.00
 FE2 D:SF4501 0.0 33.5 1.0
SG D:CYS353 2.3 32.1 1.0
S4 D:SF4501 2.3 31.4 1.0
S3 D:SF4501 2.3 35.6 1.0
S1 D:SF4501 2.3 32.5 1.0
FE4 D:SF4501 2.8 34.7 1.0
FE3 D:SF4501 2.8 31.8 1.0
FE1 D:SF4501 2.8 33.8 1.0
CB D:CYS353 3.1 34.7 1.0
OG1 D:THR346 3.6 36.3 1.0
S2 D:SF4501 3.9 32.6 1.0
N D:GLY396 4.1 35.5 1.0
CD2 D:LEU395 4.3 33.9 1.0
CA D:GLY396 4.4 36.3 1.0
CB D:THR346 4.5 36.6 1.0
CA D:CYS353 4.6 35.8 1.0
N D:CYS347 4.6 35.2 1.0
CB D:LEU395 4.6 33.0 1.0
SG D:CYS350 4.7 36.1 1.0
SG D:CYS393 4.8 32.5 1.0
CA D:THR346 4.8 35.8 1.0
CB D:CYS350 4.9 36.9 1.0
C D:CYS353 5.0 36.2 1.0
N D:GLY348 5.0 35.9 1.0
C D:LEU395 5.0 34.7 1.0

Reference:

D.Wohlwend, L.Merono, S.Bucka, K.Ritter, H.J.Jessen, T.Friedrich. Structures of 3-Acetylpyridine Adenine Dinucleotide and Adp-Ribose Bound to the Electron Input Module of Respiratory Complex I. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38503292
DOI: 10.1016/J.STR.2024.02.013
Page generated: Sat Aug 10 15:20:37 2024

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