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Iron in PDB 6hl3: Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+

Enzymatic activity of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+

All present enzymatic activity of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+:
1.6.5.11;

Protein crystallography data

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+, PDB code: 6hl3 was solved by S.Gerhardt, T.Friedrich, O.Einsle, E.Gnandt, M.Schulte, D.Fiegen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.35 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.514, 115.759, 189.635, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Other elements in 6hl3:

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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 Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ (pdb code 6hl3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+, PDB code: 6hl3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6hl3

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Iron binding site 1 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:26.2
occ:1.00
 FE1 A:FES201 0.0 26.2 1.0
S1 A:FES201 2.2 23.4 1.0
S2 A:FES201 2.2 23.4 1.0
SG A:CYS86 2.3 26.0 1.0
SG A:CYS91 2.3 25.8 1.0
FE2 A:FES201 2.7 25.3 1.0
CB A:CYS86 3.3 23.0 1.0
CB A:CYS91 3.4 22.7 1.0
N A:CYS91 3.9 22.6 1.0
CA A:CYS127 4.2 20.1 1.0
CA A:CYS91 4.2 22.9 1.0
N A:LEU128 4.3 21.7 1.0
SG A:CYS127 4.5 22.5 1.0
CB A:CYS127 4.6 19.6 1.0
CA A:CYS86 4.7 24.1 1.0
CB A:SER88 4.7 26.9 1.0
CB A:VAL136 4.7 25.4 1.0
CG2 A:VAL136 4.7 24.6 1.0
SG A:CYS131 4.8 24.3 1.0
C A:CYS127 4.8 23.8 1.0
O A:SER88 4.9 23.3 1.0
CA A:CYS131 4.9 21.3 1.0
C A:CYS86 5.0 26.6 1.0
N A:SER88 5.0 25.2 1.0
C A:VAL90 5.0 26.5 1.0

Iron binding site 2 out of 12 in 6hl3

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Iron binding site 2 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:25.3
occ:1.00
 FE2 A:FES201 0.0 25.3 1.0
S1 A:FES201 2.2 23.4 1.0
S2 A:FES201 2.2 23.4 1.0
SG A:CYS131 2.3 24.3 1.0
SG A:CYS127 2.4 22.5 1.0
FE1 A:FES201 2.7 26.2 1.0
CB A:CYS131 3.4 21.2 1.0
CB A:CYS127 3.4 19.6 1.0
CA A:CYS131 3.8 21.3 1.0
CA A:CYS127 3.8 20.1 1.0
N A:CYS131 3.9 21.1 1.0
N A:GLY129 4.0 21.5 1.0
N A:LEU128 4.1 21.7 1.0
N B:GLY99 4.2 21.8 1.0
C A:CYS127 4.3 23.8 1.0
N A:ALA130 4.4 21.8 1.0
SG A:CYS86 4.4 26.0 1.0
CA A:GLY129 4.5 20.9 1.0
SG A:CYS91 4.6 25.8 1.0
CB A:VAL90 4.8 24.1 1.0
CG2 A:VAL90 4.8 23.1 1.0
C A:ALA130 4.8 24.6 1.0
CA B:GLY99 4.9 21.2 1.0
C A:LEU128 4.9 26.3 1.0
C A:GLY129 5.0 24.1 1.0
CA B:PRO98 5.0 18.7 1.0

Iron binding site 3 out of 12 in 6hl3

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Iron binding site 3 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:29.4
occ:1.00
 FE1 B:SF4501 0.0 29.4 1.0
SG B:CYS347 2.3 30.7 1.0
S3 B:SF4501 2.3 30.8 1.0
S4 B:SF4501 2.3 26.6 1.0
S2 B:SF4501 2.3 28.1 1.0
FE2 B:SF4501 2.8 30.1 1.0
FE3 B:SF4501 2.8 29.3 1.0
FE4 B:SF4501 2.8 30.1 1.0
CB B:CYS347 3.4 26.8 1.0
N B:CYS347 3.6 27.3 1.0
CA B:CYS347 3.9 27.1 1.0
S1 B:SF4501 3.9 27.4 1.0
N B:GLY348 4.0 27.8 1.0
N B:GLN349 4.2 30.0 1.0
CD B:PRO199 4.2 25.0 1.0
C B:CYS347 4.2 30.2 1.0
CB B:GLN349 4.3 31.0 1.0
NE2 B:GLN349 4.5 25.8 1.0
CG B:PRO199 4.5 28.8 1.0
OG1 B:THR346 4.6 27.1 1.0
SG B:CYS350 4.8 28.6 1.0
SG B:CYS393 4.8 28.4 1.0
C B:THR346 4.8 31.1 1.0
CG B:GLN349 4.8 39.5 1.0
CG1 B:ILE181 4.8 21.7 1.0
N B:CYS350 4.8 27.2 1.0
CA B:GLN349 4.9 30.2 1.0
SG B:CYS353 4.9 27.6 1.0
CD1 B:ILE181 4.9 27.7 1.0
CA B:GLY348 5.0 28.7 1.0

Iron binding site 4 out of 12 in 6hl3

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Iron binding site 4 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.1
occ:1.00
 FE2 B:SF4501 0.0 30.1 1.0
S4 B:SF4501 2.3 26.6 1.0
S3 B:SF4501 2.3 30.8 1.0
S1 B:SF4501 2.3 27.4 1.0
SG B:CYS353 2.3 27.6 1.0
FE4 B:SF4501 2.7 30.1 1.0
FE3 B:SF4501 2.8 29.3 1.0
FE1 B:SF4501 2.8 29.4 1.0
CB B:CYS353 3.1 24.5 1.0
OG1 B:THR346 3.6 27.1 1.0
S2 B:SF4501 3.9 28.1 1.0
N B:GLY396 4.2 27.7 1.0
CD2 B:LEU395 4.3 32.8 1.0
CA B:GLY396 4.5 27.9 1.0
CB B:THR346 4.5 30.1 1.0
CA B:CYS353 4.5 24.8 1.0
N B:CYS347 4.6 27.3 1.0
CB B:LEU395 4.6 25.3 1.0
SG B:CYS350 4.7 28.6 1.0
CA B:THR346 4.7 25.6 1.0
CB B:CYS350 4.8 25.4 1.0
SG B:CYS393 4.8 28.4 1.0
SG B:CYS347 4.9 30.7 1.0
C B:CYS353 4.9 29.9 1.0
N B:GLY348 5.0 27.8 1.0

Iron binding site 5 out of 12 in 6hl3

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Iron binding site 5 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:29.3
occ:1.00
 FE3 B:SF4501 0.0 29.3 1.0
S1 B:SF4501 2.3 27.4 1.0
S2 B:SF4501 2.3 28.1 1.0
S4 B:SF4501 2.3 26.6 1.0
SG B:CYS393 2.3 28.4 1.0
FE4 B:SF4501 2.8 30.1 1.0
FE2 B:SF4501 2.8 30.1 1.0
FE1 B:SF4501 2.8 29.4 1.0
CB B:CYS393 3.5 25.1 1.0
N B:CYS393 3.7 27.4 1.0
S3 B:SF4501 3.9 30.8 1.0
CA B:CYS393 4.0 25.9 1.0
CG B:PRO199 4.2 28.8 1.0
CB B:LEU395 4.3 25.3 1.0
O B:CYS393 4.3 30.7 1.0
C B:CYS393 4.3 29.9 1.0
CD1 B:ILE181 4.3 27.7 1.0
N B:GLY396 4.5 27.7 1.0
N B:LEU395 4.7 25.2 1.0
CB B:PRO199 4.7 24.8 1.0
SG B:CYS347 4.8 30.7 1.0
CD B:PRO199 4.8 25.0 1.0
C B:ILE392 4.9 32.8 1.0
SG B:CYS350 4.9 28.6 1.0
SG B:CYS353 4.9 27.6 1.0
N B:ILE392 4.9 28.8 1.0
CA B:LEU395 4.9 25.3 1.0
CB B:ILE392 5.0 32.6 1.0

Iron binding site 6 out of 12 in 6hl3

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Iron binding site 6 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.1
occ:1.00
 FE4 B:SF4501 0.0 30.1 1.0
SG B:CYS350 2.3 28.6 1.0
S2 B:SF4501 2.3 28.1 1.0
S1 B:SF4501 2.3 27.4 1.0
S3 B:SF4501 2.3 30.8 1.0
FE2 B:SF4501 2.7 30.1 1.0
FE3 B:SF4501 2.8 29.3 1.0
FE1 B:SF4501 2.8 29.4 1.0
CB B:CYS350 3.2 25.4 1.0
N B:CYS350 3.8 27.2 1.0
N B:ILE392 3.9 28.8 1.0
S4 B:SF4501 3.9 26.6 1.0
CA B:CYS350 4.1 26.2 1.0
CB B:ILE392 4.3 32.6 1.0
CB B:GLN349 4.4 31.0 1.0
CB B:CYS353 4.4 24.5 1.0
N B:CYS393 4.5 27.4 1.0
CA B:SER391 4.6 27.9 1.0
CA B:ILE392 4.6 29.3 1.0
SG B:CYS353 4.6 27.6 1.0
SG B:CYS347 4.7 30.7 1.0
CG1 B:ILE392 4.7 33.4 1.0
C B:SER391 4.7 31.8 1.0
C B:GLN349 4.7 32.3 1.0
CB B:SER391 4.8 30.8 1.0
CD1 B:ILE392 4.8 39.7 1.0
N B:GLN349 4.8 30.0 1.0
CA B:GLN349 4.9 30.2 1.0
SG B:CYS393 4.9 28.4 1.0

Iron binding site 7 out of 12 in 6hl3

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Iron binding site 7 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:27.4
occ:1.00
 FE1 C:FES201 0.0 27.4 1.0
S1 C:FES201 2.2 22.5 1.0
S2 C:FES201 2.2 25.5 1.0
SG C:CYS86 2.3 28.0 1.0
SG C:CYS91 2.4 27.2 1.0
FE2 C:FES201 2.7 26.4 1.0
CB C:CYS86 3.3 25.0 1.0
CB C:CYS91 3.4 25.6 1.0
N C:CYS91 3.9 27.4 1.0
CA C:CYS127 4.2 22.3 1.0
CA C:CYS91 4.3 26.8 1.0
N C:LEU128 4.3 23.1 1.0
SG C:CYS127 4.5 25.1 1.0
CB C:CYS127 4.6 22.1 1.0
CB C:SER88 4.6 26.5 1.0
CA C:CYS86 4.7 26.4 1.0
CB C:VAL136 4.7 29.0 1.0
CG2 C:VAL136 4.8 28.4 1.0
SG C:CYS131 4.8 27.3 1.0
C C:CYS127 4.8 26.1 1.0
O C:SER88 4.9 28.0 1.0
CA C:CYS131 5.0 23.4 1.0
N C:SER88 5.0 24.7 1.0
C C:CYS86 5.0 31.1 1.0

Iron binding site 8 out of 12 in 6hl3

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Iron binding site 8 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:26.4
occ:1.00
 FE2 C:FES201 0.0 26.4 1.0
S1 C:FES201 2.2 22.5 1.0
S2 C:FES201 2.2 25.5 1.0
SG C:CYS131 2.3 27.3 1.0
SG C:CYS127 2.4 25.1 1.0
FE1 C:FES201 2.7 27.4 1.0
CB C:CYS131 3.4 23.7 1.0
CB C:CYS127 3.4 22.1 1.0
CA C:CYS131 3.8 23.4 1.0
CA C:CYS127 3.8 22.3 1.0
N C:CYS131 3.9 21.9 1.0
N C:GLY129 4.0 23.3 1.0
N C:LEU128 4.1 23.1 1.0
N D:GLY99 4.3 23.4 1.0
C C:CYS127 4.3 26.1 1.0
N C:ALA130 4.4 23.3 1.0
SG C:CYS86 4.4 28.0 1.0
CA C:GLY129 4.5 22.4 1.0
SG C:CYS91 4.7 27.2 1.0
CB C:VAL90 4.8 27.5 1.0
C C:ALA130 4.8 25.0 1.0
CG2 C:VAL90 4.8 26.8 1.0
CA D:GLY99 4.9 22.9 1.0
C C:LEU128 5.0 28.2 1.0
C C:GLY129 5.0 26.3 1.0
CA D:PRO98 5.0 21.8 1.0

Iron binding site 9 out of 12 in 6hl3

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Iron binding site 9 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:31.2
occ:1.00
 FE1 D:SF4501 0.0 31.2 1.0
SG D:CYS347 2.3 29.7 1.0
S3 D:SF4501 2.3 31.1 1.0
S4 D:SF4501 2.3 29.3 1.0
S2 D:SF4501 2.3 28.9 1.0
FE4 D:SF4501 2.8 31.6 1.0
FE2 D:SF4501 2.8 31.2 1.0
FE3 D:SF4501 2.8 30.4 1.0
CB D:CYS347 3.4 26.0 1.0
N D:CYS347 3.6 27.0 1.0
CA D:CYS347 3.9 26.9 1.0
S1 D:SF4501 3.9 30.0 1.0
N D:GLY348 4.0 29.6 1.0
N D:GLN349 4.2 30.6 1.0
CD D:PRO199 4.2 27.9 1.0
C D:CYS347 4.2 32.5 1.0
CB D:GLN349 4.3 31.9 1.0
NE2 D:GLN349 4.5 30.0 1.0
CG D:PRO199 4.6 31.6 1.0
OG1 D:THR346 4.6 30.5 1.0
SG D:CYS350 4.8 32.1 1.0
SG D:CYS393 4.8 32.6 1.0
C D:THR346 4.8 31.1 1.0
CG D:GLN349 4.8 42.4 1.0
CG1 D:ILE181 4.8 23.7 1.0
N D:CYS350 4.8 30.2 1.0
CA D:GLN349 4.9 31.0 1.0
SG D:CYS353 4.9 28.9 1.0
CD1 D:ILE181 4.9 28.9 1.0
CA D:GLY348 5.0 30.3 1.0

Iron binding site 10 out of 12 in 6hl3

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Iron binding site 10 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:31.2
occ:1.00
 FE2 D:SF4501 0.0 31.2 1.0
S3 D:SF4501 2.3 31.1 1.0
S4 D:SF4501 2.3 29.3 1.0
S1 D:SF4501 2.3 30.0 1.0
SG D:CYS353 2.3 28.9 1.0
FE4 D:SF4501 2.7 31.6 1.0
FE1 D:SF4501 2.8 31.2 1.0
FE3 D:SF4501 2.8 30.4 1.0
CB D:CYS353 3.1 26.2 1.0
OG1 D:THR346 3.6 30.5 1.0
S2 D:SF4501 3.9 28.9 1.0
N D:GLY396 4.2 29.7 1.0
CD2 D:LEU395 4.3 35.2 1.0
CA D:GLY396 4.5 30.2 1.0
CB D:THR346 4.5 32.6 1.0
CA D:CYS353 4.5 26.7 1.0
N D:CYS347 4.6 27.0 1.0
CB D:LEU395 4.6 29.4 1.0
SG D:CYS350 4.7 32.1 1.0
CA D:THR346 4.7 28.7 1.0
CB D:CYS350 4.8 29.5 1.0
SG D:CYS393 4.8 32.6 1.0
SG D:CYS347 4.9 29.7 1.0
C D:CYS353 4.9 31.3 1.0
N D:GLY348 5.0 29.6 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: Tue Aug 6 21:25:26 2024

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