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Iron in PDB 6hl2: Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form

Enzymatic activity of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form

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

Protein crystallography data

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form, PDB code: 6hl2 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) 73.48 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.190, 116.438, 189.449, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.5

Other elements in 6hl2:

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

Chlorine (Cl) 8 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 (pdb code 6hl2). 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, PDB code: 6hl2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6hl2

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:23.1
occ:1.00
 FE1 A:FES201 0.0 23.1 1.0
S1 A:FES201 2.2 17.1 1.0
S2 A:FES201 2.2 19.1 1.0
SG A:CYS86 2.3 19.9 1.0
SG A:CYS91 2.3 19.4 1.0
FE2 A:FES201 2.7 21.9 1.0
CB A:CYS86 3.2 16.7 1.0
CB A:CYS91 3.3 16.3 1.0
N A:CYS91 3.9 17.7 1.0
CA A:CYS91 4.2 17.1 1.0
CA A:CYS127 4.2 16.6 1.0
N A:LEU128 4.3 19.6 1.0
SG A:CYS127 4.5 20.1 1.0
CA A:CYS86 4.6 17.7 1.0
CB A:SER88 4.7 21.2 1.0
CB A:CYS127 4.7 16.7 1.0
CB A:VAL136 4.7 22.8 1.0
CG2 A:VAL136 4.8 22.1 1.0
O A:SER88 4.8 17.0 1.0
SG A:CYS131 4.8 22.4 1.0
C A:CYS127 4.8 21.9 1.0
N A:SER88 4.9 18.7 1.0
C A:CYS86 4.9 21.4 1.0
CA A:CYS131 4.9 18.3 1.0
C A:VAL90 5.0 21.1 1.0

Iron binding site 2 out of 12 in 6hl2

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:21.9
occ:1.00
 FE2 A:FES201 0.0 21.9 1.0
S2 A:FES201 2.2 19.1 1.0
S1 A:FES201 2.2 17.1 1.0
SG A:CYS127 2.4 20.1 1.0
SG A:CYS131 2.4 22.4 1.0
FE1 A:FES201 2.7 23.1 1.0
CB A:CYS131 3.4 18.9 1.0
CB A:CYS127 3.4 16.7 1.0
CA A:CYS131 3.8 18.3 1.0
CA A:CYS127 3.8 16.6 1.0
N A:CYS131 3.9 18.1 1.0
N A:LEU128 4.0 19.6 1.0
N A:GLY129 4.0 17.4 1.0
C A:CYS127 4.3 21.9 1.0
N B:GLY99 4.3 16.3 1.0
SG A:CYS86 4.3 19.9 1.0
N A:ALA130 4.4 16.9 1.0
SG A:CYS91 4.6 19.4 1.0
CA A:GLY129 4.6 16.9 1.0
CB A:VAL90 4.8 19.4 1.0
C A:ALA130 4.8 21.1 1.0
CG2 A:VAL90 4.8 18.6 1.0
CA B:GLY99 4.9 17.4 1.0
C A:LEU128 4.9 20.0 1.0
CA B:PRO98 5.0 16.0 1.0
C A:GLY129 5.0 19.7 1.0

Iron binding site 3 out of 12 in 6hl2

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


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

b:25.2
occ:1.00
 FE1 B:SF4501 0.0 25.2 1.0
SG B:CYS347 2.2 23.4 1.0
S3 B:SF4501 2.3 23.9 1.0
S4 B:SF4501 2.3 19.7 1.0
S2 B:SF4501 2.3 22.4 1.0
FE2 B:SF4501 2.7 25.7 1.0
FE4 B:SF4501 2.7 25.8 1.0
FE3 B:SF4501 2.8 25.3 1.0
CB B:CYS347 3.5 20.4 1.0
N B:CYS347 3.6 22.3 1.0
CA B:CYS347 3.9 20.7 1.0
S1 B:SF4501 3.9 21.6 1.0
N B:GLY348 4.0 24.1 1.0
N B:GLN349 4.1 24.0 1.0
C B:CYS347 4.2 25.7 1.0
CB B:GLN349 4.4 24.6 1.0
CD B:PRO199 4.4 22.6 1.0
NE2 B:GLN349 4.5 27.7 1.0
OG1 B:THR346 4.5 26.0 1.0
CG B:PRO199 4.7 26.0 1.0
SG B:CYS350 4.7 22.9 1.0
SG B:CYS393 4.8 23.3 1.0
C B:THR346 4.8 25.2 1.0
CG B:GLN349 4.8 36.0 1.0
CA B:GLN349 4.9 23.9 1.0
N B:CYS350 4.9 21.7 1.0
SG B:CYS353 4.9 21.9 1.0
CA B:GLY348 4.9 23.8 1.0
CG1 B:ILE181 5.0 21.2 1.0

Iron binding site 4 out of 12 in 6hl2

Go back to Iron Binding Sites List in 6hl2
Iron binding site 4 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form


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

b:25.7
occ:1.00
 FE2 B:SF4501 0.0 25.7 1.0
S4 B:SF4501 2.3 19.7 1.0
S3 B:SF4501 2.3 23.9 1.0
S1 B:SF4501 2.3 21.6 1.0
SG B:CYS353 2.4 21.9 1.0
FE4 B:SF4501 2.7 25.8 1.0
FE3 B:SF4501 2.7 25.3 1.0
FE1 B:SF4501 2.7 25.2 1.0
CB B:CYS353 3.1 19.2 1.0
OG1 B:THR346 3.7 26.0 1.0
S2 B:SF4501 3.9 22.4 1.0
N B:GLY396 4.2 21.5 1.0
CD2 B:LEU395 4.3 25.8 1.0
CA B:GLY396 4.5 21.3 1.0
CB B:THR346 4.5 21.9 1.0
CA B:CYS353 4.6 19.9 1.0
N B:CYS347 4.6 22.3 1.0
CB B:LEU395 4.6 19.7 1.0
SG B:CYS350 4.7 22.9 1.0
SG B:CYS393 4.7 23.3 1.0
CA B:THR346 4.8 21.6 1.0
CB B:CYS350 4.8 19.9 1.0
SG B:CYS347 4.9 23.4 1.0
N B:GLY348 5.0 24.1 1.0

Iron binding site 5 out of 12 in 6hl2

Go back to Iron Binding Sites List in 6hl2
Iron binding site 5 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form


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

b:25.3
occ:1.00
 FE3 B:SF4501 0.0 25.3 1.0
S1 B:SF4501 2.3 21.6 1.0
S2 B:SF4501 2.3 22.4 1.0
S4 B:SF4501 2.3 19.7 1.0
SG B:CYS393 2.3 23.3 1.0
FE4 B:SF4501 2.7 25.8 1.0
FE2 B:SF4501 2.7 25.7 1.0
FE1 B:SF4501 2.8 25.2 1.0
CB B:CYS393 3.3 20.9 1.0
N B:CYS393 3.8 23.3 1.0
S3 B:SF4501 3.9 23.9 1.0
CA B:CYS393 3.9 22.3 1.0
CG B:PRO199 4.3 26.0 1.0
C B:CYS393 4.3 27.8 1.0
O B:CYS393 4.3 27.3 1.0
CB B:LEU395 4.3 19.7 1.0
CD1 B:ILE181 4.4 21.8 1.0
N B:GLY396 4.5 21.5 1.0
SG B:CYS347 4.7 23.4 1.0
N B:LEU395 4.7 20.5 1.0
CB B:PRO199 4.7 22.3 1.0
C B:ILE392 4.8 29.0 1.0
SG B:CYS350 4.8 22.9 1.0
CD B:PRO199 4.9 22.6 1.0
SG B:CYS353 4.9 21.9 1.0
N B:ILE392 4.9 24.1 1.0
CA B:LEU395 5.0 20.2 1.0

Iron binding site 6 out of 12 in 6hl2

Go back to Iron Binding Sites List in 6hl2
Iron binding site 6 out of 12 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form


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

b:25.8
occ:1.00
 FE4 B:SF4501 0.0 25.8 1.0
SG B:CYS350 2.3 22.9 1.0
S2 B:SF4501 2.3 22.4 1.0
S1 B:SF4501 2.3 21.6 1.0
S3 B:SF4501 2.3 23.9 1.0
FE3 B:SF4501 2.7 25.3 1.0
FE2 B:SF4501 2.7 25.7 1.0
FE1 B:SF4501 2.7 25.2 1.0
CB B:CYS350 3.2 19.9 1.0
N B:CYS350 3.8 21.7 1.0
S4 B:SF4501 3.9 19.7 1.0
N B:ILE392 4.0 24.1 1.0
CA B:CYS350 4.2 20.3 1.0
CB B:ILE392 4.3 30.0 1.0
CB B:CYS353 4.4 19.2 1.0
CB B:GLN349 4.4 24.6 1.0
N B:CYS393 4.5 23.3 1.0
CA B:SER391 4.6 23.0 1.0
SG B:CYS347 4.6 23.4 1.0
SG B:CYS353 4.6 21.9 1.0
CA B:ILE392 4.7 25.6 1.0
C B:GLN349 4.7 26.6 1.0
N B:GLN349 4.8 24.0 1.0
C B:SER391 4.8 27.0 1.0
CB B:SER391 4.8 25.6 1.0
CG1 B:ILE392 4.9 32.0 1.0
SG B:CYS393 4.9 23.3 1.0
CA B:GLN349 4.9 23.9 1.0

Iron binding site 7 out of 12 in 6hl2

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:26.2
occ:1.00
 FE1 C:FES201 0.0 26.2 1.0
S1 C:FES201 2.2 21.1 1.0
S2 C:FES201 2.2 22.8 1.0
SG C:CYS86 2.3 23.5 1.0
SG C:CYS91 2.3 23.1 1.0
FE2 C:FES201 2.7 25.2 1.0
CB C:CYS86 3.3 20.5 1.0
CB C:CYS91 3.3 21.4 1.0
N C:CYS91 3.9 22.6 1.0
CA C:CYS91 4.2 22.4 1.0
N C:LEU128 4.3 21.7 1.0
CA C:CYS127 4.3 17.8 1.0
SG C:CYS127 4.5 21.1 1.0
CA C:CYS86 4.6 22.4 1.0
CB C:SER88 4.6 24.5 1.0
CB C:CYS127 4.7 17.9 1.0
CB C:VAL136 4.7 25.8 1.0
CG2 C:VAL136 4.8 25.2 1.0
SG C:CYS131 4.8 24.6 1.0
O C:SER88 4.8 26.6 1.0
C C:CYS127 4.8 22.9 1.0
N C:SER88 4.9 23.6 1.0
C C:CYS86 4.9 25.2 1.0
CA C:CYS131 4.9 21.1 1.0
C C:VAL90 5.0 25.6 1.0

Iron binding site 8 out of 12 in 6hl2

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:25.2
occ:1.00
 FE2 C:FES201 0.0 25.2 1.0
S2 C:FES201 2.2 22.8 1.0
S1 C:FES201 2.2 21.1 1.0
SG C:CYS131 2.4 24.6 1.0
SG C:CYS127 2.4 21.1 1.0
FE1 C:FES201 2.7 26.2 1.0
CB C:CYS131 3.4 21.4 1.0
CB C:CYS127 3.5 17.9 1.0
CA C:CYS131 3.8 21.1 1.0
CA C:CYS127 3.8 17.8 1.0
N C:CYS131 3.9 20.3 1.0
N C:LEU128 4.0 21.7 1.0
N C:GLY129 4.0 18.9 1.0
C C:CYS127 4.2 22.9 1.0
SG C:CYS86 4.3 23.5 1.0
N D:GLY99 4.3 20.9 1.0
N C:ALA130 4.4 21.2 1.0
CA C:GLY129 4.6 18.2 1.0
SG C:CYS91 4.6 23.1 1.0
C C:ALA130 4.8 23.4 1.0
CB C:VAL90 4.8 23.0 1.0
CG2 C:VAL90 4.8 22.5 1.0
C C:LEU128 4.9 22.4 1.0
CA D:GLY99 5.0 21.5 1.0
CA C:LEU128 5.0 21.2 1.0
C C:GLY129 5.0 24.5 1.0

Iron binding site 9 out of 12 in 6hl2

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


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

b:24.9
occ:1.00
 FE1 D:SF4501 0.0 24.9 1.0
S3 D:SF4501 2.3 22.9 1.0
SG D:CYS347 2.3 23.2 1.0
S4 D:SF4501 2.3 21.0 1.0
S2 D:SF4501 2.3 22.5 1.0
FE4 D:SF4501 2.7 25.8 1.0
FE2 D:SF4501 2.8 25.2 1.0
FE3 D:SF4501 2.8 23.2 1.0
CB D:CYS347 3.5 20.6 1.0
N D:CYS347 3.6 20.4 1.0
CA D:CYS347 3.9 20.9 1.0
S1 D:SF4501 3.9 22.3 1.0
N D:GLY348 4.0 23.8 1.0
N D:GLN349 4.1 22.4 1.0
C D:CYS347 4.2 25.9 1.0
CB D:GLN349 4.4 23.1 1.0
CD D:PRO199 4.4 22.3 1.0
OG1 D:THR346 4.5 22.3 1.0
NE2 D:GLN349 4.5 24.9 1.0
CG D:PRO199 4.7 26.4 1.0
SG D:CYS350 4.7 23.2 1.0
C D:THR346 4.8 23.7 1.0
SG D:CYS393 4.8 24.8 1.0
CG D:GLN349 4.8 35.3 1.0
CA D:GLN349 4.9 21.6 1.0
SG D:CYS353 4.9 23.0 1.0
N D:CYS350 4.9 20.5 1.0
CA D:GLY348 4.9 23.1 1.0
CG1 D:ILE181 5.0 20.1 1.0
CD1 D:ILE181 5.0 23.2 1.0

Iron binding site 10 out of 12 in 6hl2

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


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

b:25.2
occ:1.00
 FE2 D:SF4501 0.0 25.2 1.0
S3 D:SF4501 2.3 22.9 1.0
S4 D:SF4501 2.3 21.0 1.0
S1 D:SF4501 2.3 22.3 1.0
SG D:CYS353 2.3 23.0 1.0
FE4 D:SF4501 2.7 25.8 1.0
FE3 D:SF4501 2.7 23.2 1.0
FE1 D:SF4501 2.8 24.9 1.0
CB D:CYS353 3.1 20.2 1.0
OG1 D:THR346 3.6 22.3 1.0
S2 D:SF4501 3.9 22.5 1.0
N D:GLY396 4.2 22.1 1.0
CD2 D:LEU395 4.3 27.4 1.0
CA D:GLY396 4.5 22.4 1.0
CB D:THR346 4.5 23.0 1.0
CA D:CYS353 4.6 19.9 1.0
CB D:LEU395 4.6 21.3 1.0
N D:CYS347 4.6 20.4 1.0
SG D:CYS350 4.7 23.2 1.0
SG D:CYS393 4.7 24.8 1.0
CA D:THR346 4.8 21.5 1.0
CB D:CYS350 4.8 20.2 1.0
SG D:CYS347 4.9 23.2 1.0
CG D:LEU395 5.0 24.8 1.0
C D:LEU395 5.0 25.2 1.0
C D:CYS353 5.0 23.2 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 21:25:08 2024

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