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Iron in PDB 6hlm: Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+

Enzymatic activity of Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+

All present enzymatic activity of Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+:
1.6.5.11;

Protein crystallography data

The structure of Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+, PDB code: 6hlm 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) 51.49 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.690, 63.293, 124.192, 90.00, 107.18, 90.00
R / Rfree (%) 17.6 / 19.7

Other elements in 6hlm:

The structure of Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ (pdb code 6hlm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+, PDB code: 6hlm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6hlm

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Iron binding site 1 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:22.6
occ:1.00
 FE1 A:FES200 0.0 22.6 1.0
S1 A:FES200 2.2 21.6 1.0
S2 A:FES200 2.2 22.2 1.0
SG A:CYS91 2.3 22.6 1.0
SG A:CYS86 2.3 22.7 1.0
FE2 A:FES200 2.7 22.4 1.0
CB A:CYS86 3.3 20.1 1.0
CB A:CYS91 3.3 21.3 1.0
N A:CYS91 3.8 22.9 1.0
CA A:CYS91 4.2 22.2 1.0
CA A:CYS127 4.3 18.9 1.0
N A:LEU128 4.4 18.7 1.0
SG A:CYS127 4.5 20.0 1.0
CA A:CYS86 4.7 21.4 1.0
CB A:CYS127 4.7 17.8 1.0
CB A:SER88 4.7 23.6 1.0
CB A:VAL136 4.7 24.1 1.0
CG2 A:VAL136 4.8 23.6 1.0
SG A:CYS131 4.8 21.1 1.0
O A:SER88 4.9 24.3 1.0
N A:SER88 4.9 22.5 1.0
C A:VAL90 4.9 24.8 1.0
C A:CYS127 4.9 21.1 1.0
C A:CYS86 5.0 24.7 1.0

Iron binding site 2 out of 12 in 6hlm

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Iron binding site 2 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:22.4
occ:1.00
 FE2 A:FES200 0.0 22.4 1.0
S2 A:FES200 2.2 22.2 1.0
S1 A:FES200 2.2 21.6 1.0
SG A:CYS127 2.3 20.0 1.0
SG A:CYS131 2.4 21.1 1.0
FE1 A:FES200 2.7 22.6 1.0
CB A:CYS127 3.4 17.8 1.0
CB A:CYS131 3.5 19.0 1.0
N A:ASP129 3.8 18.2 1.0
CA A:CYS127 3.8 18.9 1.0
CA A:CYS131 3.9 19.8 1.0
N A:CYS131 4.0 20.1 1.0
N A:LEU128 4.1 18.7 1.0
CA A:ASP129 4.2 17.4 1.0
C A:CYS127 4.3 21.1 1.0
SG A:CYS86 4.3 22.7 1.0
N B:GLY99 4.4 17.9 1.0
N A:ALA130 4.5 21.0 1.0
SG A:CYS91 4.6 22.6 1.0
CB A:VAL90 4.7 22.4 1.0
CG2 A:VAL90 4.7 21.5 1.0
C A:LEU128 4.8 20.2 1.0
C A:ASP129 4.9 22.9 1.0
OD1 A:ASP129 4.9 22.4 1.0
C A:ALA130 4.9 22.0 1.0
CA B:PRO98 5.0 18.6 1.0

Iron binding site 3 out of 12 in 6hlm

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Iron binding site 3 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:25.9
occ:1.00
 FE1 B:SF4501 0.0 25.9 1.0
S3 B:SF4501 2.3 27.9 1.0
SG B:CYS347 2.3 26.6 1.0
S4 B:SF4501 2.3 25.7 1.0
S2 B:SF4501 2.3 25.0 1.0
FE4 B:SF4501 2.7 27.1 1.0
FE3 B:SF4501 2.7 26.5 1.0
FE2 B:SF4501 2.7 27.6 1.0
CB B:CYS347 3.4 23.4 1.0
N B:CYS347 3.6 24.2 1.0
CA B:CYS347 3.9 24.3 1.0
S1 B:SF4501 3.9 26.3 1.0
N B:GLY348 4.0 27.2 1.0
N B:GLN349 4.2 27.6 1.0
C B:CYS347 4.2 29.9 1.0
CD B:PRO199 4.3 23.5 1.0
CB B:GLN349 4.4 28.7 1.0
NE2 B:GLN349 4.5 27.0 1.0
CG B:PRO199 4.6 27.3 1.0
OG1 B:THR346 4.6 25.1 1.0
SG B:CYS350 4.7 28.0 1.0
C B:THR346 4.7 26.9 1.0
SG B:CYS393 4.8 26.6 1.0
CG B:GLN349 4.8 38.1 1.0
N B:CYS350 4.8 25.1 1.0
SG B:CYS353 4.8 25.7 1.0
CA B:GLN349 4.9 27.8 1.0
CG1 B:ILE181 4.9 21.6 1.0
CD1 B:ILE181 4.9 23.9 1.0
CA B:GLY348 5.0 26.4 1.0

Iron binding site 4 out of 12 in 6hlm

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Iron binding site 4 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:27.6
occ:1.00
 FE2 B:SF4501 0.0 27.6 1.0
S4 B:SF4501 2.3 25.7 1.0
S3 B:SF4501 2.3 27.9 1.0
S1 B:SF4501 2.3 26.3 1.0
SG B:CYS353 2.3 25.7 1.0
FE4 B:SF4501 2.7 27.1 1.0
FE3 B:SF4501 2.7 26.5 1.0
FE1 B:SF4501 2.7 25.9 1.0
CB B:CYS353 3.1 23.4 1.0
OG1 B:THR346 3.7 25.1 1.0
S2 B:SF4501 3.9 25.0 1.0
N B:GLY396 4.1 24.7 1.0
CD2 B:LEU395 4.3 25.9 1.0
CA B:GLY396 4.4 24.7 1.0
N B:CYS347 4.5 24.2 1.0
CA B:CYS353 4.6 23.8 1.0
CB B:LEU395 4.6 24.8 1.0
CB B:THR346 4.6 26.8 1.0
SG B:CYS350 4.7 28.0 1.0
CA B:THR346 4.7 23.8 1.0
SG B:CYS393 4.8 26.6 1.0
CB B:CYS350 4.8 24.5 1.0
SG B:CYS347 4.9 26.6 1.0
C B:LEU395 5.0 26.8 1.0

Iron binding site 5 out of 12 in 6hlm

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Iron binding site 5 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:26.5
occ:1.00
 FE3 B:SF4501 0.0 26.5 1.0
S1 B:SF4501 2.3 26.3 1.0
S2 B:SF4501 2.3 25.0 1.0
S4 B:SF4501 2.3 25.7 1.0
SG B:CYS393 2.3 26.6 1.0
FE2 B:SF4501 2.7 27.6 1.0
FE1 B:SF4501 2.7 25.9 1.0
FE4 B:SF4501 2.7 27.1 1.0
CB B:CYS393 3.3 24.7 1.0
N B:CYS393 3.9 27.3 1.0
S3 B:SF4501 3.9 27.9 1.0
CA B:CYS393 4.0 26.2 1.0
CG B:PRO199 4.2 27.3 1.0
C B:CYS393 4.3 30.1 1.0
O B:CYS393 4.3 28.9 1.0
CB B:LEU395 4.3 24.8 1.0
CD1 B:ILE181 4.3 23.9 1.0
N B:GLY396 4.5 24.7 1.0
N B:LEU395 4.7 26.5 1.0
SG B:CYS347 4.7 26.6 1.0
CB B:PRO199 4.7 23.8 1.0
CD B:PRO199 4.8 23.5 1.0
SG B:CYS350 4.9 28.0 1.0
C B:ILE392 4.9 33.9 1.0
SG B:CYS353 4.9 25.7 1.0
CA B:LEU395 4.9 25.3 1.0
N B:ILE392 5.0 28.8 1.0

Iron binding site 6 out of 12 in 6hlm

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Iron binding site 6 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:27.1
occ:1.00
 FE4 B:SF4501 0.0 27.1 1.0
S2 B:SF4501 2.3 25.0 1.0
SG B:CYS350 2.3 28.0 1.0
S1 B:SF4501 2.3 26.3 1.0
S3 B:SF4501 2.3 27.9 1.0
FE1 B:SF4501 2.7 25.9 1.0
FE2 B:SF4501 2.7 27.6 1.0
FE3 B:SF4501 2.7 26.5 1.0
CB B:CYS350 3.2 24.5 1.0
N B:CYS350 3.8 25.1 1.0
S4 B:SF4501 3.9 25.7 1.0
N B:ILE392 4.1 28.8 1.0
CA B:CYS350 4.1 24.9 1.0
CG1 B:ILE392 4.1 34.9 1.0
CB B:CYS353 4.4 23.4 1.0
CB B:GLN349 4.4 28.7 1.0
SG B:CYS347 4.6 26.6 1.0
CA B:SER391 4.6 28.4 1.0
N B:CYS393 4.6 27.3 1.0
SG B:CYS353 4.6 25.7 1.0
C B:GLN349 4.8 30.3 1.0
N B:GLN349 4.9 27.6 1.0
CB B:SER391 4.9 32.4 1.0
C B:SER391 4.9 32.2 1.0
SG B:CYS393 4.9 26.6 1.0
CA B:ILE392 4.9 30.1 1.0
CA B:GLN349 5.0 27.8 1.0
NE2 B:GLN349 5.0 27.0 1.0

Iron binding site 7 out of 12 in 6hlm

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Iron binding site 7 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:28.5
occ:1.00
 FE1 C:FES200 0.0 28.5 1.0
S1 C:FES200 2.2 27.5 1.0
S2 C:FES200 2.2 27.1 1.0
SG C:CYS91 2.3 27.9 1.0
SG C:CYS86 2.3 27.9 1.0
FE2 C:FES200 2.7 26.6 1.0
CB C:CYS86 3.3 25.5 1.0
CB C:CYS91 3.3 26.5 1.0
N C:CYS91 3.8 27.3 1.0
CA C:CYS91 4.2 27.7 1.0
CA C:CYS127 4.3 23.9 1.0
N C:LEU128 4.4 24.1 1.0
SG C:CYS127 4.5 25.1 1.0
CA C:CYS86 4.7 26.7 1.0
CB C:CYS127 4.7 22.6 1.0
CB C:SER88 4.7 31.0 1.0
CG2 C:VAL136 4.8 30.8 1.0
CB C:VAL136 4.8 30.9 1.0
SG C:CYS131 4.8 25.9 1.0
N C:SER88 4.9 27.9 1.0
O C:SER88 4.9 31.0 1.0
C C:CYS127 4.9 26.9 1.0
C C:VAL90 4.9 30.4 1.0
C C:CYS86 5.0 31.2 1.0

Iron binding site 8 out of 12 in 6hlm

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Iron binding site 8 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:26.6
occ:1.00
 FE2 C:FES200 0.0 26.6 1.0
S1 C:FES200 2.2 27.5 1.0
S2 C:FES200 2.2 27.1 1.0
SG C:CYS131 2.3 25.9 1.0
SG C:CYS127 2.3 25.1 1.0
FE1 C:FES200 2.7 28.5 1.0
CB C:CYS131 3.4 23.2 1.0
CB C:CYS127 3.5 22.6 1.0
N C:ASP129 3.8 23.2 1.0
CA C:CYS131 3.8 24.1 1.0
CA C:CYS127 3.9 23.9 1.0
N C:CYS131 4.0 25.4 1.0
N C:LEU128 4.1 24.1 1.0
CA C:ASP129 4.2 22.9 1.0
C C:CYS127 4.3 26.9 1.0
SG C:CYS86 4.4 27.9 1.0
N D:GLY99 4.4 23.6 1.0
N C:ALA130 4.5 24.3 1.0
SG C:CYS91 4.6 27.9 1.0
CB C:VAL90 4.6 27.1 1.0
CG2 C:VAL90 4.7 26.0 1.0
C C:LEU128 4.9 27.1 1.0
C C:ASP129 4.9 27.3 1.0
OD1 C:ASP129 4.9 27.5 1.0
C C:ALA130 4.9 28.3 1.0
CA D:PRO98 5.0 24.2 1.0

Iron binding site 9 out of 12 in 6hlm

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Iron binding site 9 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:26.6
occ:1.00
 FE1 D:SF4501 0.0 26.6 1.0
S4 D:SF4501 2.3 25.5 1.0
SG D:CYS347 2.3 27.6 1.0
S3 D:SF4501 2.3 27.0 1.0
S2 D:SF4501 2.3 26.0 1.0
FE3 D:SF4501 2.7 26.8 1.0
FE4 D:SF4501 2.7 28.1 1.0
FE2 D:SF4501 2.8 27.1 1.0
CB D:CYS347 3.4 24.7 1.0
N D:CYS347 3.6 23.9 1.0
CA D:CYS347 3.9 25.6 1.0
S1 D:SF4501 3.9 26.2 1.0
N D:GLY348 4.0 29.1 1.0
N D:GLN349 4.2 26.9 1.0
C D:CYS347 4.2 31.8 1.0
CD D:PRO199 4.3 24.0 1.0
CB D:GLN349 4.4 28.7 1.0
NE2 D:GLN349 4.5 28.2 1.0
CG D:PRO199 4.6 28.1 1.0
OG1 D:THR346 4.6 27.7 1.0
SG D:CYS350 4.7 28.9 1.0
SG D:CYS393 4.7 26.4 1.0
C D:THR346 4.8 27.6 1.0
CG D:GLN349 4.8 37.8 1.0
N D:CYS350 4.9 25.5 1.0
CA D:GLN349 4.9 27.3 1.0
SG D:CYS353 4.9 25.5 1.0
CD1 D:ILE181 4.9 23.4 1.0
CG1 D:ILE181 4.9 23.6 1.0
CA D:GLY348 5.0 28.7 1.0

Iron binding site 10 out of 12 in 6hlm

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Iron binding site 10 out of 12 in the Variant G129D of Nuoef From Aquifex Aeolicus 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 Variant G129D of Nuoef From Aquifex Aeolicus Bound to Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:27.1
occ:1.00
 FE2 D:SF4501 0.0 27.1 1.0
S3 D:SF4501 2.3 27.0 1.0
S4 D:SF4501 2.3 25.5 1.0
S1 D:SF4501 2.3 26.2 1.0
SG D:CYS353 2.3 25.5 1.0
FE4 D:SF4501 2.7 28.1 1.0
FE3 D:SF4501 2.7 26.8 1.0
FE1 D:SF4501 2.8 26.6 1.0
CB D:CYS353 3.1 22.7 1.0
OG1 D:THR346 3.7 27.7 1.0
S2 D:SF4501 3.9 26.0 1.0
N D:GLY396 4.1 27.2 1.0
CD2 D:LEU395 4.3 27.2 1.0
CA D:GLY396 4.4 27.7 1.0
N D:CYS347 4.5 23.9 1.0
CA D:CYS353 4.5 23.3 1.0
CB D:THR346 4.6 27.4 1.0
CB D:LEU395 4.6 24.6 1.0
SG D:CYS350 4.7 28.9 1.0
CA D:THR346 4.8 25.2 1.0
SG D:CYS393 4.8 26.4 1.0
CB D:CYS350 4.8 25.1 1.0
SG D:CYS347 4.9 27.6 1.0
C D:LEU395 5.0 29.2 1.0
C D:CYS353 5.0 27.2 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 21:29:52 2024

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