Iron in PDB 9fif: Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions

Protein crystallography data

The structure of Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions, PDB code: 9fif was solved by D.Wohlwend, T.Friedrich, S.Goeppert-Asadollahpour, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.04 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.399, 116.035, 189.72, 90, 90, 90
R / Rfree (%) 16.3 / 18.9

Other elements in 9fif:

The structure of Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions also contains other interesting chemical elements:

Sodium (Na) 7 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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions (pdb code 9fif). 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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions, PDB code: 9fif:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 9fif

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Iron binding site 1 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:20.9
occ:1.00
 FE1 A:FES201 0.0 20.9 1.0
S2 A:FES201 2.2 20.4 1.0
S1 A:FES201 2.2 20.3 1.0
SG A:CYS86 2.3 21.2 1.0
SG A:CYS91 2.3 21.6 1.0
FE2 A:FES201 2.7 20.0 1.0
CB A:CYS86 3.3 20.7 1.0
CB A:CYS91 3.3 21.6 1.0
N A:CYS91 3.9 21.4 1.0
CA A:CYS91 4.2 21.7 1.0
CA A:CYS127 4.2 19.6 1.0
N A:LEU128 4.3 20.1 1.0
SG A:CYS127 4.5 19.9 1.0
CA A:CYS86 4.6 20.9 1.0
CB A:CYS127 4.7 20.6 1.0
CG2 A:VAL136 4.7 21.7 1.0
SG A:CYS131 4.8 20.6 1.0
CB A:SER88 4.8 21.0 1.0
CB A:VAL136 4.8 21.4 1.0
C A:CYS127 4.9 20.2 1.0
CA A:CYS131 4.9 20.8 1.0
O A:SER88 4.9 20.8 1.0
C A:VAL90 4.9 21.6 1.0
C A:CYS86 4.9 20.9 1.0
N A:SER88 5.0 20.1 1.0

Iron binding site 2 out of 12 in 9fif

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Iron binding site 2 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:20.0
occ:1.00
 FE2 A:FES201 0.0 20.0 1.0
S1 A:FES201 2.2 20.3 1.0
S2 A:FES201 2.2 20.4 1.0
SG A:CYS127 2.3 19.9 1.0
SG A:CYS131 2.3 20.6 1.0
FE1 A:FES201 2.7 20.9 1.0
CB A:CYS131 3.4 20.9 1.0
CB A:CYS127 3.4 20.6 1.0
CA A:CYS127 3.7 19.6 1.0
CA A:CYS131 3.8 20.8 1.0
N A:CYS131 4.0 20.2 1.0
N A:LEU128 4.0 20.1 1.0
N A:GLY129 4.1 20.6 1.0
N B:GLY99 4.2 19.1 1.0
C A:CYS127 4.3 20.2 1.0
SG A:CYS86 4.3 21.2 1.0
N A:ALA130 4.4 19.9 1.0
SG A:CYS91 4.6 21.6 1.0
CA A:GLY129 4.7 20.8 1.0
C A:ALA130 4.8 20.4 1.0
CB A:VAL90 4.8 20.7 1.0
CG2 A:VAL90 4.9 21.2 1.0
CA B:GLY99 4.9 20.6 1.0
C A:LEU128 5.0 20.2 1.0
CA B:PRO98 5.0 19.4 1.0

Iron binding site 3 out of 12 in 9fif

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Iron binding site 3 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.8
occ:1.00
 FE1 B:SF4501 0.0 20.8 1.0
SG B:CYS393 2.2 20.8 1.0
S4 B:SF4501 2.3 23.1 1.0
S3 B:SF4501 2.3 21.3 1.0
S2 B:SF4501 2.3 20.8 1.0
FE2 B:SF4501 2.7 22.4 1.0
FE3 B:SF4501 2.8 21.2 1.0
FE4 B:SF4501 2.8 20.7 1.0
CB B:CYS393 3.3 21.9 1.0
N B:CYS393 3.8 23.7 1.0
S1 B:SF4501 3.9 21.8 1.0
CA B:CYS393 3.9 23.6 1.0
CG B:PRO199 4.2 21.2 1.0
C B:CYS393 4.3 24.7 1.0
CB B:LEU395 4.3 22.5 1.0
O B:CYS393 4.3 24.6 1.0
CD1 B:ILE181 4.5 21.7 1.0
N B:GLY396 4.5 23.2 1.0
N B:LEU395 4.7 21.7 1.0
CB B:PRO199 4.7 22.1 1.0
SG B:CYS347 4.8 22.0 1.0
C B:ILE392 4.8 25.2 1.0
SG B:CYS350 4.8 22.9 1.0
CD B:PRO199 4.9 21.3 1.0
SG B:CYS353 4.9 20.4 1.0
CA B:LEU395 4.9 22.3 1.0
N B:ILE392 5.0 25.4 1.0
CG1 B:ILE392 5.0 30.2 1.0

Iron binding site 4 out of 12 in 9fif

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Iron binding site 4 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:22.4
occ:1.00
 FE2 B:SF4501 0.0 22.4 1.0
SG B:CYS350 2.3 22.9 1.0
S4 B:SF4501 2.3 23.1 1.0
S3 B:SF4501 2.3 21.3 1.0
S1 B:SF4501 2.3 21.8 1.0
FE3 B:SF4501 2.7 21.2 1.0
FE4 B:SF4501 2.7 20.7 1.0
FE1 B:SF4501 2.7 20.8 1.0
CB B:CYS350 3.3 21.9 1.0
N B:CYS350 3.8 21.0 1.0
S2 B:SF4501 3.9 20.8 1.0
N B:ILE392 4.1 25.4 1.0
CG1 B:ILE392 4.1 30.2 1.0
CA B:CYS350 4.2 22.1 1.0
CB B:GLN349 4.3 25.7 1.0
CB B:CYS353 4.4 21.6 1.0
SG B:CYS353 4.6 20.4 1.0
N B:CYS393 4.6 23.7 1.0
SG B:CYS347 4.7 22.0 1.0
CA B:SER391 4.7 24.5 1.0
C B:GLN349 4.7 23.3 1.0
N B:GLN349 4.8 23.5 1.0
SG B:CYS393 4.9 20.8 1.0
CA B:GLN349 4.9 24.1 1.0
CB B:SER391 4.9 26.2 1.0
C B:SER391 4.9 25.6 1.0
CD1 B:ILE392 4.9 31.0 1.0
CA B:ILE392 4.9 27.1 1.0

Iron binding site 5 out of 12 in 9fif

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Iron binding site 5 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:21.2
occ:1.00
 FE3 B:SF4501 0.0 21.2 1.0
S1 B:SF4501 2.3 21.8 1.0
SG B:CYS347 2.3 22.0 1.0
S2 B:SF4501 2.3 20.8 1.0
S4 B:SF4501 2.3 23.1 1.0
FE2 B:SF4501 2.7 22.4 1.0
FE1 B:SF4501 2.8 20.8 1.0
FE4 B:SF4501 2.8 20.7 1.0
CB B:CYS347 3.5 22.4 1.0
N B:CYS347 3.7 21.7 1.0
S3 B:SF4501 3.9 21.3 1.0
CA B:CYS347 3.9 22.4 1.0
N B:GLY348 4.0 23.5 1.0
N B:GLN349 4.1 23.5 1.0
C B:CYS347 4.2 23.5 1.0
CB B:GLN349 4.3 25.7 1.0
CD B:PRO199 4.3 21.3 1.0
OE1 B:GLN349 4.5 26.9 1.0
OG1 B:THR346 4.5 21.7 1.0
CG B:PRO199 4.6 21.2 1.0
SG B:CYS350 4.7 22.9 1.0
SG B:CYS393 4.7 20.8 1.0
CG B:GLN349 4.8 27.6 1.0
CA B:GLN349 4.8 24.1 1.0
C B:THR346 4.8 22.6 1.0
SG B:CYS353 4.8 20.4 1.0
N B:CYS350 4.9 21.0 1.0
CA B:GLY348 5.0 24.7 1.0

Iron binding site 6 out of 12 in 9fif

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Iron binding site 6 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:20.7
occ:1.00
 FE4 B:SF4501 0.0 20.7 1.0
S2 B:SF4501 2.3 20.8 1.0
S1 B:SF4501 2.3 21.8 1.0
SG B:CYS353 2.3 20.4 1.0
S3 B:SF4501 2.3 21.3 1.0
FE2 B:SF4501 2.7 22.4 1.0
FE1 B:SF4501 2.8 20.8 1.0
FE3 B:SF4501 2.8 21.2 1.0
CB B:CYS353 3.1 21.6 1.0
OG1 B:THR346 3.6 21.7 1.0
S4 B:SF4501 3.9 23.1 1.0
N B:GLY396 4.2 23.2 1.0
CD2 B:LEU395 4.3 23.4 1.0
CA B:GLY396 4.4 23.0 1.0
CB B:THR346 4.5 23.1 1.0
CA B:CYS353 4.6 21.6 1.0
CB B:LEU395 4.6 22.5 1.0
N B:CYS347 4.6 21.7 1.0
SG B:CYS350 4.7 22.9 1.0
CA B:THR346 4.7 23.3 1.0
SG B:CYS393 4.7 20.8 1.0
CB B:CYS350 4.9 21.9 1.0
SG B:CYS347 4.9 22.0 1.0
C B:CYS353 5.0 21.7 1.0
CG B:LEU395 5.0 22.2 1.0

Iron binding site 7 out of 12 in 9fif

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Iron binding site 7 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:19.9
occ:1.00
 FE1 C:FES201 0.0 19.9 1.0
S2 C:FES201 2.2 20.4 1.0
S1 C:FES201 2.2 20.1 1.0
SG C:CYS91 2.3 20.6 1.0
SG C:CYS86 2.3 20.7 1.0
FE2 C:FES201 2.7 19.8 1.0
CB C:CYS86 3.3 18.8 1.0
CB C:CYS91 3.3 20.1 1.0
N C:CYS91 3.8 19.2 1.0
CA C:CYS127 4.2 19.3 1.0
CA C:CYS91 4.2 20.0 1.0
N C:LEU128 4.4 19.7 1.0
SG C:CYS127 4.5 19.8 1.0
CB C:CYS127 4.6 19.5 1.0
CA C:CYS86 4.6 19.1 1.0
CB C:SER88 4.7 21.4 1.0
SG C:CYS131 4.7 20.6 1.0
CG2 C:VAL136 4.8 21.9 1.0
CB C:VAL136 4.8 21.4 1.0
C C:CYS127 4.9 19.7 1.0
O C:SER88 4.9 20.4 1.0
CA C:CYS131 4.9 20.2 1.0
C C:VAL90 4.9 19.9 1.0
N C:SER88 4.9 19.8 1.0
C C:CYS86 5.0 19.3 1.0
CB C:VAL90 5.0 19.6 1.0

Iron binding site 8 out of 12 in 9fif

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Iron binding site 8 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:19.8
occ:1.00
 FE2 C:FES201 0.0 19.8 1.0
S1 C:FES201 2.2 20.1 1.0
S2 C:FES201 2.2 20.4 1.0
SG C:CYS131 2.3 20.6 1.0
SG C:CYS127 2.3 19.8 1.0
FE1 C:FES201 2.7 19.9 1.0
CB C:CYS131 3.4 19.9 1.0
CB C:CYS127 3.4 19.5 1.0
CA C:CYS127 3.7 19.3 1.0
CA C:CYS131 3.8 20.2 1.0
N C:CYS131 4.0 20.3 1.0
N C:LEU128 4.1 19.7 1.0
N C:GLY129 4.1 19.6 1.0
N D:GLY99 4.2 18.8 1.0
C C:CYS127 4.3 19.7 1.0
SG C:CYS86 4.4 20.7 1.0
N C:ALA130 4.4 20.2 1.0
SG C:CYS91 4.6 20.6 1.0
CA C:GLY129 4.7 21.1 1.0
CB C:VAL90 4.8 19.6 1.0
C C:ALA130 4.8 20.2 1.0
CG2 C:VAL90 4.8 19.2 1.0
CA D:GLY99 4.9 19.2 1.0
CA D:PRO98 4.9 19.2 1.0
C C:LEU128 5.0 19.5 1.0

Iron binding site 9 out of 12 in 9fif

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Iron binding site 9 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:22.0
occ:1.00
 FE1 D:SF4501 0.0 22.0 1.0
SG D:CYS350 2.3 22.9 1.0
S4 D:SF4501 2.3 22.0 1.0
S3 D:SF4501 2.3 21.5 1.0
S2 D:SF4501 2.3 21.2 1.0
FE2 D:SF4501 2.7 20.7 1.0
FE4 D:SF4501 2.7 20.5 1.0
FE3 D:SF4501 2.8 20.7 1.0
CB D:CYS350 3.3 21.5 1.0
N D:CYS350 3.8 21.0 1.0
S1 D:SF4501 3.9 21.1 1.0
CG1 D:ILE392 4.0 29.7 1.0
N D:ILE392 4.0 25.4 1.0
CA D:CYS350 4.2 20.9 1.0
CB D:CYS353 4.4 21.0 1.0
CB D:GLN349 4.5 25.6 1.0
SG D:CYS353 4.6 20.9 1.0
SG D:CYS347 4.6 22.2 1.0
CA D:SER391 4.6 26.0 1.0
N D:CYS393 4.7 23.2 1.0
C D:GLN349 4.8 22.6 1.0
CD1 D:ILE392 4.8 30.5 1.0
N D:GLN349 4.8 22.7 1.0
CB D:SER391 4.8 25.3 1.0
C D:SER391 4.9 26.3 1.0
SG D:CYS393 4.9 21.1 1.0
CA D:ILE392 4.9 27.0 1.0
CA D:GLN349 5.0 23.7 1.0

Iron binding site 10 out of 12 in 9fif

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Iron binding site 10 out of 12 in the Crystal Structure of Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions


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 Nuoef Variant P228R(Nuof) From Aquifex Aeolicus Bound to Nadh Under Anoxic Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:20.7
occ:1.00
 FE2 D:SF4501 0.0 20.7 1.0
SG D:CYS347 2.2 22.2 1.0
S1 D:SF4501 2.3 21.1 1.0
S3 D:SF4501 2.3 21.5 1.0
S4 D:SF4501 2.3 22.0 1.0
FE1 D:SF4501 2.7 22.0 1.0
FE3 D:SF4501 2.7 20.7 1.0
FE4 D:SF4501 2.8 20.5 1.0
CB D:CYS347 3.5 22.6 1.0
N D:CYS347 3.7 22.4 1.0
S2 D:SF4501 3.9 21.2 1.0
CA D:CYS347 3.9 22.5 1.0
N D:GLY348 4.0 23.3 1.0
N D:GLN349 4.2 22.7 1.0
C D:CYS347 4.2 23.7 1.0
CD D:PRO199 4.4 20.8 1.0
OE1 D:GLN349 4.4 28.4 1.0
CB D:GLN349 4.4 25.6 1.0
OG1 D:THR346 4.5 21.7 1.0
CG D:PRO199 4.6 20.8 1.0
SG D:CYS350 4.7 22.9 1.0
SG D:CYS393 4.7 21.1 1.0
C D:THR346 4.8 22.5 1.0
CG D:GLN349 4.8 28.3 1.0
SG D:CYS353 4.8 20.9 1.0
CA D:GLN349 4.9 23.7 1.0
N D:CYS350 4.9 21.0 1.0
CG1 D:ILE181 5.0 19.7 1.0

Reference:

S.Goppert-Asadollahpour, D.Wohlwend, T.Friedrich. Structural Robustness of the Nadh Binding Site in Nadh:Ubiquinone Oxidoreductase (Complex I). Biochim Biophys Acta V.1865 49491 2024BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 38960077
DOI: 10.1016/J.BBABIO.2024.149491
Page generated: Sat Aug 10 20:39:17 2024

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