Atomistry » Iron » PDB 6hbi-6hsm » 6hl3
Atomistry »
  Iron »
    PDB 6hbi-6hsm »
      6hl3 »

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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Go back to Iron Binding Sites List in 6hl3
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy