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Iron in PDB 6zkg: Complex I with Nadh, Closed

Enzymatic activity of Complex I with Nadh, Closed

All present enzymatic activity of Complex I with Nadh, Closed:
1.6.99.3; 7.1.1.2;

Other elements in 6zkg:

The structure of Complex I with Nadh, Closed also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Complex I with Nadh, Closed (pdb code 6zkg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Complex I with Nadh, Closed, PDB code: 6zkg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6zkg

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Iron binding site 1 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:36.3
occ:1.00
FE1 1:SF4501 0.0 36.3 1.0
S2 1:SF4501 2.3 35.8 1.0
S3 1:SF4501 2.3 46.3 1.0
S4 1:SF4501 2.3 75.8 1.0
SG 1:CYS365 2.3 17.1 1.0
FE2 1:SF4501 2.7 41.7 1.0
FE3 1:SF4501 2.7 25.8 1.0
FE4 1:SF4501 2.8 19.9 1.0
CB 1:CYS365 2.9 9.7 1.0
OG 1:SER358 3.1 23.3 1.0
S1 1:SF4501 4.2 67.8 1.0
CD2 1:LEU407 4.3 25.6 1.0
CA 1:CYS365 4.3 13.6 1.0
CB 1:SER358 4.4 27.7 1.0
N 1:CYS359 4.5 16.3 1.0
C 1:CYS365 4.8 11.5 1.0
N 1:GLY360 4.8 21.3 1.0
CA 1:SER358 4.8 27.3 1.0
N 1:ARG366 4.8 10.6 1.0
CB 1:LEU407 4.9 15.2 1.0
C 1:SER358 5.0 24.1 1.0
N 1:GLY408 5.0 29.2 1.0

Iron binding site 2 out of 28 in 6zkg

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Iron binding site 2 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:41.7
occ:1.00
FE2 1:SF4501 0.0 41.7 1.0
S3 1:SF4501 2.3 46.3 1.0
S1 1:SF4501 2.3 67.8 1.0
S4 1:SF4501 2.4 75.8 1.0
FE3 1:SF4501 2.5 25.8 1.0
FE4 1:SF4501 2.5 19.9 1.0
FE1 1:SF4501 2.7 36.3 1.0
SG 1:CYS362 3.1 20.6 1.0
N 1:CYS362 3.4 25.3 1.0
S2 1:SF4501 3.8 35.8 1.0
CB 1:CYS362 3.9 34.9 1.0
CB 1:GLN361 4.0 16.8 1.0
N 1:GLN361 4.1 19.1 1.0
CA 1:CYS362 4.1 28.2 1.0
O 1:CYS362 4.3 23.5 1.0
CB 1:CYS365 4.3 9.7 1.0
C 1:GLN361 4.4 27.0 1.0
CA 1:GLN361 4.4 28.8 1.0
CD1 1:ILE404 4.6 7.6 1.0
C 1:CYS362 4.6 51.4 1.0
SG 1:CYS365 4.7 17.1 1.0
CB 1:ILE404 4.7 20.4 1.0
SG 1:CYS359 4.8 31.8 1.0
CG1 1:ILE404 4.8 16.4 1.0
N 1:ILE404 4.9 19.1 1.0
OE1 1:GLN361 4.9 11.8 1.0
CG 1:GLN361 5.0 9.6 1.0

Iron binding site 3 out of 28 in 6zkg

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Iron binding site 3 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:25.8
occ:1.00
FE3 1:SF4501 0.0 25.8 1.0
S4 1:SF4501 2.3 75.8 1.0
S1 1:SF4501 2.3 67.8 1.0
S2 1:SF4501 2.4 35.8 1.0
FE4 1:SF4501 2.4 19.9 1.0
FE2 1:SF4501 2.5 41.7 1.0
FE1 1:SF4501 2.7 36.3 1.0
SG 1:CYS359 3.0 31.8 1.0
S3 1:SF4501 3.7 46.3 1.0
CD 1:PRO203 3.9 17.7 1.0
N 1:CYS359 4.0 16.3 1.0
CB 1:CYS359 4.0 20.0 1.0
CB 1:GLN361 4.2 16.8 1.0
CG 1:PRO203 4.3 18.9 1.0
N 1:GLN361 4.3 19.1 1.0
CA 1:CYS359 4.4 13.8 1.0
CG1 1:ILE185 4.4 18.3 1.0
N 1:GLY360 4.4 21.3 1.0
CD1 1:ILE185 4.5 23.4 1.0
OE1 1:GLN361 4.7 11.8 1.0
C 1:CYS359 4.7 18.9 1.0
SG 1:CYS405 4.7 19.4 1.0
OG 1:SER358 4.7 23.3 1.0
CA 1:GLN361 4.9 28.8 1.0
SG 1:CYS365 5.0 17.1 1.0

Iron binding site 4 out of 28 in 6zkg

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Iron binding site 4 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:19.9
occ:1.00
FE4 1:SF4501 0.0 19.9 1.0
S2 1:SF4501 2.3 35.8 1.0
S1 1:SF4501 2.3 67.8 1.0
S3 1:SF4501 2.4 46.3 1.0
FE3 1:SF4501 2.4 25.8 1.0
FE2 1:SF4501 2.5 41.7 1.0
FE1 1:SF4501 2.8 36.3 1.0
SG 1:CYS405 3.0 19.4 1.0
N 1:CYS405 3.8 28.6 1.0
S4 1:SF4501 3.8 75.8 1.0
CB 1:CYS405 4.0 41.2 1.0
CA 1:CYS405 4.3 34.2 1.0
CG 1:PRO203 4.5 18.9 1.0
O 1:CYS405 4.5 27.8 1.0
CB 1:ILE404 4.5 20.4 1.0
N 1:ILE404 4.6 19.1 1.0
C 1:CYS405 4.6 32.4 1.0
CD1 1:ILE185 4.8 23.4 1.0
CB 1:LEU407 4.8 15.2 1.0
C 1:ILE404 4.8 23.9 1.0
CD 1:PRO203 4.9 17.7 1.0
SG 1:CYS365 4.9 17.1 1.0
CA 1:ILE404 4.9 21.8 1.0
SG 1:CYS362 4.9 20.6 1.0
CB 1:CYS365 5.0 9.7 1.0
N 1:GLY408 5.0 29.2 1.0

Iron binding site 5 out of 28 in 6zkg

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Iron binding site 5 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:0.1
occ:1.00
FE1 2:FES300 0.0 0.1 1.0
S2 2:FES300 2.2 69.1 1.0
S1 2:FES300 2.2 71.4 1.0
SG 2:CYS103 2.3 65.0 1.0
SG 2:CYS108 2.3 73.8 1.0
FE2 2:FES300 3.0 50.8 1.0
CB 2:CYS103 3.5 37.9 1.0
CB 2:CYS108 3.5 71.4 1.0
OG1 2:THR105 3.6 53.1 1.0
CA 2:CYS144 4.2 37.4 1.0
N 2:LEU145 4.3 33.1 1.0
N 2:CYS108 4.3 41.0 1.0
CA 2:CYS108 4.5 52.2 1.0
O 2:CYS103 4.6 35.6 1.0
C 2:CYS103 4.6 35.8 1.0
CA 2:CYS103 4.7 35.7 1.0
SG 2:CYS144 4.7 56.7 1.0
CB 2:CYS144 4.7 49.0 1.0
SG 2:CYS148 4.8 73.3 1.0
C 2:CYS144 4.8 32.8 1.0
N 2:THR105 4.8 33.9 1.0
SD 2:MET153 4.8 61.1 1.0
CB 2:THR105 4.9 45.3 1.0
CG 2:MET153 5.0 43.0 1.0

Iron binding site 6 out of 28 in 6zkg

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Iron binding site 6 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:50.8
occ:1.00
FE2 2:FES300 0.0 50.8 1.0
S2 2:FES300 2.2 69.1 1.0
S1 2:FES300 2.2 71.4 1.0
SG 2:CYS148 2.3 73.3 1.0
SG 2:CYS144 2.3 56.7 1.0
FE1 2:FES300 3.0 0.1 1.0
CB 2:CYS144 3.4 49.0 1.0
N 2:GLY146 3.7 37.1 1.0
CA 2:CYS144 3.8 37.4 1.0
CB 2:CYS148 3.8 56.5 1.0
N 2:LEU145 4.0 33.1 1.0
C 2:CYS144 4.2 32.8 1.0
CA 2:CYS148 4.2 43.4 1.0
CA 2:GLY146 4.2 33.9 1.0
N 2:ALA147 4.2 32.2 1.0
N 2:CYS148 4.3 41.2 1.0
CA 1:PRO102 4.3 36.6 1.0
N 1:GLY103 4.3 40.6 1.0
OG1 2:THR105 4.4 53.1 1.0
C 2:GLY146 4.6 30.4 1.0
SG 2:CYS103 4.7 65.0 1.0
C 2:LEU145 4.8 37.7 1.0
CB 1:PRO102 4.8 33.6 1.0
C 2:ALA147 4.8 40.7 1.0
C 1:PRO102 4.9 41.3 1.0
SG 2:CYS108 4.9 73.8 1.0
CG 2:PRO107 5.0 44.2 1.0
CA 2:LEU145 5.0 33.4 1.0
O 1:GLU101 5.0 43.3 1.0

Iron binding site 7 out of 28 in 6zkg

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Iron binding site 7 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:63.3
occ:1.00
FE1 3:SF4801 0.0 63.3 1.0
S3 3:SF4801 2.3 73.2 1.0
S2 3:SF4801 2.3 63.3 1.0
S4 3:SF4801 2.3 63.3 1.0
SG 3:CYS114 2.3 29.6 1.0
FE4 3:SF4801 2.7 63.3 1.0
FE3 3:SF4801 2.7 63.3 1.0
FE2 3:SF4801 2.7 63.3 1.0
CB 3:CYS114 3.4 16.5 1.0
S1 3:SF4801 3.9 67.8 1.0
CG 3:GLN117 4.0 28.8 1.0
NE2 3:HIS101 4.3 34.5 1.0
NE2 3:GLN117 4.3 26.4 1.0
CB 3:LEU116 4.4 12.8 1.0
CD 3:GLN117 4.5 22.4 1.0
N 3:GLY206 4.6 32.3 1.0
N 3:GLN117 4.6 43.9 1.0
CA 3:VAL205 4.7 7.2 1.0
CD2 3:LEU116 4.7 11.0 1.0
SG 3:CYS108 4.7 55.7 1.0
CA 3:CYS114 4.8 16.1 1.0
SG 3:CYS105 4.8 50.5 1.0
CB 3:GLN110 4.8 6.2 1.0
CG 3:LEU116 4.9 6.5 1.0
CB 3:GLN117 5.0 25.4 1.0
CB 3:VAL205 5.0 13.0 1.0
CG 3:GLN110 5.0 13.5 1.0

Iron binding site 8 out of 28 in 6zkg

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Iron binding site 8 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:63.3
occ:1.00
FE2 3:SF4801 0.0 63.3 1.0
S4 3:SF4801 2.3 63.3 1.0
S3 3:SF4801 2.3 73.2 1.0
S1 3:SF4801 2.3 67.8 1.0
SG 3:CYS105 2.3 50.5 1.0
FE3 3:SF4801 2.7 63.3 1.0
FE4 3:SF4801 2.7 63.3 1.0
FE1 3:SF4801 2.7 63.3 1.0
NE2 3:GLN117 3.3 26.4 1.0
CB 3:CYS105 3.4 32.8 1.0
CA 3:CYS105 3.5 32.8 1.0
N 3:CYS105 3.8 52.6 1.0
S2 3:SF4801 3.9 63.3 1.0
CG 3:GLN117 4.0 28.8 1.0
CE 4:MET342 4.1 42.8 1.0
CD 3:GLN117 4.1 22.4 1.0
NE2 3:HIS101 4.4 34.5 1.0
C 3:ASP104 4.7 24.9 1.0
CD2 3:HIS101 4.8 28.9 1.0
SG 3:CYS108 4.8 55.7 1.0
CB 3:CYS108 4.8 14.2 1.0
SG 3:CYS114 4.9 29.6 1.0
C 3:CYS105 4.9 12.7 1.0
CG1 4:ILE346 4.9 10.9 1.0

Iron binding site 9 out of 28 in 6zkg

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Iron binding site 9 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:63.3
occ:1.00
FE3 3:SF4801 0.0 63.3 1.0
NE2 3:HIS101 2.0 34.5 1.0
S2 3:SF4801 2.3 63.3 1.0
S1 3:SF4801 2.3 67.8 1.0
S4 3:SF4801 2.3 63.3 1.0
FE2 3:SF4801 2.7 63.3 1.0
FE1 3:SF4801 2.7 63.3 1.0
FE4 3:SF4801 2.7 63.3 1.0
CD2 3:HIS101 2.9 28.9 1.0
CE1 3:HIS101 3.0 47.2 1.0
S3 3:SF4801 3.9 73.2 1.0
ND1 3:HIS101 4.1 24.6 1.0
CG 3:HIS101 4.1 40.2 1.0
CD2 3:LEU116 4.3 11.0 1.0
CE 4:MET342 4.4 42.8 1.0
O 3:PRO102 4.5 22.7 1.0
SG 3:CYS105 4.7 50.5 1.0
CG 3:ARG152 4.8 31.1 1.0
SG 3:CYS114 4.8 29.6 1.0
CB 3:ARG152 4.8 21.4 1.0
SG 3:CYS108 4.9 55.7 1.0
CD 3:ARG152 4.9 49.3 1.0

Iron binding site 10 out of 28 in 6zkg

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Iron binding site 10 out of 28 in the Complex I with Nadh, Closed


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Complex I with Nadh, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:63.3
occ:1.00
FE4 3:SF4801 0.0 63.3 1.0
S2 3:SF4801 2.3 63.3 1.0
S3 3:SF4801 2.3 73.2 1.0
S1 3:SF4801 2.3 67.8 1.0
SG 3:CYS108 2.3 55.7 1.0
FE1 3:SF4801 2.7 63.3 1.0
FE2 3:SF4801 2.7 63.3 1.0
FE3 3:SF4801 2.7 63.3 1.0
CB 3:CYS108 3.1 14.2 1.0
S4 3:SF4801 3.9 63.3 1.0
N 3:GLY206 4.3 32.3 1.0
CD 3:ARG152 4.4 49.3 1.0
CB 3:GLN110 4.4 6.2 1.0
CA 3:GLY206 4.5 15.8 1.0
CA 3:CYS105 4.5 32.8 1.0
CA 3:CYS108 4.6 9.8 1.0
NE2 3:HIS101 4.6 34.5 1.0
N 3:CYS105 4.6 52.6 1.0
SG 3:CYS114 4.7 29.6 1.0
SG 3:CYS105 4.8 50.5 1.0
NH1 3:ARG152 4.8 25.5 1.0
N 3:GLY111 4.9 11.4 1.0
C 3:ASP104 4.9 24.9 1.0
NE 3:ARG152 4.9 39.0 1.0
NE2 3:GLN117 5.0 26.4 1.0

Reference:

D.Kampjut, L.A.Sazanov. The Coupling Mechanism of Mammalian Respiratory Complex I. Science V. 370 2020.
ISSN: ESSN 1095-9203
PubMed: 32972993
DOI: 10.1126/SCIENCE.ABC4209
Page generated: Wed Aug 6 17:50:32 2025

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