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Iron in PDB 6zkj: Complex I with Nadh, OPEN3

Enzymatic activity of Complex I with Nadh, OPEN3

All present enzymatic activity of Complex I with Nadh, OPEN3:
1.6.99.3; 7.1.1.2;

Other elements in 6zkj:

The structure of Complex I with Nadh, OPEN3 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, OPEN3 (pdb code 6zkj). 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, OPEN3, PDB code: 6zkj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6zkj

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Iron binding site 1 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:21.4
occ:1.00
FE1 1:SF4501 0.0 21.4 1.0
S2 1:SF4501 2.3 19.3 1.0
S3 1:SF4501 2.3 31.8 1.0
S4 1:SF4501 2.3 62.6 1.0
SG 1:CYS365 2.3 19.0 1.0
FE2 1:SF4501 2.7 37.0 1.0
FE3 1:SF4501 2.7 26.8 1.0
FE4 1:SF4501 2.8 31.5 1.0
CB 1:CYS365 2.9 18.9 1.0
OG 1:SER358 3.3 17.9 1.0
S1 1:SF4501 4.2 57.3 1.0
CA 1:CYS365 4.3 20.5 1.0
CD2 1:LEU407 4.4 33.2 1.0
N 1:CYS359 4.4 22.4 1.0
CB 1:SER358 4.5 24.2 1.0
CB 1:LEU407 4.7 20.1 1.0
C 1:CYS365 4.7 23.1 1.0
N 1:ARG366 4.8 21.9 1.0
N 1:GLY360 4.8 20.3 1.0
CA 1:SER358 4.8 27.5 1.0
CG 1:LEU407 5.0 30.2 1.0
C 1:SER358 5.0 32.5 1.0

Iron binding site 2 out of 28 in 6zkj

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Iron binding site 2 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:37.0
occ:1.00
FE2 1:SF4501 0.0 37.0 1.0
S3 1:SF4501 2.3 31.8 1.0
S1 1:SF4501 2.3 57.3 1.0
S4 1:SF4501 2.4 62.6 1.0
FE3 1:SF4501 2.5 26.8 1.0
FE4 1:SF4501 2.5 31.5 1.0
FE1 1:SF4501 2.7 21.4 1.0
SG 1:CYS362 3.1 32.3 1.0
N 1:CYS362 3.4 24.3 1.0
S2 1:SF4501 3.8 19.3 1.0
CB 1:CYS362 3.9 18.4 1.0
CB 1:GLN361 4.0 19.0 1.0
CA 1:CYS362 4.1 19.8 1.0
N 1:GLN361 4.1 20.0 1.0
CB 1:CYS365 4.2 18.9 1.0
O 1:CYS362 4.3 20.2 1.0
C 1:GLN361 4.3 20.6 1.0
CA 1:GLN361 4.4 40.4 1.0
CB 1:ILE404 4.6 26.5 1.0
C 1:CYS362 4.6 15.0 1.0
CD1 1:ILE404 4.7 17.8 1.0
SG 1:CYS365 4.7 19.0 1.0
N 1:ILE404 4.7 26.2 1.0
CG1 1:ILE404 4.8 16.7 1.0
SG 1:CYS359 4.8 35.1 1.0
OE1 1:GLN361 4.9 19.1 1.0
CG 1:GLN361 4.9 21.2 1.0

Iron binding site 3 out of 28 in 6zkj

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Iron binding site 3 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:26.8
occ:1.00
FE3 1:SF4501 0.0 26.8 1.0
S4 1:SF4501 2.3 62.6 1.0
S1 1:SF4501 2.3 57.3 1.0
S2 1:SF4501 2.4 19.3 1.0
FE4 1:SF4501 2.4 31.5 1.0
FE2 1:SF4501 2.5 37.0 1.0
FE1 1:SF4501 2.7 21.4 1.0
SG 1:CYS359 3.0 35.1 1.0
S3 1:SF4501 3.7 31.8 1.0
CD 1:PRO203 3.8 19.3 1.0
CB 1:CYS359 3.9 20.5 1.0
N 1:CYS359 4.0 22.4 1.0
CB 1:GLN361 4.1 19.0 1.0
CG 1:PRO203 4.1 24.1 1.0
N 1:GLN361 4.2 20.0 1.0
CA 1:CYS359 4.4 25.4 1.0
N 1:GLY360 4.4 20.3 1.0
OE1 1:GLN361 4.5 19.1 1.0
CG1 1:ILE185 4.6 22.8 1.0
C 1:CYS359 4.7 19.5 1.0
SG 1:CYS405 4.7 29.5 1.0
CA 1:GLN361 4.8 40.4 1.0
CD1 1:ILE185 4.8 36.1 1.0
OG 1:SER358 5.0 17.9 1.0
SG 1:CYS365 5.0 19.0 1.0

Iron binding site 4 out of 28 in 6zkj

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Iron binding site 4 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:31.5
occ:1.00
FE4 1:SF4501 0.0 31.5 1.0
S2 1:SF4501 2.3 19.3 1.0
S1 1:SF4501 2.3 57.3 1.0
S3 1:SF4501 2.3 31.8 1.0
FE3 1:SF4501 2.4 26.8 1.0
FE2 1:SF4501 2.5 37.0 1.0
FE1 1:SF4501 2.8 21.4 1.0
SG 1:CYS405 3.0 29.5 1.0
N 1:CYS405 3.7 18.8 1.0
S4 1:SF4501 3.8 62.6 1.0
CB 1:CYS405 3.9 20.5 1.0
CG 1:PRO203 4.2 24.1 1.0
CA 1:CYS405 4.2 22.5 1.0
O 1:CYS405 4.4 25.9 1.0
C 1:CYS405 4.5 20.6 1.0
CB 1:ILE404 4.5 26.5 1.0
N 1:ILE404 4.6 26.2 1.0
CD 1:PRO203 4.6 19.3 1.0
C 1:ILE404 4.7 24.4 1.0
CB 1:LEU407 4.7 20.1 1.0
CB 1:PRO203 4.8 22.6 1.0
CD1 1:ILE185 4.8 36.1 1.0
CA 1:ILE404 4.8 24.5 1.0
SG 1:CYS365 4.9 19.0 1.0
SG 1:CYS362 4.9 32.3 1.0
CB 1:CYS365 4.9 18.9 1.0

Iron binding site 5 out of 28 in 6zkj

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Iron binding site 5 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:0.7
occ:1.00
FE1 2:FES300 0.0 0.7 1.0
S2 2:FES300 2.2 47.5 1.0
S1 2:FES300 2.2 50.7 1.0
SG 2:CYS108 2.3 51.1 1.0
SG 2:CYS103 2.3 43.9 1.0
FE2 2:FES300 3.0 45.6 1.0
CB 2:CYS103 3.3 33.9 1.0
CB 2:CYS108 3.3 42.8 1.0
OG1 2:THR105 3.5 53.4 1.0
N 2:CYS108 4.2 37.5 1.0
CA 2:CYS144 4.3 30.2 1.0
CA 2:CYS108 4.3 39.0 1.0
N 2:LEU145 4.4 28.7 1.0
SD 2:MET153 4.5 59.0 1.0
CA 2:CYS103 4.6 35.2 1.0
C 2:CYS103 4.6 29.0 1.0
O 2:CYS103 4.6 37.6 1.0
SG 2:CYS144 4.7 58.3 1.0
N 2:THR105 4.8 33.6 1.0
CB 2:CYS144 4.8 37.9 1.0
CB 2:THR105 4.8 34.1 1.0
CG 2:MET153 4.9 54.7 1.0
C 2:CYS144 4.9 30.9 1.0
SG 2:CYS148 4.9 40.6 1.0

Iron binding site 6 out of 28 in 6zkj

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Iron binding site 6 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:45.6
occ:1.00
FE2 2:FES300 0.0 45.6 1.0
S2 2:FES300 2.2 47.5 1.0
S1 2:FES300 2.2 50.7 1.0
SG 2:CYS148 2.3 40.6 1.0
SG 2:CYS144 2.3 58.3 1.0
FE1 2:FES300 3.0 0.7 1.0
CB 2:CYS144 3.4 37.9 1.0
N 2:GLY146 3.7 32.1 1.0
CB 2:CYS148 3.7 42.9 1.0
CA 2:CYS144 3.8 30.2 1.0
CA 2:CYS148 4.1 41.9 1.0
N 2:ALA147 4.1 40.0 1.0
N 2:LEU145 4.1 28.7 1.0
CA 2:GLY146 4.2 31.2 1.0
C 2:CYS144 4.2 30.9 1.0
N 2:CYS148 4.2 44.4 1.0
OG1 2:THR105 4.2 53.4 1.0
N 1:GLY103 4.3 31.2 1.0
CA 1:PRO102 4.4 35.1 1.0
SG 2:CYS103 4.6 43.9 1.0
C 2:GLY146 4.6 37.8 1.0
C 2:ALA147 4.7 45.3 1.0
C 2:LEU145 4.8 34.6 1.0
SG 2:CYS108 4.9 51.1 1.0
O 1:GLU101 4.9 52.6 1.0
CB 2:PRO107 4.9 31.8 1.0
C 1:PRO102 4.9 33.9 1.0
CG 2:PRO107 5.0 31.9 1.0
O 2:CYS144 5.0 34.8 1.0

Iron binding site 7 out of 28 in 6zkj

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Iron binding site 7 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE1 3:SF4801 0.0 74.9 1.0
S2 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
SG 3:CYS114 2.3 35.3 1.0
FE4 3:SF4801 2.7 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE3 3:SF4801 2.7 74.9 1.0
CB 3:CYS114 3.4 19.7 1.0
S1 3:SF4801 3.9 74.9 1.0
CG 3:GLN117 4.0 17.7 1.0
NE2 3:HIS101 4.2 46.2 1.0
NE2 3:GLN117 4.4 21.3 1.0
CD 3:GLN117 4.4 17.3 1.0
CB 3:LEU116 4.4 14.2 1.0
N 3:GLN117 4.6 55.5 1.0
N 3:GLY206 4.6 8.3 1.0
CD2 3:LEU116 4.7 9.6 1.0
CA 3:CYS114 4.8 22.1 1.0
SG 3:CYS108 4.8 22.0 1.0
CA 3:VAL205 4.8 13.8 1.0
SG 3:CYS105 4.8 28.4 1.0
CB 3:GLN110 4.8 13.6 1.0
CB 3:GLN117 4.9 28.1 1.0
CE1 3:HIS101 4.9 58.8 1.0
CG 3:GLN110 4.9 18.1 1.0
CB 3:VAL205 5.0 24.6 1.0

Iron binding site 8 out of 28 in 6zkj

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Iron binding site 8 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE2 3:SF4801 0.0 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
SG 3:CYS105 2.3 28.4 1.0
FE3 3:SF4801 2.7 74.9 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE4 3:SF4801 2.7 74.9 1.0
NE2 3:GLN117 3.4 21.3 1.0
CB 3:CYS105 3.4 8.8 1.0
CA 3:CYS105 3.5 5.2 1.0
N 3:CYS105 3.8 10.7 1.0
S2 3:SF4801 3.9 74.9 1.0
CG 3:GLN117 4.1 17.7 1.0
CE 4:MET342 4.1 53.3 1.0
CD 3:GLN117 4.1 17.3 1.0
NE2 3:HIS101 4.2 46.2 1.0
C 3:ASP104 4.7 12.1 1.0
CD2 3:HIS101 4.7 47.9 1.0
SG 3:CYS108 4.8 22.0 1.0
SG 3:CYS114 4.8 35.3 1.0
C 3:CYS105 4.8 14.8 1.0
CB 3:CYS108 4.9 19.0 1.0
CG1 4:ILE346 4.9 17.6 1.0

Iron binding site 9 out of 28 in 6zkj

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Iron binding site 9 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE3 3:SF4801 0.0 74.9 1.0
NE2 3:HIS101 1.9 46.2 1.0
S2 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE4 3:SF4801 2.7 74.9 1.0
CE1 3:HIS101 2.8 58.8 1.0
CD2 3:HIS101 2.9 47.9 1.0
S3 3:SF4801 3.9 74.9 1.0
ND1 3:HIS101 3.9 33.8 1.0
CG 3:HIS101 4.0 51.9 1.0
CD2 3:LEU116 4.3 9.6 1.0
O 3:PRO102 4.4 26.9 1.0
CE 4:MET342 4.5 53.3 1.0
CB 3:ARG152 4.7 33.1 1.0
SG 3:CYS105 4.7 28.4 1.0
CG 3:ARG152 4.7 42.8 1.0
SG 3:CYS114 4.8 35.3 1.0
SG 3:CYS108 4.9 22.0 1.0
CD 3:ARG152 4.9 60.9 1.0
N 3:GLY206 5.0 8.3 1.0

Iron binding site 10 out of 28 in 6zkj

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Iron binding site 10 out of 28 in the Complex I with Nadh, OPEN3


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, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE4 3:SF4801 0.0 74.9 1.0
S2 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
SG 3:CYS108 2.3 22.0 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE3 3:SF4801 2.7 74.9 1.0
CB 3:CYS108 3.1 19.0 1.0
S4 3:SF4801 3.9 74.9 1.0
N 3:GLY206 4.2 8.3 1.0
CD 3:ARG152 4.3 60.9 1.0
CA 3:GLY206 4.4 12.3 1.0
CB 3:GLN110 4.5 13.6 1.0
NE2 3:HIS101 4.5 46.2 1.0
CA 3:CYS105 4.5 5.2 1.0
CA 3:CYS108 4.6 13.1 1.0
SG 3:CYS114 4.7 35.3 1.0
N 3:CYS105 4.8 10.7 1.0
NE 3:ARG152 4.8 50.7 1.0
SG 3:CYS105 4.8 28.4 1.0
N 3:GLY111 4.9 10.6 1.0
C 3:ASP104 4.9 12.1 1.0
CG 3:ARG152 4.9 42.8 1.0
NH1 3:ARG152 4.9 35.5 1.0
O 3:ASP104 5.0 15.0 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 7 19:36:00 2024

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