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Iron in PDB 6zkc: Complex I During Turnover, Closed

Enzymatic activity of Complex I During Turnover, Closed

All present enzymatic activity of Complex I During Turnover, Closed:
1.6.99.3; 7.1.1.2;

Other elements in 6zkc:

The structure of Complex I During Turnover, 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 During Turnover, Closed (pdb code 6zkc). 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 During Turnover, Closed, PDB code: 6zkc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6zkc

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Iron binding site 1 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:34.8
occ:1.00
 FE1 1:SF4501 0.0 34.8 1.0
S2 1:SF4501 2.3 71.1 1.0
S3 1:SF4501 2.3 41.0 1.0
S4 1:SF4501 2.3 55.6 1.0
SG 1:CYS365 2.3 60.3 1.0
FE2 1:SF4501 2.7 76.9 1.0
FE3 1:SF4501 2.7 53.1 1.0
FE4 1:SF4501 2.8 23.5 1.0
CB 1:CYS365 2.9 40.3 1.0
OG 1:SER358 3.4 31.6 1.0
S1 1:SF4501 4.2 75.1 1.0
CA 1:CYS365 4.3 39.1 1.0
CD2 1:LEU407 4.4 25.1 1.0
N 1:CYS359 4.5 36.5 1.0
CB 1:SER358 4.6 31.6 1.0
C 1:CYS365 4.7 32.3 1.0
N 1:ARG366 4.8 37.5 1.0
N 1:GLY360 4.8 41.5 1.0
CB 1:LEU407 4.8 39.8 1.0
CA 1:SER358 4.9 38.7 1.0

Iron binding site 2 out of 28 in 6zkc

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Iron binding site 2 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:76.9
occ:1.00
 FE2 1:SF4501 0.0 76.9 1.0
S3 1:SF4501 2.3 41.0 1.0
S1 1:SF4501 2.3 75.1 1.0
S4 1:SF4501 2.4 55.6 1.0
FE3 1:SF4501 2.5 53.1 1.0
FE4 1:SF4501 2.5 23.5 1.0
FE1 1:SF4501 2.7 34.8 1.0
SG 1:CYS362 3.1 37.4 1.0
N 1:CYS362 3.4 29.7 1.0
S2 1:SF4501 3.8 71.1 1.0
CB 1:GLN361 3.9 23.4 1.0
CB 1:CYS362 3.9 53.8 1.0
N 1:GLN361 4.1 34.0 1.0
CA 1:CYS362 4.1 46.6 1.0
CB 1:CYS365 4.3 40.3 1.0
CA 1:GLN361 4.3 32.3 1.0
C 1:GLN361 4.3 34.5 1.0
O 1:CYS362 4.4 39.6 1.0
CB 1:ILE404 4.6 37.6 1.0
CD1 1:ILE404 4.6 33.5 1.0
C 1:CYS362 4.7 47.1 1.0
SG 1:CYS365 4.7 60.3 1.0
N 1:ILE404 4.8 35.7 1.0
SG 1:CYS359 4.8 56.0 1.0
CG1 1:ILE404 4.8 34.3 1.0
OE1 1:GLN361 4.8 17.1 1.0
CG 1:GLN361 4.8 17.9 1.0

Iron binding site 3 out of 28 in 6zkc

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Iron binding site 3 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:53.1
occ:1.00
 FE3 1:SF4501 0.0 53.1 1.0
S4 1:SF4501 2.3 55.6 1.0
S1 1:SF4501 2.3 75.1 1.0
S2 1:SF4501 2.4 71.1 1.0
FE4 1:SF4501 2.4 23.5 1.0
FE2 1:SF4501 2.5 76.9 1.0
FE1 1:SF4501 2.7 34.8 1.0
SG 1:CYS359 2.9 56.0 1.0
S3 1:SF4501 3.7 41.0 1.0
CD 1:PRO203 3.8 42.4 1.0
CB 1:CYS359 3.9 44.9 1.0
N 1:CYS359 4.0 36.5 1.0
CB 1:GLN361 4.1 23.4 1.0
CG 1:PRO203 4.2 45.8 1.0
N 1:GLN361 4.2 34.0 1.0
CA 1:CYS359 4.4 38.8 1.0
N 1:GLY360 4.4 41.5 1.0
OE1 1:GLN361 4.5 17.1 1.0
CG1 1:ILE185 4.5 61.8 1.0
C 1:CYS359 4.6 45.5 1.0
CD1 1:ILE185 4.6 70.8 1.0
SG 1:CYS405 4.7 49.4 1.0
CA 1:GLN361 4.8 32.3 1.0
SG 1:CYS365 5.0 60.3 1.0

Iron binding site 4 out of 28 in 6zkc

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Iron binding site 4 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:23.5
occ:1.00
 FE4 1:SF4501 0.0 23.5 1.0
S2 1:SF4501 2.3 71.1 1.0
S1 1:SF4501 2.3 75.1 1.0
S3 1:SF4501 2.4 41.0 1.0
FE3 1:SF4501 2.4 53.1 1.0
FE2 1:SF4501 2.5 76.9 1.0
FE1 1:SF4501 2.8 34.8 1.0
SG 1:CYS405 3.0 49.4 1.0
N 1:CYS405 3.6 41.3 1.0
S4 1:SF4501 3.8 55.6 1.0
CB 1:CYS405 4.0 45.8 1.0
CA 1:CYS405 4.2 42.6 1.0
CG 1:PRO203 4.2 45.8 1.0
O 1:CYS405 4.4 50.1 1.0
CB 1:ILE404 4.5 37.6 1.0
C 1:CYS405 4.5 47.9 1.0
N 1:ILE404 4.6 35.7 1.0
CD 1:PRO203 4.7 42.4 1.0
C 1:ILE404 4.7 32.4 1.0
CB 1:LEU407 4.8 39.8 1.0
CB 1:PRO203 4.8 38.4 1.0
CA 1:ILE404 4.8 31.9 1.0
SG 1:CYS365 4.9 60.3 1.0
CD1 1:ILE185 4.9 70.8 1.0
SG 1:CYS362 4.9 37.4 1.0
CB 1:CYS365 5.0 40.3 1.0

Iron binding site 5 out of 28 in 6zkc

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Iron binding site 5 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed 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 82.9 1.0
S1 2:FES300 2.2 81.3 1.0
SG 2:CYS103 2.3 90.8 1.0
SG 2:CYS108 2.3 68.7 1.0
FE2 2:FES300 3.0 80.8 1.0
CB 2:CYS103 3.4 61.5 1.0
CB 2:CYS108 3.5 49.9 1.0
OG1 2:THR105 3.7 41.5 1.0
N 2:CYS108 4.3 43.6 1.0
CA 2:CYS144 4.3 57.6 1.0
N 2:LEU145 4.4 53.3 1.0
CA 2:CYS108 4.5 48.1 1.0
O 2:CYS103 4.6 33.2 1.0
SD 2:MET153 4.6 66.3 1.0
SG 2:CYS144 4.6 94.3 1.0
CA 2:CYS103 4.7 46.8 1.0
C 2:CYS103 4.7 35.1 1.0
CB 2:CYS144 4.8 71.9 1.0
SG 2:CYS148 4.9 74.8 1.0
CG 2:MET153 4.9 65.4 1.0
N 2:THR105 4.9 35.5 1.0
C 2:CYS144 4.9 60.1 1.0

Iron binding site 6 out of 28 in 6zkc

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Iron binding site 6 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:80.8
occ:1.00
 FE2 2:FES300 0.0 80.8 1.0
S2 2:FES300 2.2 82.9 1.0
S1 2:FES300 2.2 81.3 1.0
SG 2:CYS148 2.3 74.8 1.0
SG 2:CYS144 2.3 94.3 1.0
FE1 2:FES300 3.0 0.7 1.0
CB 2:CYS144 3.5 71.9 1.0
N 2:GLY146 3.7 41.8 1.0
CB 2:CYS148 3.8 69.8 1.0
CA 2:CYS144 3.9 57.6 1.0
CA 2:GLY146 4.1 34.9 1.0
CA 2:CYS148 4.1 59.6 1.0
N 2:ALA147 4.1 37.6 1.0
N 2:LEU145 4.2 53.3 1.0
N 2:CYS148 4.2 56.3 1.0
N 1:GLY103 4.3 46.0 1.0
OG1 2:THR105 4.3 41.5 1.0
CA 1:PRO102 4.4 42.9 1.0
C 2:CYS144 4.4 60.1 1.0
C 2:GLY146 4.5 32.8 1.0
SG 2:CYS103 4.6 90.8 1.0
O 1:GLU101 4.7 55.4 1.0
C 2:ALA147 4.7 53.1 1.0
C 2:LEU145 4.8 50.5 1.0
C 1:PRO102 4.9 45.2 1.0
SG 2:CYS108 4.9 68.7 1.0

Iron binding site 7 out of 28 in 6zkc

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Iron binding site 7 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:66.9
occ:1.00
 FE1 3:SF4801 0.0 66.9 1.0
S3 3:SF4801 2.3 66.9 1.0
S2 3:SF4801 2.3 66.9 1.0
S4 3:SF4801 2.3 66.9 1.0
SG 3:CYS114 2.3 45.1 1.0
FE4 3:SF4801 2.7 66.9 1.0
FE2 3:SF4801 2.7 66.9 1.0
FE3 3:SF4801 2.7 66.9 1.0
CB 3:CYS114 3.4 32.6 1.0
S1 3:SF4801 3.9 66.9 1.0
CG 3:GLN117 4.0 42.2 1.0
NE2 3:HIS101 4.2 38.6 1.0
NE2 3:GLN117 4.4 56.5 1.0
CD 3:GLN117 4.5 45.3 1.0
CB 3:LEU116 4.5 38.0 1.0
N 3:GLY206 4.7 23.9 1.0
N 3:GLN117 4.7 47.5 1.0
SG 3:CYS108 4.7 46.8 1.0
CD2 3:LEU116 4.7 44.1 1.0
CA 3:CYS114 4.8 31.4 1.0
CA 3:VAL205 4.8 28.8 1.0
SG 3:CYS105 4.8 53.0 1.0
CB 3:GLN110 4.8 29.0 1.0
CE1 3:HIS101 4.9 50.7 1.0
CG 3:GLN110 4.9 30.8 1.0
CB 3:GLN117 5.0 42.3 1.0
CB 3:VAL205 5.0 33.9 1.0

Iron binding site 8 out of 28 in 6zkc

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Iron binding site 8 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:66.9
occ:1.00
 FE2 3:SF4801 0.0 66.9 1.0
S4 3:SF4801 2.3 66.9 1.0
S1 3:SF4801 2.3 66.9 1.0
S3 3:SF4801 2.3 66.9 1.0
SG 3:CYS105 2.3 53.0 1.0
FE3 3:SF4801 2.7 66.9 1.0
FE4 3:SF4801 2.7 66.9 1.0
FE1 3:SF4801 2.7 66.9 1.0
CB 3:CYS105 3.4 39.7 1.0
NE2 3:GLN117 3.4 56.5 1.0
CA 3:CYS105 3.5 29.4 1.0
N 3:CYS105 3.8 36.3 1.0
S2 3:SF4801 3.9 66.9 1.0
CE 4:MET342 4.1 16.1 1.0
CG 3:GLN117 4.1 42.2 1.0
CD 3:GLN117 4.2 45.3 1.0
NE2 3:HIS101 4.2 38.6 1.0
C 3:ASP104 4.6 32.6 1.0
CD2 3:HIS101 4.7 40.0 1.0
SG 3:CYS108 4.8 46.8 1.0
C 3:CYS105 4.8 25.5 1.0
SG 3:CYS114 4.8 45.1 1.0
CB 3:CYS108 4.8 29.1 1.0
CG1 4:ILE346 4.9 17.8 1.0

Iron binding site 9 out of 28 in 6zkc

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Iron binding site 9 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:66.9
occ:1.00
 FE3 3:SF4801 0.0 66.9 1.0
NE2 3:HIS101 1.9 38.6 1.0
S2 3:SF4801 2.3 66.9 1.0
S1 3:SF4801 2.3 66.9 1.0
S4 3:SF4801 2.3 66.9 1.0
FE2 3:SF4801 2.7 66.9 1.0
FE1 3:SF4801 2.7 66.9 1.0
FE4 3:SF4801 2.7 66.9 1.0
CE1 3:HIS101 2.8 50.7 1.0
CD2 3:HIS101 3.0 40.0 1.0
S3 3:SF4801 3.9 66.9 1.0
ND1 3:HIS101 4.0 50.3 1.0
CG 3:HIS101 4.1 43.8 1.0
CD2 3:LEU116 4.4 44.1 1.0
O 3:PRO102 4.5 20.4 1.0
CE 4:MET342 4.5 16.1 1.0
CB 3:ARG152 4.7 41.9 1.0
CG 3:ARG152 4.7 52.8 1.0
SG 3:CYS105 4.7 53.0 1.0
SG 3:CYS114 4.8 45.1 1.0
SG 3:CYS108 4.8 46.8 1.0
CD 3:ARG152 4.8 52.9 1.0
N 3:GLY206 5.0 23.9 1.0

Iron binding site 10 out of 28 in 6zkc

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Iron binding site 10 out of 28 in the Complex I During Turnover, 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 During Turnover, Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:66.9
occ:1.00
 FE4 3:SF4801 0.0 66.9 1.0
S2 3:SF4801 2.3 66.9 1.0
S3 3:SF4801 2.3 66.9 1.0
S1 3:SF4801 2.3 66.9 1.0
SG 3:CYS108 2.3 46.8 1.0
FE1 3:SF4801 2.7 66.9 1.0
FE2 3:SF4801 2.7 66.9 1.0
FE3 3:SF4801 2.7 66.9 1.0
CB 3:CYS108 3.1 29.1 1.0
S4 3:SF4801 3.9 66.9 1.0
N 3:GLY206 4.3 23.9 1.0
CD 3:ARG152 4.4 52.9 1.0
CB 3:GLN110 4.5 29.0 1.0
CA 3:CYS105 4.5 29.4 1.0
CA 3:GLY206 4.5 26.4 1.0
CA 3:CYS108 4.6 26.5 1.0
NE2 3:HIS101 4.6 38.6 1.0
SG 3:CYS114 4.7 45.1 1.0
N 3:CYS105 4.7 36.3 1.0
N 3:GLY111 4.8 39.8 1.0
SG 3:CYS105 4.8 53.0 1.0
NH1 3:ARG152 4.9 37.0 1.0
O 3:ASP104 4.9 37.7 1.0
C 3:ASP104 4.9 32.6 1.0
NE 3:ARG152 4.9 42.6 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 18:46:27 2024

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