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Iron in PDB 6zk9: Peripheral Domain of Open Complex I During Turnover

Enzymatic activity of Peripheral Domain of Open Complex I During Turnover

All present enzymatic activity of Peripheral Domain of Open Complex I During Turnover:
1.6.99.3; 7.1.1.2;

Other elements in 6zk9:

The structure of Peripheral Domain of Open Complex I During Turnover 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 Peripheral Domain of Open Complex I During Turnover (pdb code 6zk9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Peripheral Domain of Open Complex I During Turnover, PDB code: 6zk9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6zk9

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Iron binding site 1 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:39.3
occ:1.00
 FE1 1:SF4501 0.0 39.3 1.0
S2 1:SF4501 2.3 37.1 1.0
S3 1:SF4501 2.3 49.6 1.0
S4 1:SF4501 2.3 80.5 1.0
SG 1:CYS365 2.3 35.7 1.0
FE3 1:SF4501 2.7 44.6 1.0
FE2 1:SF4501 2.7 54.9 1.0
CB 1:CYS365 2.8 28.6 1.0
FE4 1:SF4501 2.9 49.4 1.0
OG 1:SER358 3.4 35.8 1.0
S1 1:SF4501 4.2 53.0 1.0
CD2 1:LEU407 4.2 51.0 1.0
CA 1:CYS365 4.2 38.4 1.0
N 1:CYS359 4.3 40.2 1.0
CB 1:SER358 4.5 42.0 1.0
CA 1:SER358 4.6 45.3 1.0
CB 1:LEU407 4.6 37.9 1.0
C 1:CYS365 4.7 41.0 1.0
N 1:ARG366 4.8 39.8 1.0
N 1:GLY360 4.8 32.9 1.0
SG 1:CYS362 4.8 50.1 1.0
C 1:SER358 4.8 50.4 1.0
CG 1:LEU407 4.9 48.1 1.0
N 1:GLY408 5.0 49.8 1.0

Iron binding site 2 out of 28 in 6zk9

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Iron binding site 2 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:54.9
occ:1.00
 FE2 1:SF4501 0.0 54.9 1.0
S3 1:SF4501 2.3 49.6 1.0
S1 1:SF4501 2.3 53.0 1.0
S4 1:SF4501 2.4 80.5 1.0
FE3 1:SF4501 2.5 44.6 1.0
FE4 1:SF4501 2.6 49.4 1.0
FE1 1:SF4501 2.7 39.3 1.0
SG 1:CYS362 2.9 50.1 1.0
N 1:CYS362 3.3 27.5 1.0
CB 1:CYS362 3.6 31.1 1.0
S2 1:SF4501 3.8 37.1 1.0
CA 1:CYS362 3.9 31.4 1.0
CB 1:CYS365 4.1 28.6 1.0
CB 1:GLN361 4.2 35.9 1.0
O 1:CYS362 4.3 28.6 1.0
N 1:GLN361 4.3 37.9 1.0
C 1:GLN361 4.3 38.5 1.0
CB 1:ILE404 4.5 44.4 1.0
CA 1:GLN361 4.5 58.3 1.0
C 1:CYS362 4.5 27.3 1.0
N 1:ILE404 4.5 44.1 1.0
SG 1:CYS365 4.6 35.7 1.0
CD1 1:ILE404 4.7 35.6 1.0
CG1 1:ILE404 4.8 31.7 1.0
CB 1:THR403 4.9 38.1 1.0

Iron binding site 3 out of 28 in 6zk9

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Iron binding site 3 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:44.6
occ:1.00
 FE3 1:SF4501 0.0 44.6 1.0
S4 1:SF4501 2.3 80.5 1.0
S1 1:SF4501 2.3 53.0 1.0
S2 1:SF4501 2.4 37.1 1.0
FE4 1:SF4501 2.4 49.4 1.0
FE2 1:SF4501 2.5 54.9 1.0
FE1 1:SF4501 2.7 39.3 1.0
SG 1:CYS359 2.9 52.9 1.0
S3 1:SF4501 3.7 49.6 1.0
N 1:CYS359 3.7 40.2 1.0
CB 1:CYS359 3.9 38.3 1.0
N 1:GLN361 3.9 37.9 1.0
CB 1:GLN361 4.0 35.9 1.0
N 1:GLY360 4.1 32.9 1.0
CD 1:PRO203 4.1 37.2 1.0
CA 1:CYS359 4.2 43.3 1.0
C 1:CYS359 4.4 37.4 1.0
CA 1:GLN361 4.5 58.3 1.0
CG 1:PRO203 4.5 42.0 1.0
N 1:CYS362 4.6 27.5 1.0
OE1 1:GLN361 4.7 32.5 1.0
CG1 1:ILE185 4.8 40.5 1.0
CD1 1:ILE185 4.8 42.5 1.0
C 1:SER358 4.8 50.4 1.0
C 1:GLY360 4.9 38.2 1.0
SG 1:CYS365 4.9 35.7 1.0
OG 1:SER358 5.0 35.8 1.0
CA 1:GLY360 5.0 33.1 1.0

Iron binding site 4 out of 28 in 6zk9

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Iron binding site 4 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:49.4
occ:1.00
 FE4 1:SF4501 0.0 49.4 1.0
S2 1:SF4501 2.3 37.1 1.0
S1 1:SF4501 2.3 53.0 1.0
S3 1:SF4501 2.4 49.6 1.0
FE3 1:SF4501 2.4 44.6 1.0
FE2 1:SF4501 2.6 54.9 1.0
FE1 1:SF4501 2.9 39.3 1.0
SG 1:CYS405 3.0 47.4 1.0
S4 1:SF4501 3.9 80.5 1.0
N 1:CYS405 3.9 33.9 1.0
CB 1:CYS405 4.0 38.4 1.0
CG 1:PRO203 4.1 42.0 1.0
CA 1:CYS405 4.4 40.4 1.0
CB 1:LEU407 4.4 37.9 1.0
CD1 1:ILE185 4.5 42.5 1.0
CD 1:PRO203 4.5 37.2 1.0
O 1:CYS405 4.5 39.4 1.0
C 1:CYS405 4.6 38.4 1.0
CB 1:ILE404 4.8 44.4 1.0
CB 1:PRO203 4.9 40.5 1.0
C 1:ILE404 4.9 42.2 1.0
N 1:LEU407 5.0 41.8 1.0
SG 1:CYS365 5.0 35.7 1.0
N 1:ILE404 5.0 44.1 1.0

Iron binding site 5 out of 28 in 6zk9

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Iron binding site 5 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 FE1 2:FES300 0.0 0.6 1.0
S2 2:FES300 2.2 65.4 1.0
S1 2:FES300 2.2 68.5 1.0
SG 2:CYS103 2.3 57.2 1.0
SG 2:CYS108 2.3 60.1 1.0
FE2 2:FES300 3.0 63.4 1.0
CB 2:CYS103 3.3 51.8 1.0
CB 2:CYS108 3.3 46.1 1.0
OG1 2:THR105 3.5 67.4 1.0
N 2:CYS108 4.1 55.4 1.0
CA 2:CYS144 4.2 48.1 1.0
CA 2:CYS108 4.3 56.8 1.0
N 2:LEU145 4.3 46.6 1.0
CA 2:CYS103 4.5 53.1 1.0
SD 2:MET153 4.6 76.9 1.0
C 2:CYS103 4.6 46.9 1.0
SG 2:CYS144 4.7 72.0 1.0
CB 2:CYS144 4.7 55.8 1.0
O 2:CYS103 4.7 55.5 1.0
C 2:CYS144 4.8 48.8 1.0
N 2:THR105 4.8 51.5 1.0
CG 2:MET153 4.9 72.5 1.0
CB 2:THR105 4.9 52.0 1.0
SG 2:CYS148 4.9 58.5 1.0

Iron binding site 6 out of 28 in 6zk9

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Iron binding site 6 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:63.4
occ:1.00
 FE2 2:FES300 0.0 63.4 1.0
S2 2:FES300 2.2 65.4 1.0
S1 2:FES300 2.2 68.5 1.0
SG 2:CYS148 2.3 58.5 1.0
SG 2:CYS144 2.3 72.0 1.0
FE1 2:FES300 3.0 0.6 1.0
CB 2:CYS144 3.4 55.8 1.0
CB 2:CYS148 3.6 60.8 1.0
CA 2:CYS144 3.7 48.1 1.0
N 2:GLY146 3.7 49.9 1.0
CA 2:CYS148 3.9 59.8 1.0
N 2:LEU145 4.0 46.6 1.0
N 2:CYS148 4.1 62.2 1.0
C 2:CYS144 4.1 48.8 1.0
N 2:ALA147 4.1 57.9 1.0
OG1 2:THR105 4.2 67.4 1.0
CA 2:GLY146 4.3 49.1 1.0
N 1:GLY103 4.3 49.1 1.0
CA 1:PRO102 4.4 53.0 1.0
SG 2:CYS103 4.6 57.2 1.0
C 2:ALA147 4.6 63.2 1.0
C 2:GLY146 4.7 55.6 1.0
C 2:LEU145 4.8 52.5 1.0
O 1:HOH649 4.8 52.0 1.0
SG 2:CYS108 4.9 60.1 1.0
CB 2:PRO107 4.9 49.7 1.0
CG 2:PRO107 4.9 49.8 1.0
C 1:PRO102 4.9 51.8 1.0
CA 2:LEU145 4.9 48.1 1.0
O 2:CYS144 5.0 50.5 1.0

Iron binding site 7 out of 28 in 6zk9

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Iron binding site 7 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:92.8
occ:1.00
 FE1 3:SF4801 0.0 92.8 1.0
S2 3:SF4801 2.3 92.8 1.0
S3 3:SF4801 2.3 92.8 1.0
S4 3:SF4801 2.3 92.8 1.0
SG 3:CYS114 2.3 42.5 1.0
FE2 3:SF4801 2.7 92.8 1.0
FE4 3:SF4801 2.7 92.8 1.0
FE3 3:SF4801 2.7 92.8 1.0
CB 3:CYS114 3.3 37.6 1.0
S1 3:SF4801 3.9 92.8 1.0
CG 3:GLN117 3.9 35.2 1.0
NE2 3:HIS101 4.3 64.0 1.0
CB 3:LEU116 4.4 32.0 1.0
N 3:GLN117 4.4 73.4 1.0
CD 3:GLN117 4.4 35.2 1.0
CB 3:GLN110 4.5 31.5 1.0
CG 3:GLN110 4.6 36.0 1.0
NE2 3:GLN117 4.6 35.1 1.0
CA 3:CYS114 4.7 40.0 1.0
CB 3:GLN117 4.7 46.0 1.0
SG 3:CYS108 4.7 31.9 1.0
CD2 3:LEU116 4.7 26.4 1.0
N 3:GLY206 4.7 26.1 1.0
SG 3:CYS105 4.8 46.3 1.0
CA 3:VAL205 4.9 31.7 1.0
CG 3:LEU116 5.0 36.1 1.0

Iron binding site 8 out of 28 in 6zk9

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Iron binding site 8 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:92.8
occ:1.00
 FE2 3:SF4801 0.0 92.8 1.0
S4 3:SF4801 2.3 92.8 1.0
S3 3:SF4801 2.3 92.8 1.0
S1 3:SF4801 2.3 92.8 1.0
SG 3:CYS105 2.3 46.3 1.0
FE3 3:SF4801 2.7 92.8 1.0
FE1 3:SF4801 2.7 92.8 1.0
FE4 3:SF4801 2.7 92.8 1.0
CB 3:CYS105 3.3 26.6 1.0
CA 3:CYS105 3.5 20.2 1.0
NE2 3:GLN117 3.7 35.1 1.0
N 3:CYS105 3.7 15.7 1.0
S2 3:SF4801 3.9 92.8 1.0
CG 3:GLN117 3.9 35.2 1.0
CE 4:MET342 4.0 27.2 1.0
CD 3:GLN117 4.2 35.2 1.0
NE2 3:HIS101 4.3 64.0 1.0
C 3:ASP104 4.7 29.9 1.0
CD2 3:HIS101 4.7 50.0 1.0
CG1 4:ILE346 4.8 35.5 1.0
SG 3:CYS114 4.8 42.5 1.0
SG 3:CYS108 4.8 31.9 1.0
C 3:CYS105 4.9 32.7 1.0
CB 3:CYS108 4.9 22.4 1.0

Iron binding site 9 out of 28 in 6zk9

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Iron binding site 9 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:92.8
occ:1.00
 FE3 3:SF4801 0.0 92.8 1.0
NE2 3:HIS101 1.8 64.0 1.0
S2 3:SF4801 2.3 92.8 1.0
S4 3:SF4801 2.3 92.8 1.0
S1 3:SF4801 2.3 92.8 1.0
FE2 3:SF4801 2.7 92.8 1.0
FE1 3:SF4801 2.7 92.8 1.0
FE4 3:SF4801 2.8 92.8 1.0
CD2 3:HIS101 2.8 50.0 1.0
CE1 3:HIS101 2.9 76.7 1.0
S3 3:SF4801 3.9 92.8 1.0
ND1 3:HIS101 4.0 51.6 1.0
CG 3:HIS101 4.0 69.7 1.0
CD2 3:LEU116 4.2 26.4 1.0
CE 4:MET342 4.3 27.2 1.0
O 3:PRO102 4.5 29.0 1.0
SG 3:CYS105 4.7 46.3 1.0
SG 3:CYS114 4.8 42.5 1.0
SG 3:CYS108 4.9 31.9 1.0
CG 3:ARG152 4.9 60.7 1.0
CB 3:ARG152 5.0 50.9 1.0

Iron binding site 10 out of 28 in 6zk9

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Iron binding site 10 out of 28 in the Peripheral Domain of Open Complex I During Turnover


Mono view


Stereo pair view

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

b:92.8
occ:1.00
 FE4 3:SF4801 0.0 92.8 1.0
S2 3:SF4801 2.3 92.8 1.0
S3 3:SF4801 2.3 92.8 1.0
S1 3:SF4801 2.3 92.8 1.0
SG 3:CYS108 2.3 31.9 1.0
FE1 3:SF4801 2.7 92.8 1.0
FE2 3:SF4801 2.7 92.8 1.0
FE3 3:SF4801 2.8 92.8 1.0
CB 3:CYS108 3.1 22.4 1.0
S4 3:SF4801 3.9 92.8 1.0
CB 3:GLN110 4.1 31.5 1.0
N 3:GLY206 4.3 26.1 1.0
CA 3:CYS105 4.5 20.2 1.0
NE2 3:HIS101 4.5 64.0 1.0
CD 3:ARG152 4.5 78.8 1.0
CA 3:GLY206 4.5 30.1 1.0
CA 3:CYS108 4.6 30.9 1.0
N 3:CYS105 4.6 15.7 1.0
SG 3:CYS114 4.7 42.5 1.0
N 3:GLY111 4.8 28.5 1.0
NE 3:ARG152 4.8 68.6 1.0
SG 3:CYS105 4.8 46.3 1.0
C 3:ASP104 4.9 29.9 1.0
N 3:GLN110 4.9 31.9 1.0
CA 3:GLN110 4.9 33.3 1.0
O 3:ASP104 5.0 32.8 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 18:45:58 2024

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