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Iron in PDB 6zkf: Complex I During Turnover, OPEN3

Enzymatic activity of Complex I During Turnover, OPEN3

All present enzymatic activity of Complex I During Turnover, OPEN3:
7.1.1.2;

Other elements in 6zkf:

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

Iron binding site 1 out of 28 in 6zkf

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Iron binding site 1 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:22.4
occ:1.00
FE1 1:SF4501 0.0 22.4 1.0
S2 1:SF4501 2.3 31.2 1.0
S3 1:SF4501 2.3 32.8 1.0
S4 1:SF4501 2.3 63.6 1.0
SG 1:CYS365 2.3 23.4 1.0
FE3 1:SF4501 2.7 27.8 1.0
FE2 1:SF4501 2.7 38.0 1.0
CB 1:CYS365 2.8 11.8 1.0
FE4 1:SF4501 2.8 32.5 1.0
OG 1:SER358 3.3 18.9 1.0
S1 1:SF4501 4.2 46.9 1.0
CA 1:CYS365 4.2 21.5 1.0
CD2 1:LEU407 4.4 34.2 1.0
N 1:CYS359 4.4 23.4 1.0
CB 1:SER358 4.5 25.2 1.0
C 1:CYS365 4.6 24.2 1.0
CA 1:SER358 4.7 28.5 1.0
N 1:ARG366 4.7 22.9 1.0
CB 1:LEU407 4.7 26.2 1.0
N 1:GLY360 4.8 27.6 1.0
C 1:SER358 4.9 33.5 1.0
N 1:GLY408 5.0 41.8 1.0
SG 1:CYS362 5.0 52.2 1.0
N 1:CYS365 5.0 20.4 1.0

Iron binding site 2 out of 28 in 6zkf

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Iron binding site 2 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:38.0
occ:1.00
FE2 1:SF4501 0.0 38.0 1.0
S3 1:SF4501 2.3 32.8 1.0
S1 1:SF4501 2.3 46.9 1.0
S4 1:SF4501 2.4 63.6 1.0
FE3 1:SF4501 2.5 27.8 1.0
FE4 1:SF4501 2.5 32.5 1.0
FE1 1:SF4501 2.7 22.4 1.0
SG 1:CYS362 3.0 52.2 1.0
N 1:CYS362 3.3 27.4 1.0
S2 1:SF4501 3.8 31.2 1.0
CB 1:CYS362 3.8 35.5 1.0
CA 1:CYS362 4.1 26.6 1.0
CB 1:GLN361 4.1 27.3 1.0
CB 1:CYS365 4.2 11.8 1.0
N 1:GLN361 4.2 25.0 1.0
O 1:CYS362 4.3 31.2 1.0
C 1:GLN361 4.3 29.1 1.0
CA 1:GLN361 4.4 41.4 1.0
CB 1:ILE404 4.5 27.5 1.0
C 1:CYS362 4.6 25.4 1.0
N 1:ILE404 4.6 27.2 1.0
SG 1:CYS365 4.7 23.4 1.0
CD1 1:ILE404 4.8 18.8 1.0
CG1 1:ILE404 4.8 21.9 1.0
OE1 1:GLN361 4.9 15.8 1.0
SG 1:CYS359 5.0 36.1 1.0

Iron binding site 3 out of 28 in 6zkf

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Iron binding site 3 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:27.8
occ:1.00
FE3 1:SF4501 0.0 27.8 1.0
S4 1:SF4501 2.3 63.6 1.0
S1 1:SF4501 2.3 46.9 1.0
S2 1:SF4501 2.4 31.2 1.0
FE4 1:SF4501 2.4 32.5 1.0
FE2 1:SF4501 2.5 38.0 1.0
FE1 1:SF4501 2.7 22.4 1.0
SG 1:CYS359 2.9 36.1 1.0
S3 1:SF4501 3.7 32.8 1.0
N 1:CYS359 3.8 23.4 1.0
CB 1:CYS359 3.9 25.5 1.0
N 1:GLN361 4.0 25.0 1.0
CD 1:PRO203 4.1 20.7 1.0
CB 1:GLN361 4.1 27.3 1.0
N 1:GLY360 4.2 27.6 1.0
CA 1:CYS359 4.2 26.4 1.0
C 1:CYS359 4.4 23.3 1.0
CG 1:PRO203 4.4 25.2 1.0
OE1 1:GLN361 4.6 15.8 1.0
CD1 1:ILE185 4.6 25.7 1.0
CA 1:GLN361 4.6 41.4 1.0
CG1 1:ILE185 4.7 23.6 1.0
SG 1:CYS405 4.8 30.6 1.0
N 1:CYS362 4.8 27.4 1.0
C 1:SER358 4.9 33.5 1.0
OG 1:SER358 4.9 18.9 1.0
SG 1:CYS365 5.0 23.4 1.0

Iron binding site 4 out of 28 in 6zkf

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Iron binding site 4 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:32.5
occ:1.00
FE4 1:SF4501 0.0 32.5 1.0
S2 1:SF4501 2.3 31.2 1.0
S1 1:SF4501 2.3 46.9 1.0
S3 1:SF4501 2.4 32.8 1.0
FE3 1:SF4501 2.4 27.8 1.0
FE2 1:SF4501 2.5 38.0 1.0
FE1 1:SF4501 2.8 22.4 1.0
SG 1:CYS405 3.0 30.6 1.0
N 1:CYS405 3.7 28.8 1.0
S4 1:SF4501 3.8 63.6 1.0
CB 1:CYS405 4.0 32.3 1.0
CA 1:CYS405 4.2 29.6 1.0
CG 1:PRO203 4.3 25.2 1.0
O 1:CYS405 4.4 38.1 1.0
C 1:CYS405 4.5 32.8 1.0
CB 1:LEU407 4.6 26.2 1.0
CB 1:ILE404 4.6 27.5 1.0
CD1 1:ILE185 4.6 25.7 1.0
CD 1:PRO203 4.7 20.7 1.0
N 1:ILE404 4.8 27.2 1.0
C 1:ILE404 4.8 29.3 1.0
SG 1:CYS365 4.9 23.4 1.0
SG 1:CYS362 5.0 52.2 1.0
CB 1:PRO203 5.0 29.0 1.0
CA 1:ILE404 5.0 25.5 1.0
CB 1:CYS365 5.0 11.8 1.0
N 1:LEU407 5.0 25.0 1.0

Iron binding site 5 out of 28 in 6zkf

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Iron binding site 5 out of 28 in the Complex I During Turnover, 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 During Turnover, 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 48.5 1.0
S1 2:FES300 2.2 51.7 1.0
SG 2:CYS103 2.3 40.3 1.0
SG 2:CYS108 2.3 73.5 1.0
FE2 2:FES300 3.0 55.1 1.0
CB 2:CYS108 3.4 45.8 1.0
CB 2:CYS103 3.4 36.1 1.0
OG1 2:THR105 3.5 50.5 1.0
N 2:CYS108 4.2 38.5 1.0
CA 2:CYS144 4.3 40.2 1.0
N 2:LEU145 4.3 37.9 1.0
CA 2:CYS108 4.4 40.0 1.0
SD 2:MET153 4.5 70.4 1.0
CA 2:CYS103 4.7 36.2 1.0
SG 2:CYS144 4.7 56.6 1.0
C 2:CYS103 4.7 30.1 1.0
CG 2:MET153 4.8 60.1 1.0
O 2:CYS103 4.8 38.6 1.0
CB 2:CYS144 4.8 44.4 1.0
C 2:CYS144 4.9 37.5 1.0
CB 2:THR105 4.9 39.9 1.0
N 2:THR105 4.9 34.6 1.0
SG 2:CYS148 5.0 61.1 1.0

Iron binding site 6 out of 28 in 6zkf

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Iron binding site 6 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:55.1
occ:1.00
FE2 2:FES300 0.0 55.1 1.0
S2 2:FES300 2.2 48.5 1.0
S1 2:FES300 2.2 51.7 1.0
SG 2:CYS148 2.3 61.1 1.0
SG 2:CYS144 2.3 56.6 1.0
FE1 2:FES300 3.0 0.7 1.0
CB 2:CYS144 3.4 44.4 1.0
CB 2:CYS148 3.6 70.2 1.0
CA 2:CYS144 3.8 40.2 1.0
CA 2:CYS148 3.9 61.8 1.0
N 2:GLY146 3.9 33.1 1.0
N 2:CYS148 4.1 55.8 1.0
N 2:LEU145 4.1 37.9 1.0
N 2:ALA147 4.2 47.6 1.0
C 2:CYS144 4.2 37.5 1.0
OG1 2:THR105 4.3 50.5 1.0
N 1:GLY103 4.3 42.2 1.0
CA 1:PRO102 4.4 40.9 1.0
CA 2:GLY146 4.4 32.2 1.0
C 2:ALA147 4.6 50.8 1.0
SG 2:CYS103 4.6 40.3 1.0
C 2:GLY146 4.7 38.8 1.0
C 2:LEU145 4.9 35.6 1.0
SG 2:CYS108 4.9 73.5 1.0
C 1:PRO102 4.9 43.5 1.0
CB 1:PRO102 5.0 46.2 1.0
CG 2:PRO107 5.0 32.9 1.0

Iron binding site 7 out of 28 in 6zkf

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Iron binding site 7 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:75.9
occ:1.00
FE1 3:SF4801 0.0 75.9 1.0
S3 3:SF4801 2.3 75.9 1.0
S2 3:SF4801 2.3 75.9 1.0
S4 3:SF4801 2.3 75.9 1.0
SG 3:CYS114 2.3 25.6 1.0
FE4 3:SF4801 2.7 75.9 1.0
FE2 3:SF4801 2.7 75.9 1.0
FE3 3:SF4801 2.7 75.9 1.0
CB 3:CYS114 3.3 20.7 1.0
S1 3:SF4801 3.9 75.9 1.0
NE2 3:HIS101 4.1 47.2 1.0
CG 3:GLN117 4.3 24.2 1.0
CB 3:LEU116 4.5 15.2 1.0
CG 3:GLN110 4.5 21.4 1.0
CB 3:GLN110 4.5 15.1 1.0
CD 3:GLN117 4.7 20.4 1.0
N 3:GLY206 4.7 12.7 1.0
N 3:GLN117 4.7 56.5 1.0
CA 3:CYS114 4.7 23.1 1.0
SG 3:CYS108 4.7 15.1 1.0
CD2 3:LEU116 4.8 14.5 1.0
CA 3:VAL205 4.8 14.8 1.0
SG 3:CYS105 4.8 29.4 1.0
CE1 3:HIS101 4.8 59.8 1.0
NE2 3:GLN117 4.8 29.1 1.0
CB 3:VAL205 4.9 25.7 1.0

Iron binding site 8 out of 28 in 6zkf

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Iron binding site 8 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:75.9
occ:1.00
FE2 3:SF4801 0.0 75.9 1.0
S4 3:SF4801 2.3 75.9 1.0
S3 3:SF4801 2.3 75.9 1.0
S1 3:SF4801 2.3 75.9 1.0
SG 3:CYS105 2.3 29.4 1.0
FE4 3:SF4801 2.7 75.9 1.0
FE3 3:SF4801 2.7 75.9 1.0
FE1 3:SF4801 2.7 75.9 1.0
CB 3:CYS105 3.4 11.9 1.0
CA 3:CYS105 3.5 12.1 1.0
NE2 3:GLN117 3.8 29.1 1.0
N 3:CYS105 3.8 27.0 1.0
S2 3:SF4801 3.9 75.9 1.0
CE 4:MET342 4.1 10.4 1.0
NE2 3:HIS101 4.1 47.2 1.0
CG 3:GLN117 4.2 24.2 1.0
CD 3:GLN117 4.3 20.4 1.0
C 3:ASP104 4.6 14.6 1.0
CD2 3:HIS101 4.7 33.1 1.0
SG 3:CYS108 4.8 15.1 1.0
C 3:CYS105 4.8 15.8 1.0
SG 3:CYS114 4.8 25.6 1.0
CB 3:CYS108 4.9 15.6 1.0
CG1 4:ILE346 5.0 18.6 1.0

Iron binding site 9 out of 28 in 6zkf

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Iron binding site 9 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:75.9
occ:1.00
FE3 3:SF4801 0.0 75.9 1.0
NE2 3:HIS101 1.8 47.2 1.0
S2 3:SF4801 2.3 75.9 1.0
S1 3:SF4801 2.3 75.9 1.0
S4 3:SF4801 2.3 75.9 1.0
FE2 3:SF4801 2.7 75.9 1.0
CE1 3:HIS101 2.7 59.8 1.0
FE1 3:SF4801 2.7 75.9 1.0
FE4 3:SF4801 2.7 75.9 1.0
CD2 3:HIS101 2.9 33.1 1.0
ND1 3:HIS101 3.9 34.8 1.0
S3 3:SF4801 3.9 75.9 1.0
CG 3:HIS101 4.0 52.9 1.0
CD2 3:LEU116 4.4 14.5 1.0
CG 3:ARG152 4.5 43.8 1.0
O 3:PRO102 4.5 14.1 1.0
CE 4:MET342 4.5 10.4 1.0
CB 3:ARG152 4.7 34.1 1.0
SG 3:CYS105 4.8 29.4 1.0
SG 3:CYS114 4.8 25.6 1.0
CD 3:ARG152 4.8 61.9 1.0
SG 3:CYS108 4.8 15.1 1.0

Iron binding site 10 out of 28 in 6zkf

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Iron binding site 10 out of 28 in the Complex I During Turnover, 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 During Turnover, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:75.9
occ:1.00
FE4 3:SF4801 0.0 75.9 1.0
S2 3:SF4801 2.3 75.9 1.0
S1 3:SF4801 2.3 75.9 1.0
S3 3:SF4801 2.3 75.9 1.0
SG 3:CYS108 2.3 15.1 1.0
FE2 3:SF4801 2.7 75.9 1.0
FE1 3:SF4801 2.7 75.9 1.0
FE3 3:SF4801 2.7 75.9 1.0
CB 3:CYS108 3.1 15.6 1.0
S4 3:SF4801 3.9 75.9 1.0
CB 3:GLN110 4.2 15.1 1.0
N 3:GLY206 4.3 12.7 1.0
CD 3:ARG152 4.3 61.9 1.0
CA 3:CYS105 4.4 12.1 1.0
CA 3:GLY206 4.6 13.3 1.0
NE2 3:HIS101 4.6 47.2 1.0
NE 3:ARG152 4.6 51.7 1.0
CA 3:CYS108 4.6 17.8 1.0
N 3:CYS105 4.7 27.0 1.0
SG 3:CYS114 4.8 25.6 1.0
SG 3:CYS105 4.8 29.4 1.0
N 3:GLY111 4.8 11.6 1.0
C 3:ASP104 4.9 14.6 1.0
O 3:ASP104 4.9 16.0 1.0
N 3:GLN110 4.9 15.0 1.0
CA 3:GLN110 4.9 16.4 1.0
CG 3:ARG152 4.9 43.8 1.0
C 3:GLN110 4.9 16.0 1.0
CZ 3:ARG152 5.0 42.3 1.0
CG 3:GLN110 5.0 21.4 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 7 18:54:11 2024

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