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Iron in PDB 7z7r: Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State

Enzymatic activity of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State

All present enzymatic activity of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State:
1.6.5.11; 1.6.5.3;

Other elements in 7z7r:

The structure of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State (pdb code 7z7r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State, PDB code: 7z7r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 7z7r

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Iron binding site 1 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:37.0
occ:1.00
 FE1 F:SF4501 0.0 37.0 1.0
S4 F:SF4501 2.3 42.6 1.0
S3 F:SF4501 2.3 63.7 1.0
S2 F:SF4501 2.3 57.3 1.0
SG F:CYS354 2.3 31.9 1.0
FE2 F:SF4501 2.6 40.2 1.0
FE3 F:SF4501 2.7 44.3 1.0
FE4 F:SF4501 2.8 39.5 1.0
CB F:CYS354 3.5 32.6 1.0
N F:CYS354 3.7 26.5 1.0
S1 F:SF4501 3.9 44.4 1.0
O F:CYS354 4.0 52.6 1.0
CA F:CYS354 4.0 30.6 1.0
CB F:CYS357 4.1 48.6 1.0
CB F:PHE397 4.1 42.5 1.0
N F:PHE397 4.2 61.9 1.0
C F:CYS354 4.4 37.9 1.0
N F:CYS398 4.4 44.5 1.0
SG F:CYS357 4.5 60.2 1.0
CB F:THR396 4.6 51.5 1.0
CA F:PHE397 4.7 42.7 1.0
CB F:TRP353 4.7 33.9 1.0
C F:TRP353 4.8 28.6 1.0
SG F:CYS398 4.8 54.7 1.0
SG F:CYS351 4.9 33.9 1.0
N F:TRP353 4.9 44.0 1.0

Iron binding site 2 out of 32 in 7z7r

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Iron binding site 2 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:40.2
occ:1.00
 FE2 F:SF4501 0.0 40.2 1.0
S4 F:SF4501 2.3 42.6 1.0
S3 F:SF4501 2.3 63.7 1.0
S1 F:SF4501 2.3 44.4 1.0
SG F:CYS357 2.3 60.2 1.0
FE1 F:SF4501 2.6 37.0 1.0
FE4 F:SF4501 2.7 39.5 1.0
FE3 F:SF4501 2.7 44.3 1.0
CB F:CYS357 3.0 48.6 1.0
OG F:SER350 3.2 48.6 1.0
CD2 F:HIS400 3.9 73.9 1.0
S2 F:SF4501 3.9 57.3 1.0
CB F:SER350 4.3 42.8 1.0
N F:CYS351 4.5 48.1 1.0
CA F:CYS357 4.5 45.0 1.0
CG F:HIS400 4.6 66.6 1.0
SG F:CYS354 4.6 31.9 1.0
CA F:SER350 4.6 40.1 1.0
CB F:HIS400 4.6 53.1 1.0
N F:ARG358 4.8 31.4 1.0
NE2 F:HIS400 4.9 71.9 1.0
C F:CYS357 4.9 50.1 1.0
SG F:CYS351 4.9 33.9 1.0
SG F:CYS398 4.9 54.7 1.0
O F:CYS354 4.9 52.6 1.0
N F:GLY352 5.0 58.7 1.0

Iron binding site 3 out of 32 in 7z7r

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Iron binding site 3 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:44.3
occ:1.00
 FE3 F:SF4501 0.0 44.3 1.0
S4 F:SF4501 2.3 42.6 1.0
S2 F:SF4501 2.3 57.3 1.0
S1 F:SF4501 2.3 44.4 1.0
SG F:CYS398 2.3 54.7 1.0
FE4 F:SF4501 2.6 39.5 1.0
FE2 F:SF4501 2.7 40.2 1.0
FE1 F:SF4501 2.7 37.0 1.0
CB F:CYS398 3.4 35.0 1.0
S3 F:SF4501 3.9 63.7 1.0
N F:CYS398 3.9 44.5 1.0
CB F:HIS400 3.9 53.1 1.0
CA F:CYS398 4.0 44.9 1.0
O F:CYS398 4.2 54.2 1.0
C F:CYS398 4.2 47.7 1.0
CD1 F:ILE179 4.4 76.0 1.0
N F:HIS400 4.5 51.0 1.0
CG F:PRO197 4.6 53.1 1.0
SG F:CYS351 4.7 33.9 1.0
CG F:HIS400 4.7 66.6 1.0
CD2 F:HIS400 4.8 73.9 1.0
CA F:HIS400 4.8 50.9 1.0
SG F:CYS354 4.9 31.9 1.0
SG F:CYS357 4.9 60.2 1.0
N F:ALA399 5.0 43.8 1.0

Iron binding site 4 out of 32 in 7z7r

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Iron binding site 4 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:39.5
occ:1.00
 FE4 F:SF4501 0.0 39.5 1.0
S2 F:SF4501 2.3 57.3 1.0
S3 F:SF4501 2.3 63.7 1.0
S1 F:SF4501 2.3 44.4 1.0
SG F:CYS351 2.3 33.9 1.0
FE3 F:SF4501 2.6 44.3 1.0
FE2 F:SF4501 2.7 40.2 1.0
FE1 F:SF4501 2.8 37.0 1.0
CB F:CYS351 3.4 43.4 1.0
N F:CYS351 3.7 48.1 1.0
N F:TRP353 3.8 44.0 1.0
S4 F:SF4501 3.9 42.6 1.0
N F:GLY352 3.9 58.7 1.0
CA F:CYS351 3.9 51.7 1.0
CB F:TRP353 4.0 33.9 1.0
C F:CYS351 4.1 61.2 1.0
OG F:SER350 4.3 48.6 1.0
CA F:TRP353 4.5 31.8 1.0
N F:CYS354 4.5 26.5 1.0
CD F:PRO197 4.6 49.3 1.0
SG F:CYS398 4.7 54.7 1.0
C F:GLY352 4.8 51.6 1.0
CG F:PRO197 4.8 53.1 1.0
CA F:GLY352 4.9 47.3 1.0
SG F:CYS357 4.9 60.2 1.0
C F:SER350 4.9 48.6 1.0
SG F:CYS354 4.9 31.9 1.0
CG1 F:ILE179 5.0 70.5 1.0

Iron binding site 5 out of 32 in 7z7r

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Iron binding site 5 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:75.2
occ:1.00
 FE1 E:FES201 0.0 75.2 1.0
S2 E:FES201 2.2 63.8 1.0
S1 E:FES201 2.2 74.8 1.0
SG E:CYS92 2.3 68.1 1.0
SG E:CYS97 2.3 53.6 1.0
FE2 E:FES201 2.7 58.8 1.0
CB E:CYS92 3.4 65.4 1.0
CB E:CYS97 3.7 57.5 1.0
ND2 E:ASN142 3.8 73.6 1.0
N E:CYS97 4.1 74.9 1.0
N E:LEU134 4.3 54.5 1.0
CA E:CYS133 4.3 57.9 1.0
CB E:SER94 4.4 72.6 1.0
SG E:CYS133 4.4 66.3 1.0
CA E:CYS97 4.5 72.6 1.0
CB E:CYS133 4.7 54.9 1.0
SG E:CYS137 4.7 82.2 1.0
CA E:CYS92 4.8 70.6 1.0
C E:CYS133 4.9 58.0 1.0
CA E:CYS137 4.9 63.2 1.0
N E:SER94 4.9 53.7 1.0
O E:CYS92 5.0 75.5 1.0
CG E:ASN142 5.0 66.6 1.0
C E:CYS92 5.0 74.3 1.0

Iron binding site 6 out of 32 in 7z7r

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Iron binding site 6 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:58.8
occ:1.00
 FE2 E:FES201 0.0 58.8 1.0
S2 E:FES201 2.2 63.8 1.0
S1 E:FES201 2.2 74.8 1.0
SG E:CYS137 2.3 82.2 1.0
SG E:CYS133 2.3 66.3 1.0
FE1 E:FES201 2.7 75.2 1.0
CB E:CYS137 3.5 66.3 1.0
CB E:CYS133 3.5 54.9 1.0
N E:CYS137 3.8 63.5 1.0
CA E:CYS137 3.9 63.2 1.0
N E:GLY135 4.0 86.6 1.0
CA E:CYS133 4.0 57.9 1.0
N E:LEU134 4.0 54.5 1.0
N E:ASN136 4.3 70.8 1.0
C E:CYS133 4.3 58.0 1.0
N F:GLY97 4.3 84.3 1.0
SG E:CYS92 4.4 68.1 1.0
CA E:GLY135 4.5 70.9 1.0
C E:ASN136 4.6 62.5 1.0
SG E:CYS97 4.7 53.6 1.0
C E:GLY135 4.8 81.9 1.0
ND2 E:ASN142 4.8 73.6 1.0
CG2 E:VAL96 4.8 58.6 1.0
CA F:PRO96 4.8 75.2 1.0
CB E:VAL96 4.8 66.8 1.0
C E:LEU134 4.9 72.5 1.0
CA E:LEU134 5.0 60.9 1.0

Iron binding site 7 out of 32 in 7z7r

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Iron binding site 7 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:31.8
occ:1.00
 FE1 G:SF41001 0.0 31.8 1.0
S2 G:SF41001 2.3 90.2 1.0
S3 G:SF41001 2.3 57.4 1.0
S4 G:SF41001 2.3 45.1 1.0
SG G:CYS114 2.3 47.0 1.0
FE4 G:SF41001 2.7 35.0 1.0
FE3 G:SF41001 2.7 48.6 1.0
FE2 G:SF41001 2.7 32.2 1.0
CB G:CYS114 3.3 39.1 1.0
NE2 G:HIS101 3.8 51.2 1.0
S1 G:SF41001 3.9 50.9 1.0
CG G:GLN117 4.2 72.0 1.0
CE1 G:HIS101 4.4 48.7 1.0
CA G:CYS114 4.6 56.3 1.0
CB G:LEU116 4.7 37.0 1.0
CD G:GLN117 4.7 66.5 1.0
N G:GLN117 4.8 56.7 1.0
NE2 G:GLN117 4.8 77.2 1.0
SG G:CYS108 4.8 34.3 1.0
CG2 G:THR205 4.8 44.2 1.0
N G:GLY206 4.8 36.9 1.0
SG G:CYS105 4.8 62.9 1.0
CD2 G:LEU116 4.8 58.2 1.0
CA G:THR205 4.9 37.2 1.0
CB G:GLU110 4.9 49.1 1.0
CD2 G:HIS101 4.9 50.3 1.0
CB G:THR205 4.9 42.9 1.0

Iron binding site 8 out of 32 in 7z7r

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Iron binding site 8 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:32.2
occ:1.00
 FE2 G:SF41001 0.0 32.2 1.0
S3 G:SF41001 2.3 57.4 1.0
S1 G:SF41001 2.3 50.9 1.0
S4 G:SF41001 2.3 45.1 1.0
SG G:CYS105 2.3 62.9 1.0
FE4 G:SF41001 2.7 35.0 1.0
FE3 G:SF41001 2.7 48.6 1.0
FE1 G:SF41001 2.7 31.8 1.0
CB G:CYS105 3.4 37.2 1.0
NE2 G:HIS101 3.5 51.2 1.0
CA G:CYS105 3.6 34.8 1.0
S2 G:SF41001 3.9 90.2 1.0
N G:CYS105 4.0 30.5 1.0
NE2 G:GLN117 4.0 77.2 1.0
CD2 G:HIS101 4.2 50.3 1.0
CD1 C:ILE516 4.4 63.3 1.0
CE1 G:HIS101 4.5 48.7 1.0
CG G:GLN117 4.5 72.0 1.0
CD G:GLN117 4.7 66.5 1.0
C G:ASP104 4.7 39.0 1.0
SG G:CYS108 4.8 34.3 1.0
CG1 C:ILE516 4.8 50.1 1.0
SG G:CYS114 4.8 47.0 1.0
CB G:CYS108 5.0 39.1 1.0
CD1 C:ILE512 5.0 45.4 1.0
C G:CYS105 5.0 39.7 1.0

Iron binding site 9 out of 32 in 7z7r

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Iron binding site 9 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:48.6
occ:1.00
 FE3 G:SF41001 0.0 48.6 1.0
NE2 G:HIS101 2.1 51.2 1.0
S2 G:SF41001 2.3 90.2 1.0
S4 G:SF41001 2.3 45.1 1.0
S1 G:SF41001 2.3 50.9 1.0
CE1 G:HIS101 2.3 48.7 1.0
FE2 G:SF41001 2.7 32.2 1.0
FE1 G:SF41001 2.7 31.8 1.0
FE4 G:SF41001 2.7 35.0 1.0
CD2 G:HIS101 3.4 50.3 1.0
ND1 G:HIS101 3.6 40.4 1.0
CB G:ARG152 3.7 42.5 1.0
CG G:ARG152 3.9 50.7 1.0
S3 G:SF41001 3.9 57.4 1.0
CD G:ARG152 4.1 42.6 1.0
CG G:HIS101 4.1 45.1 1.0
CA G:ARG152 4.5 37.3 1.0
O G:ARG152 4.5 52.8 1.0
SG G:CYS105 4.8 62.9 1.0
SG G:CYS108 4.8 34.3 1.0
SG G:CYS114 4.8 47.0 1.0
CD2 G:LEU116 4.8 58.2 1.0
N G:GLY206 4.9 36.9 1.0
CB G:THR205 4.9 42.9 1.0
CG2 G:THR205 5.0 44.2 1.0

Iron binding site 10 out of 32 in 7z7r

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Iron binding site 10 out of 32 in the Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Complex I From E. Coli, Lmng-Purified, Apo, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:35.0
occ:1.00
 FE4 G:SF41001 0.0 35.0 1.0
S2 G:SF41001 2.3 90.2 1.0
S3 G:SF41001 2.3 57.4 1.0
S1 G:SF41001 2.3 50.9 1.0
SG G:CYS108 2.3 34.3 1.0
FE1 G:SF41001 2.7 31.8 1.0
FE2 G:SF41001 2.7 32.2 1.0
FE3 G:SF41001 2.7 48.6 1.0
CB G:CYS108 3.2 39.1 1.0
S4 G:SF41001 3.9 45.1 1.0
CD G:ARG152 4.1 42.6 1.0
CB G:GLU110 4.3 49.1 1.0
N G:GLY111 4.5 38.3 1.0
N G:GLY206 4.6 36.9 1.0
CA G:CYS105 4.6 34.8 1.0
CA G:CYS108 4.7 39.8 1.0
NE2 G:HIS101 4.7 51.2 1.0
C G:GLU110 4.7 45.5 1.0
NE G:ARG152 4.7 53.0 1.0
SG G:CYS114 4.7 47.0 1.0
CA G:GLY206 4.7 38.3 1.0
NH1 G:ARG152 4.8 67.5 1.0
SG G:CYS105 4.8 62.9 1.0
CG G:ARG152 4.8 50.7 1.0
N G:GLU110 4.8 46.3 1.0
CA G:GLU110 4.8 46.6 1.0
O G:ASP104 5.0 45.1 1.0
CZ G:ARG152 5.0 59.6 1.0

Reference:

V.Kravchuk, O.Petrova, D.Kampjut, A.Wojciechowska-Bason, Z.Breese, L.Sazanov. A Universal Coupling Mechanism of Respiratory Complex I. Nature V. 609 808 2022.
ISSN: ESSN 1476-4687
PubMed: 36104567
DOI: 10.1038/S41586-022-05199-7
Page generated: Fri Aug 9 13:00:58 2024

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