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Iron in PDB 7p61: Complex I From E. Coli, Ddm-Purified, with Nadh, Resting State

Other elements in 7p61:

The structure of Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State (pdb code 7p61). 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, Ddm-Purified, with Nadh, Resting State, PDB code: 7p61:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 7p61

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Iron binding site 1 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:51.1
occ:1.00
 FE1 F:SF4501 0.0 51.1 1.0
S3 F:SF4501 2.3 122.1 1.0
S4 F:SF4501 2.3 64.2 1.0
S2 F:SF4501 2.3 53.7 1.0
SG F:CYS354 2.3 42.8 1.0
FE2 F:SF4501 2.6 83.0 1.0
FE3 F:SF4501 2.7 46.8 1.0
FE4 F:SF4501 2.8 40.5 1.0
CB F:CYS354 3.5 29.9 1.0
N F:CYS354 3.7 25.6 1.0
S1 F:SF4501 3.9 66.9 1.0
CA F:CYS354 4.0 19.0 1.0
O F:CYS354 4.1 17.4 1.0
CB F:CYS357 4.1 31.8 1.0
CB F:PHE397 4.2 32.2 1.0
N F:PHE397 4.4 28.1 1.0
C F:CYS354 4.4 18.2 1.0
SG F:CYS357 4.5 43.4 1.0
N F:CYS398 4.6 33.7 1.0
CB F:TRP353 4.8 37.7 1.0
CA F:PHE397 4.8 29.2 1.0
SG F:CYS398 4.8 47.9 1.0
SG F:CYS351 4.9 26.1 1.0
C F:TRP353 4.9 27.9 1.0
CB F:THR396 4.9 34.7 1.0

Iron binding site 2 out of 32 in 7p61

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Iron binding site 2 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:83.0
occ:1.00
 FE2 F:SF4501 0.0 83.0 1.0
S4 F:SF4501 2.3 64.2 1.0
S3 F:SF4501 2.3 122.1 1.0
S1 F:SF4501 2.3 66.9 1.0
SG F:CYS357 2.3 43.4 1.0
FE1 F:SF4501 2.6 51.1 1.0
FE4 F:SF4501 2.7 40.5 1.0
FE3 F:SF4501 2.7 46.8 1.0
CB F:CYS357 3.0 31.8 1.0
S2 F:SF4501 3.9 53.7 1.0
CB F:SER350 4.0 29.9 1.0
ND1 F:HIS400 4.1 38.7 1.0
CB F:HIS400 4.4 35.6 1.0
O F:CYS351 4.4 43.1 1.0
CG F:HIS400 4.4 40.1 1.0
CA F:CYS357 4.5 27.1 1.0
OG F:SER350 4.5 15.9 1.0
SG F:CYS354 4.6 42.8 1.0
N F:CYS351 4.6 35.9 1.0
SG F:CYS398 4.9 47.9 1.0
SG F:CYS351 4.9 26.1 1.0
CE1 F:HIS400 4.9 36.6 1.0
C F:CYS357 4.9 26.7 1.0
N F:ARG358 5.0 23.1 1.0
CA F:SER350 5.0 36.0 1.0

Iron binding site 3 out of 32 in 7p61

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Iron binding site 3 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:46.8
occ:1.00
 FE3 F:SF4501 0.0 46.8 1.0
S4 F:SF4501 2.3 64.2 1.0
S2 F:SF4501 2.3 53.7 1.0
S1 F:SF4501 2.3 66.9 1.0
SG F:CYS398 2.3 47.9 1.0
FE4 F:SF4501 2.7 40.5 1.0
FE2 F:SF4501 2.7 83.0 1.0
FE1 F:SF4501 2.7 51.1 1.0
CB F:CYS398 3.4 36.5 1.0
CB F:HIS400 3.8 35.6 1.0
S3 F:SF4501 3.9 122.1 1.0
N F:CYS398 4.0 33.7 1.0
CA F:CYS398 4.1 33.8 1.0
C F:CYS398 4.4 30.2 1.0
CG F:PRO197 4.5 35.0 1.0
O F:CYS398 4.5 33.2 1.0
CD1 F:ILE179 4.5 65.1 1.0
N F:HIS400 4.5 30.8 1.0
CG F:HIS400 4.7 40.1 1.0
SG F:CYS351 4.7 26.1 1.0
CA F:HIS400 4.8 30.6 1.0
SG F:CYS354 4.9 42.8 1.0
SG F:CYS357 4.9 43.4 1.0

Iron binding site 4 out of 32 in 7p61

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Iron binding site 4 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:40.5
occ:1.00
 FE4 F:SF4501 0.0 40.5 1.0
S3 F:SF4501 2.3 122.1 1.0
S1 F:SF4501 2.3 66.9 1.0
S2 F:SF4501 2.3 53.7 1.0
SG F:CYS351 2.3 26.1 1.0
FE3 F:SF4501 2.7 46.8 1.0
FE2 F:SF4501 2.7 83.0 1.0
FE1 F:SF4501 2.8 51.1 1.0
CB F:CYS351 3.5 26.9 1.0
O F:CYS351 3.8 43.1 1.0
C F:CYS351 3.9 30.1 1.0
S4 F:SF4501 3.9 64.2 1.0
N F:CYS351 3.9 35.9 1.0
CA F:CYS351 4.0 30.7 1.0
N F:TRP353 4.0 38.3 1.0
CB F:TRP353 4.1 37.7 1.0
N F:GLY352 4.5 34.7 1.0
N F:CYS354 4.5 25.6 1.0
CD F:PRO197 4.6 38.1 1.0
CA F:TRP353 4.6 32.9 1.0
SG F:CYS398 4.7 47.9 1.0
CG F:PRO197 4.8 35.0 1.0
SG F:CYS357 4.9 43.4 1.0
SG F:CYS354 4.9 42.8 1.0
CD1 F:ILE179 5.0 65.1 1.0

Iron binding site 5 out of 32 in 7p61

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Iron binding site 5 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:43.1
occ:1.00
 FE1 E:FES201 0.0 43.1 1.0
S2 E:FES201 2.2 70.5 1.0
S1 E:FES201 2.2 53.0 1.0
SG E:CYS97 2.3 79.5 1.0
SG E:CYS92 2.3 63.3 1.0
FE2 E:FES201 2.7 46.5 1.0
CB E:CYS97 3.4 39.0 1.0
CB E:CYS92 3.4 42.6 1.0
N E:CYS97 4.1 53.5 1.0
CA E:CYS97 4.3 54.0 1.0
CB E:SER94 4.4 61.1 1.0
CB E:ASN142 4.5 54.0 1.0
N E:LEU134 4.5 45.8 1.0
ND2 E:ASN142 4.6 80.0 1.0
CA E:CYS137 4.7 46.0 1.0
SG E:CYS137 4.7 68.1 1.0
CA E:CYS92 4.8 39.9 1.0
CB E:CYS137 4.9 56.2 1.0
CB E:LEU134 4.9 62.1 1.0
SG E:CYS133 4.9 76.7 1.0
OG E:SER94 5.0 86.3 1.0

Iron binding site 6 out of 32 in 7p61

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Iron binding site 6 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:46.5
occ:1.00
 FE2 E:FES201 0.0 46.5 1.0
S2 E:FES201 2.2 70.5 1.0
S1 E:FES201 2.2 53.0 1.0
SG E:CYS137 2.3 68.1 1.0
FE1 E:FES201 2.7 43.1 1.0
SG E:CYS133 3.1 76.7 1.0
CB E:CYS137 3.3 56.2 1.0
CA E:CYS137 3.6 46.0 1.0
N E:CYS137 3.8 41.5 1.0
N E:GLY135 3.9 53.0 1.0
N E:ASN136 4.2 45.5 1.0
SG E:CYS92 4.2 63.3 1.0
N E:LEU134 4.3 45.8 1.0
N F:GLY97 4.3 65.1 1.0
C E:ASN136 4.4 39.4 1.0
CA E:GLY135 4.5 52.0 1.0
CB E:CYS133 4.5 62.1 1.0
SG E:CYS97 4.7 79.5 1.0
C E:GLY135 4.7 49.4 1.0
CA F:PRO96 4.8 55.9 1.0
CA E:CYS133 4.8 49.8 1.0
CB E:SER94 4.8 61.1 1.0
C E:LEU134 4.9 45.8 1.0
C E:CYS133 4.9 53.3 1.0
CB E:VAL96 5.0 48.4 1.0
CA E:ASN136 5.0 43.9 1.0
CA E:LEU134 5.0 46.1 1.0

Iron binding site 7 out of 32 in 7p61

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Iron binding site 7 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:125.0
occ:1.00
 FE1 G:SF41001 0.0 125.0 1.0
S2 G:SF41001 2.3 34.7 1.0
S3 G:SF41001 2.3 58.6 1.0
S4 G:SF41001 2.3 25.5 1.0
SG G:CYS114 2.3 31.8 1.0
FE4 G:SF41001 2.7 11.3 1.0
FE3 G:SF41001 2.7 22.3 1.0
FE2 G:SF41001 2.7 23.8 1.0
CB G:CYS114 3.4 31.1 1.0
S1 G:SF41001 3.9 128.2 1.0
CG G:GLN117 4.0 47.0 1.0
NE2 G:GLN117 4.2 48.3 1.0
NE2 G:HIS101 4.3 21.2 1.0
CB G:LEU116 4.5 17.6 1.0
CB G:GLU110 4.6 26.0 1.0
CD G:GLN117 4.6 42.9 1.0
CA G:CYS114 4.8 29.8 1.0
SG G:CYS108 4.8 31.3 1.0
N G:GLY206 4.8 19.4 1.0
CD2 G:LEU116 4.8 56.9 1.0
N G:GLN117 4.8 18.6 1.0
CA G:THR205 4.8 21.3 1.0
SG G:CYS105 4.9 50.8 1.0
CE1 G:HIS101 4.9 18.4 1.0

Iron binding site 8 out of 32 in 7p61

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Iron binding site 8 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:23.8
occ:1.00
 FE2 G:SF41001 0.0 23.8 1.0
S1 G:SF41001 2.3 128.2 1.0
S3 G:SF41001 2.3 58.6 1.0
S4 G:SF41001 2.3 25.5 1.0
SG G:CYS105 2.3 50.8 1.0
FE4 G:SF41001 2.7 11.3 1.0
FE3 G:SF41001 2.7 22.3 1.0
FE1 G:SF41001 2.7 125.0 1.0
CB G:CYS105 3.4 26.2 1.0
CA G:CYS105 3.7 22.9 1.0
NE2 G:GLN117 3.8 48.3 1.0
NE2 G:HIS101 3.8 21.2 1.0
S2 G:SF41001 3.9 34.7 1.0
CD1 C:ILE516 4.2 66.0 1.0
N G:CYS105 4.2 47.8 1.0
CD2 G:HIS101 4.5 32.5 1.0
CG G:GLN117 4.6 47.0 1.0
CD G:GLN117 4.7 42.9 1.0
SG G:CYS108 4.8 31.3 1.0
CE1 G:HIS101 4.8 18.4 1.0
CB G:CYS108 4.8 29.9 1.0
SG G:CYS114 4.9 31.8 1.0
C G:CYS105 4.9 23.0 1.0
C G:ASP104 4.9 50.2 1.0

Iron binding site 9 out of 32 in 7p61

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Iron binding site 9 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:22.3
occ:1.00
 FE3 G:SF41001 0.0 22.3 1.0
NE2 G:HIS101 2.1 21.2 1.0
S2 G:SF41001 2.3 34.7 1.0
S1 G:SF41001 2.3 128.2 1.0
S4 G:SF41001 2.3 25.5 1.0
CE1 G:HIS101 2.5 18.4 1.0
FE1 G:SF41001 2.7 125.0 1.0
FE2 G:SF41001 2.7 23.8 1.0
FE4 G:SF41001 2.7 11.3 1.0
CD2 G:HIS101 3.4 32.5 1.0
CG G:ARG152 3.7 30.9 1.0
ND1 G:HIS101 3.8 32.3 1.0
S3 G:SF41001 3.9 58.6 1.0
CB G:ARG152 4.1 20.8 1.0
CG G:HIS101 4.2 25.5 1.0
CD2 G:LEU116 4.4 56.9 1.0
O G:ARG152 4.5 24.6 1.0
CA G:ARG152 4.7 28.9 1.0
SG G:CYS105 4.8 50.8 1.0
SG G:CYS114 4.8 31.8 1.0
SG G:CYS108 4.8 31.3 1.0
N G:GLY206 4.9 19.4 1.0
CB G:THR205 5.0 27.0 1.0

Iron binding site 10 out of 32 in 7p61

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Iron binding site 10 out of 32 in the Complex I From E. Coli, Ddm-Purified, with Nadh, Resting 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, Ddm-Purified, with Nadh, Resting State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:11.3
occ:1.00
 FE4 G:SF41001 0.0 11.3 1.0
S2 G:SF41001 2.3 34.7 1.0
S1 G:SF41001 2.3 128.2 1.0
S3 G:SF41001 2.3 58.6 1.0
SG G:CYS108 2.3 31.3 1.0
FE2 G:SF41001 2.7 23.8 1.0
FE1 G:SF41001 2.7 125.0 1.0
FE3 G:SF41001 2.7 22.3 1.0
CB G:CYS108 3.2 29.9 1.0
S4 G:SF41001 3.9 25.5 1.0
CG G:ARG152 4.1 30.9 1.0
CB G:GLU110 4.5 26.0 1.0
N G:GLY206 4.5 19.4 1.0
CA G:GLY206 4.6 21.5 1.0
CA G:CYS105 4.7 22.9 1.0
CA G:CYS108 4.7 26.0 1.0
NE2 G:HIS101 4.7 21.2 1.0
CZ G:ARG152 4.7 39.2 1.0
NE G:ARG152 4.8 51.3 1.0
SG G:CYS105 4.8 50.8 1.0
SG G:CYS114 4.8 31.8 1.0
O G:ASP104 4.9 47.5 1.0
NH1 G:ARG152 4.9 26.0 1.0
CG G:GLU110 5.0 52.9 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: Thu Aug 8 14:58:41 2024

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