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Iron in PDB 7p7c: Complex I From E. Coli, Ddm/Lmng-Purified, Apo, Open State

Other elements in 7p7c:

The structure of Complex I From E. Coli, Ddm/Lmng-Purified, Apo, Open 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/Lmng-Purified, Apo, Open State (pdb code 7p7c). 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/Lmng-Purified, Apo, Open State, PDB code: 7p7c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 7p7c

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

b:16.4
occ:1.00
 FE1 F:SF4501 0.0 16.4 1.0
S3 F:SF4501 2.3 20.5 1.0
S4 F:SF4501 2.3 16.0 1.0
S2 F:SF4501 2.3 18.0 1.0
SG F:CYS354 2.3 16.4 1.0
FE2 F:SF4501 2.6 18.2 1.0
FE3 F:SF4501 2.8 18.4 1.0
FE4 F:SF4501 2.8 17.4 1.0
CB F:CYS354 3.4 15.1 1.0
N F:CYS354 3.7 12.5 1.0
S1 F:SF4501 3.9 13.2 1.0
CB F:CYS357 4.0 12.1 1.0
CA F:CYS354 4.0 11.3 1.0
N F:PHE397 4.2 21.7 1.0
CB F:PHE397 4.2 14.8 1.0
O F:CYS354 4.2 18.4 1.0
SG F:CYS357 4.4 17.3 1.0
N F:CYS398 4.5 19.2 1.0
C F:CYS354 4.5 14.9 1.0
CA F:PHE397 4.7 20.0 1.0
CB F:THR396 4.7 22.4 1.0
CB F:TRP353 4.7 8.9 1.0
C F:TRP353 4.8 12.1 1.0
N F:TRP353 4.9 12.8 1.0
SG F:CYS398 4.9 19.8 1.0
SG F:CYS351 4.9 15.7 1.0

Iron binding site 2 out of 32 in 7p7c

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

b:18.2
occ:1.00
 FE2 F:SF4501 0.0 18.2 1.0
S4 F:SF4501 2.3 16.0 1.0
S1 F:SF4501 2.3 13.2 1.0
S3 F:SF4501 2.3 20.5 1.0
SG F:CYS357 2.3 17.3 1.0
FE1 F:SF4501 2.6 16.4 1.0
FE3 F:SF4501 2.7 18.4 1.0
FE4 F:SF4501 2.7 17.4 1.0
CB F:CYS357 3.0 12.1 1.0
ND1 F:HIS400 3.6 24.7 1.0
OG F:SER350 3.6 22.6 1.0
S2 F:SF4501 3.9 18.0 1.0
N F:CYS351 4.3 12.0 1.0
CB F:SER350 4.4 23.3 1.0
CG F:HIS400 4.4 24.3 1.0
CA F:SER350 4.4 18.7 1.0
CB F:HIS400 4.4 18.9 1.0
CE1 F:HIS400 4.5 19.1 1.0
CA F:CYS357 4.5 18.8 1.0
SG F:CYS354 4.5 16.4 1.0
SG F:CYS398 4.8 19.8 1.0
SG F:CYS351 4.9 15.7 1.0
C F:SER350 4.9 21.5 1.0
N F:ALA401 5.0 30.1 1.0
C F:CYS357 5.0 16.6 1.0
CB F:ALA401 5.0 35.8 1.0

Iron binding site 3 out of 32 in 7p7c

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

b:18.4
occ:1.00
 FE3 F:SF4501 0.0 18.4 1.0
S4 F:SF4501 2.3 16.0 1.0
S2 F:SF4501 2.3 18.0 1.0
S1 F:SF4501 2.3 13.2 1.0
SG F:CYS398 2.3 19.8 1.0
FE4 F:SF4501 2.6 17.4 1.0
FE2 F:SF4501 2.7 18.2 1.0
FE1 F:SF4501 2.8 16.4 1.0
CB F:CYS398 3.4 22.2 1.0
N F:CYS398 3.9 19.2 1.0
S3 F:SF4501 3.9 20.5 1.0
CB F:HIS400 3.9 18.9 1.0
CA F:CYS398 4.0 15.7 1.0
C F:CYS398 4.2 15.0 1.0
CG F:PRO197 4.3 27.1 1.0
O F:CYS398 4.3 26.0 1.0
N F:HIS400 4.5 18.9 1.0
CD1 F:ILE179 4.6 18.3 1.0
SG F:CYS351 4.7 15.7 1.0
CG F:HIS400 4.7 24.3 1.0
ND1 F:HIS400 4.7 24.7 1.0
CD F:PRO197 4.8 27.6 1.0
CA F:HIS400 4.8 18.0 1.0
C F:PHE397 4.9 20.0 1.0
SG F:CYS354 4.9 16.4 1.0
SG F:CYS357 4.9 17.3 1.0
N F:ALA399 4.9 16.8 1.0

Iron binding site 4 out of 32 in 7p7c

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

b:17.4
occ:1.00
 FE4 F:SF4501 0.0 17.4 1.0
S3 F:SF4501 2.3 20.5 1.0
S2 F:SF4501 2.3 18.0 1.0
S1 F:SF4501 2.3 13.2 1.0
SG F:CYS351 2.3 15.7 1.0
FE3 F:SF4501 2.6 18.4 1.0
FE2 F:SF4501 2.7 18.2 1.0
FE1 F:SF4501 2.8 16.4 1.0
CB F:CYS351 3.4 12.1 1.0
N F:CYS351 3.7 12.0 1.0
S4 F:SF4501 3.9 16.0 1.0
N F:TRP353 3.9 12.8 1.0
CA F:CYS351 3.9 11.4 1.0
CB F:TRP353 4.0 8.9 1.0
N F:GLY352 4.0 12.7 1.0
C F:CYS351 4.2 8.9 1.0
CD F:PRO197 4.4 27.6 1.0
CA F:TRP353 4.5 11.1 1.0
N F:CYS354 4.6 12.5 1.0
CG F:PRO197 4.6 27.1 1.0
OG F:SER350 4.6 22.6 1.0
SG F:CYS398 4.7 19.8 1.0
C F:SER350 4.8 21.5 1.0
C F:GLY352 4.9 14.9 1.0
SG F:CYS357 4.9 17.3 1.0
SG F:CYS354 5.0 16.4 1.0
CA F:GLY352 5.0 12.2 1.0
CG1 F:ILE179 5.0 22.6 1.0

Iron binding site 5 out of 32 in 7p7c

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

b:28.5
occ:1.00
 FE1 E:FES201 0.0 28.5 1.0
S2 E:FES201 2.2 33.7 1.0
S1 E:FES201 2.2 29.9 1.0
SG E:CYS92 2.3 30.6 1.0
SG E:CYS97 2.3 26.8 1.0
FE2 E:FES201 2.7 32.4 1.0
CB E:CYS97 3.4 27.3 1.0
CB E:CYS92 3.5 29.4 1.0
ND2 E:ASN142 4.0 33.8 1.0
N E:CYS97 4.0 28.0 1.0
CA E:CYS133 4.2 31.3 1.0
O E:HOH311 4.2 34.2 1.0
CA E:CYS97 4.3 28.4 1.0
N E:LEU134 4.4 29.1 1.0
CB E:CYS133 4.4 34.9 1.0
CB E:SER94 4.5 37.6 1.0
SG E:CYS133 4.5 34.7 1.0
SG E:CYS137 4.7 37.5 1.0
CA E:CYS92 4.8 31.3 1.0
C E:CYS133 4.9 31.3 1.0
CA E:CYS137 4.9 35.7 1.0
N E:SER94 4.9 21.8 1.0

Iron binding site 6 out of 32 in 7p7c

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

b:32.4
occ:1.00
 FE2 E:FES201 0.0 32.4 1.0
S2 E:FES201 2.2 33.7 1.0
S1 E:FES201 2.2 29.9 1.0
SG E:CYS133 2.3 34.7 1.0
SG E:CYS137 2.3 37.5 1.0
FE1 E:FES201 2.7 28.5 1.0
CB E:CYS133 3.2 34.9 1.0
CB E:CYS137 3.4 44.8 1.0
CA E:CYS137 3.8 35.7 1.0
CA E:CYS133 3.8 31.3 1.0
N E:CYS137 3.9 35.0 1.0
N E:LEU134 3.9 29.1 1.0
N E:GLY135 4.0 25.6 1.0
C E:CYS133 4.2 31.3 1.0
N E:ASN136 4.2 34.7 1.0
N F:GLY97 4.3 32.2 1.0
SG E:CYS92 4.4 30.6 1.0
C E:ASN136 4.5 34.3 1.0
CA E:GLY135 4.6 27.4 1.0
SG E:CYS97 4.7 26.8 1.0
CB E:VAL96 4.9 32.2 1.0
C E:GLY135 4.9 36.0 1.0
CG2 E:VAL96 4.9 34.2 1.0
C E:LEU134 4.9 28.1 1.0
CA F:PRO96 4.9 32.9 1.0
CA E:LEU134 5.0 26.9 1.0
ND2 E:ASN142 5.0 33.8 1.0

Iron binding site 7 out of 32 in 7p7c

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

b:157.3
occ:1.00
 FE1 G:SF41001 0.0 157.3 1.0
S3 G:SF41001 2.3 18.2 1.0
S2 G:SF41001 2.3 22.2 1.0
S4 G:SF41001 2.3 43.0 1.0
SG G:CYS114 2.3 23.0 1.0
FE4 G:SF41001 2.7 12.6 1.0
FE3 G:SF41001 2.7 88.4 1.0
FE2 G:SF41001 2.7 84.0 1.0
CB G:CYS114 3.3 14.1 1.0
CG G:GLN117 3.9 21.4 1.0
S1 G:SF41001 3.9 21.2 1.0
NE2 G:HIS101 4.4 23.1 1.0
CD G:GLN117 4.4 17.2 1.0
N G:GLN117 4.5 12.4 1.0
CB G:LEU116 4.5 20.0 1.0
CB G:GLU110 4.6 25.4 1.0
CD2 G:LEU116 4.7 22.3 1.0
CB G:GLN117 4.7 21.7 1.0
CA G:CYS114 4.7 19.4 1.0
SG G:CYS108 4.8 16.2 1.0
N G:GLY206 4.8 20.6 1.0
NE2 G:GLN117 4.8 17.5 1.0
CA G:THR205 4.9 16.4 1.0
SG G:CYS105 4.9 16.3 1.0
CG G:LEU116 4.9 19.1 1.0
CG G:GLU110 4.9 43.1 1.0
OE1 G:GLN117 5.0 18.7 1.0

Iron binding site 8 out of 32 in 7p7c

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

b:84.0
occ:1.00
 FE2 G:SF41001 0.0 84.0 1.0
S1 G:SF41001 2.3 21.2 1.0
S3 G:SF41001 2.3 18.2 1.0
S4 G:SF41001 2.3 43.0 1.0
SG G:CYS105 2.3 16.3 1.0
FE3 G:SF41001 2.7 88.4 1.0
FE4 G:SF41001 2.7 12.6 1.0
FE1 G:SF41001 2.7 157.3 1.0
CB G:CYS105 3.4 6.0 1.0
CA G:CYS105 3.6 8.6 1.0
NE2 G:GLN117 3.8 17.5 1.0
S2 G:SF41001 3.9 22.2 1.0
N G:CYS105 3.9 6.5 1.0
CG G:GLN117 4.0 21.4 1.0
CD G:GLN117 4.2 17.2 1.0
NE2 G:HIS101 4.2 23.1 1.0
CG1 C:ILE516 4.5 15.5 1.0
CD2 G:HIS101 4.7 16.3 1.0
CD1 C:ILE512 4.7 25.9 1.0
SG G:CYS108 4.8 16.2 1.0
C G:ASP104 4.8 11.2 1.0
CD1 C:ILE516 4.8 9.9 1.0
SG G:CYS114 4.9 23.0 1.0
CB G:CYS108 4.9 16.5 1.0
C G:CYS105 5.0 19.0 1.0

Iron binding site 9 out of 32 in 7p7c

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

b:88.4
occ:1.00
 FE3 G:SF41001 0.0 88.4 1.0
NE2 G:HIS101 1.9 23.1 1.0
S2 G:SF41001 2.3 22.2 1.0
S1 G:SF41001 2.3 21.2 1.0
S4 G:SF41001 2.3 43.0 1.0
FE2 G:SF41001 2.7 84.0 1.0
FE1 G:SF41001 2.7 157.3 1.0
FE4 G:SF41001 2.7 12.6 1.0
CE1 G:HIS101 2.9 7.0 1.0
CD2 G:HIS101 3.0 16.3 1.0
S3 G:SF41001 3.9 18.2 1.0
ND1 G:HIS101 4.0 6.0 1.0
CG G:HIS101 4.1 9.5 1.0
CD2 G:LEU116 4.2 22.3 1.0
CB G:ARG152 4.4 21.5 1.0
CD G:ARG152 4.6 18.8 1.0
SG G:CYS105 4.8 16.3 1.0
CG G:ARG152 4.8 25.3 1.0
SG G:CYS114 4.8 23.0 1.0
SG G:CYS108 4.9 16.2 1.0

Iron binding site 10 out of 32 in 7p7c

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

b:12.6
occ:1.00
 FE4 G:SF41001 0.0 12.6 1.0
S2 G:SF41001 2.3 22.2 1.0
S1 G:SF41001 2.3 21.2 1.0
S3 G:SF41001 2.3 18.2 1.0
SG G:CYS108 2.3 16.2 1.0
FE1 G:SF41001 2.7 157.3 1.0
FE2 G:SF41001 2.7 84.0 1.0
FE3 G:SF41001 2.7 88.4 1.0
CB G:CYS108 3.2 16.5 1.0
S4 G:SF41001 3.9 43.0 1.0
CD G:ARG152 4.0 18.8 1.0
CB G:GLU110 4.3 25.4 1.0
NE G:ARG152 4.4 20.1 1.0
N G:GLY206 4.5 20.6 1.0
NE2 G:HIS101 4.6 23.1 1.0
CA G:CYS105 4.6 8.6 1.0
CA G:CYS108 4.6 16.7 1.0
CA G:GLY206 4.7 11.4 1.0
SG G:CYS114 4.7 23.0 1.0
N G:GLY111 4.8 14.9 1.0
SG G:CYS105 4.8 16.3 1.0
N G:CYS105 4.9 6.5 1.0
N G:GLU110 4.9 13.3 1.0
CA G:GLU110 5.0 15.4 1.0
CZ G:ARG152 5.0 18.6 1.0
CG G:ARG152 5.0 25.3 1.0
C G:GLU110 5.0 10.8 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 15:08:44 2024

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