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Iron in PDB 7z84: Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State

Enzymatic activity of Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State

All present enzymatic activity of Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State:
1.6.99.5;

Other elements in 7z84:

The structure of Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State (pdb code 7z84). 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, Under Turnover at pH 8, Open-Ready State, PDB code: 7z84:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 7z84

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Iron binding site 1 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:17.8
occ:1.00
 FE1 F:SF4501 0.0 17.8 1.0
S4 F:SF4501 2.3 23.4 1.0
S3 F:SF4501 2.3 18.7 1.0
S2 F:SF4501 2.3 18.0 1.0
SG F:CYS354 2.3 12.7 1.0
FE2 F:SF4501 2.6 20.9 1.0
FE3 F:SF4501 2.7 24.2 1.0
FE4 F:SF4501 2.8 19.2 1.0
CB F:CYS354 3.4 13.3 1.0
N F:CYS354 3.7 9.1 1.0
S1 F:SF4501 3.9 21.1 1.0
CA F:CYS354 4.0 9.6 1.0
O F:CYS354 4.1 15.4 1.0
CB F:CYS357 4.1 18.0 1.0
N F:PHE397 4.2 18.5 1.0
CB F:PHE397 4.2 23.3 1.0
C F:CYS354 4.4 11.1 1.0
SG F:CYS357 4.5 22.2 1.0
N F:CYS398 4.5 18.3 1.0
CB F:THR396 4.6 32.3 1.0
CA F:PHE397 4.7 23.4 1.0
CB F:TRP353 4.8 14.6 1.0
C F:TRP353 4.8 9.3 1.0
SG F:CYS398 4.8 21.6 1.0
SG F:CYS351 4.9 14.7 1.0
N F:TRP353 4.9 10.7 1.0

Iron binding site 2 out of 32 in 7z84

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Iron binding site 2 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:20.9
occ:1.00
 FE2 F:SF4501 0.0 20.9 1.0
S4 F:SF4501 2.3 23.4 1.0
S3 F:SF4501 2.3 18.7 1.0
S1 F:SF4501 2.3 21.1 1.0
SG F:CYS357 2.3 22.2 1.0
FE1 F:SF4501 2.6 17.8 1.0
FE4 F:SF4501 2.7 19.2 1.0
FE3 F:SF4501 2.7 24.2 1.0
CB F:CYS357 3.0 18.0 1.0
OG F:SER350 3.4 27.1 1.0
ND1 F:HIS400 3.6 39.1 1.0
S2 F:SF4501 3.9 18.0 1.0
CB F:SER350 4.3 23.5 1.0
CG F:HIS400 4.3 38.2 1.0
CE1 F:HIS400 4.4 35.3 1.0
N F:CYS351 4.4 17.5 1.0
CB F:HIS400 4.4 28.6 1.0
CA F:CYS357 4.5 13.2 1.0
CA F:SER350 4.6 19.9 1.0
SG F:CYS354 4.6 12.7 1.0
SG F:CYS398 4.9 21.6 1.0
SG F:CYS351 4.9 14.7 1.0
N F:ARG358 4.9 12.2 1.0
C F:CYS357 5.0 10.3 1.0

Iron binding site 3 out of 32 in 7z84

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Iron binding site 3 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:24.2
occ:1.00
 FE3 F:SF4501 0.0 24.2 1.0
S4 F:SF4501 2.3 23.4 1.0
S2 F:SF4501 2.3 18.0 1.0
S1 F:SF4501 2.3 21.1 1.0
SG F:CYS398 2.3 21.6 1.0
FE4 F:SF4501 2.6 19.2 1.0
FE2 F:SF4501 2.7 20.9 1.0
FE1 F:SF4501 2.7 17.8 1.0
CB F:CYS398 3.4 15.8 1.0
CB F:HIS400 3.9 28.6 1.0
S3 F:SF4501 3.9 18.7 1.0
N F:CYS398 3.9 18.3 1.0
CA F:CYS398 4.1 17.2 1.0
CG F:PRO197 4.4 26.3 1.0
C F:CYS398 4.4 26.4 1.0
N F:HIS400 4.5 25.9 1.0
O F:CYS398 4.6 32.8 1.0
CG F:HIS400 4.6 38.2 1.0
CD1 F:ILE179 4.7 42.8 1.0
ND1 F:HIS400 4.7 39.1 1.0
SG F:CYS351 4.7 14.7 1.0
CA F:HIS400 4.8 26.6 1.0
SG F:CYS354 4.8 12.7 1.0
SG F:CYS357 4.9 22.2 1.0
C F:PHE397 4.9 25.9 1.0
CD F:PRO197 5.0 30.0 1.0
N F:ALA399 5.0 23.9 1.0

Iron binding site 4 out of 32 in 7z84

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Iron binding site 4 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:19.2
occ:1.00
 FE4 F:SF4501 0.0 19.2 1.0
S3 F:SF4501 2.3 18.7 1.0
S2 F:SF4501 2.3 18.0 1.0
S1 F:SF4501 2.3 21.1 1.0
SG F:CYS351 2.3 14.7 1.0
FE3 F:SF4501 2.6 24.2 1.0
FE2 F:SF4501 2.7 20.9 1.0
FE1 F:SF4501 2.8 17.8 1.0
CB F:CYS351 3.4 16.1 1.0
N F:CYS351 3.7 17.5 1.0
S4 F:SF4501 3.9 23.4 1.0
N F:TRP353 3.9 10.7 1.0
CA F:CYS351 4.0 12.0 1.0
CB F:TRP353 4.0 14.6 1.0
N F:GLY352 4.1 14.7 1.0
C F:CYS351 4.2 16.7 1.0
OG F:SER350 4.4 27.1 1.0
CD F:PRO197 4.5 30.0 1.0
N F:CYS354 4.5 9.1 1.0
CA F:TRP353 4.5 7.5 1.0
CG F:PRO197 4.7 26.3 1.0
SG F:CYS398 4.7 21.6 1.0
SG F:CYS357 4.9 22.2 1.0
C F:SER350 4.9 27.2 1.0
C F:GLY352 4.9 14.7 1.0
SG F:CYS354 5.0 12.7 1.0
CG1 F:ILE179 5.0 34.6 1.0

Iron binding site 5 out of 32 in 7z84

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Iron binding site 5 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:32.0
occ:1.00
 FE1 E:FES201 0.0 32.0 1.0
S2 E:FES201 2.2 42.5 1.0
S1 E:FES201 2.2 34.3 1.0
SG E:CYS92 2.3 36.0 1.0
SG E:CYS97 2.3 34.4 1.0
FE2 E:FES201 2.7 39.1 1.0
CB E:CYS97 3.5 39.2 1.0
CB E:CYS92 3.5 31.7 1.0
ND2 E:ASN142 3.9 46.7 1.0
N E:CYS97 4.1 30.1 1.0
CA E:CYS133 4.2 30.4 1.0
N E:LEU134 4.4 35.2 1.0
CA E:CYS97 4.4 32.5 1.0
CB E:CYS133 4.4 35.6 1.0
SG E:CYS133 4.5 47.1 1.0
CB E:SER94 4.5 36.1 1.0
SG E:CYS137 4.7 40.6 1.0
N E:SER94 4.8 25.9 1.0
C E:CYS133 4.9 33.2 1.0
CA E:CYS137 4.9 42.4 1.0
CA E:CYS92 4.9 32.9 1.0
CG E:ASN142 5.0 39.9 1.0

Iron binding site 6 out of 32 in 7z84

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Iron binding site 6 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:39.1
occ:1.00
 FE2 E:FES201 0.0 39.1 1.0
S2 E:FES201 2.2 42.5 1.0
S1 E:FES201 2.2 34.3 1.0
SG E:CYS137 2.3 40.6 1.0
SG E:CYS133 2.3 47.1 1.0
FE1 E:FES201 2.7 32.0 1.0
CB E:CYS133 3.3 35.6 1.0
CB E:CYS137 3.4 47.1 1.0
CA E:CYS137 3.8 42.4 1.0
CA E:CYS133 3.8 30.4 1.0
N E:CYS137 3.9 40.9 1.0
N E:LEU134 4.0 35.2 1.0
N E:GLY135 4.0 30.2 1.0
N E:ASN136 4.2 40.9 1.0
C E:CYS133 4.2 33.2 1.0
N F:GLY97 4.3 48.9 1.0
SG E:CYS92 4.4 36.0 1.0
C E:ASN136 4.4 40.6 1.0
CA E:GLY135 4.6 35.4 1.0
SG E:CYS97 4.7 34.4 1.0
CA F:PRO96 4.8 46.4 1.0
C E:GLY135 4.8 40.1 1.0
CB E:VAL96 4.8 33.5 1.0
CG2 E:VAL96 4.8 36.1 1.0
ND2 E:ASN142 4.9 46.7 1.0
C E:LEU134 4.9 32.6 1.0
CA E:ASN136 5.0 37.3 1.0
O E:ASN136 5.0 42.7 1.0

Iron binding site 7 out of 32 in 7z84

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Iron binding site 7 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:12.2
occ:1.00
 FE1 G:SF41001 0.0 12.2 1.0
S3 G:SF41001 2.3 1.2 1.0
S2 G:SF41001 2.3 19.9 1.0
S4 G:SF41001 2.3 11.9 1.0
SG G:CYS114 2.3 7.0 1.0
FE4 G:SF41001 2.7 12.2 1.0
FE3 G:SF41001 2.7 19.4 1.0
FE2 G:SF41001 2.7 7.1 1.0
CB G:CYS114 3.3 7.5 1.0
S1 G:SF41001 3.9 4.2 1.0
CG G:GLN117 4.2 2.8 1.0
NE2 G:HIS101 4.3 0.9 1.0
CB G:LEU116 4.5 12.9 1.0
CD G:GLN117 4.5 3.5 1.0
CB G:GLU110 4.6 17.7 1.0
N G:GLN117 4.6 6.0 1.0
CD2 G:LEU116 4.7 9.2 1.0
CA G:CYS114 4.7 4.3 1.0
SG G:CYS108 4.8 1.7 1.0
OE1 G:GLN117 4.8 4.6 1.0
CA G:THR205 4.8 1.9 1.0
SG G:CYS105 4.8 7.3 1.0
CG G:GLU110 4.8 34.3 1.0
N G:GLY206 4.9 6.6 1.0
CB G:GLN117 4.9 8.1 1.0
CG G:LEU116 4.9 12.3 1.0

Iron binding site 8 out of 32 in 7z84

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

b:7.1
occ:1.00
 FE2 G:SF41001 0.0 7.1 1.0
S1 G:SF41001 2.3 4.2 1.0
S3 G:SF41001 2.3 1.2 1.0
S4 G:SF41001 2.3 11.9 1.0
SG G:CYS105 2.3 7.3 1.0
FE4 G:SF41001 2.7 12.2 1.0
FE3 G:SF41001 2.7 19.4 1.0
FE1 G:SF41001 2.7 12.2 1.0
CB G:CYS105 3.4 2.2 1.0
CA G:CYS105 3.6 1.0 1.0
S2 G:SF41001 3.9 19.9 1.0
N G:CYS105 3.9 4.3 1.0
NE2 G:HIS101 4.1 0.9 1.0
NE2 G:GLN117 4.1 3.6 1.0
CG G:GLN117 4.4 2.8 1.0
CD G:GLN117 4.4 3.5 1.0
CD2 G:HIS101 4.6 3.3 1.0
CG1 C:ILE516 4.6 9.5 1.0
CD1 C:ILE512 4.6 26.9 1.0
C G:ASP104 4.7 5.7 1.0
CD1 C:ILE516 4.8 5.9 1.0
SG G:CYS108 4.8 1.7 1.0
SG G:CYS114 4.8 7.0 1.0
CB G:CYS108 4.9 4.5 1.0
C G:CYS105 5.0 4.7 1.0

Iron binding site 9 out of 32 in 7z84

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Iron binding site 9 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:19.4
occ:1.00
 FE3 G:SF41001 0.0 19.4 1.0
NE2 G:HIS101 1.9 0.9 1.0
S2 G:SF41001 2.3 19.9 1.0
S1 G:SF41001 2.3 4.2 1.0
S4 G:SF41001 2.3 11.9 1.0
FE2 G:SF41001 2.7 7.1 1.0
FE1 G:SF41001 2.7 12.2 1.0
FE4 G:SF41001 2.7 12.2 1.0
CE1 G:HIS101 2.8 1.8 1.0
CD2 G:HIS101 3.1 3.3 1.0
S3 G:SF41001 3.9 1.2 1.0
ND1 G:HIS101 4.0 0.0 1.0
CG G:ARG152 4.1 3.1 1.0
CG G:HIS101 4.1 1.4 1.0
CB G:ARG152 4.2 3.5 1.0
CD2 G:LEU116 4.3 9.2 1.0
CD G:ARG152 4.5 5.3 1.0
SG G:CYS105 4.8 7.3 1.0
SG G:CYS114 4.8 7.0 1.0
SG G:CYS108 4.8 1.7 1.0
O G:ARG152 4.9 14.7 1.0
CA G:ARG152 4.9 4.3 1.0

Iron binding site 10 out of 32 in 7z84

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Iron binding site 10 out of 32 in the Complex I From E. Coli, Ddm/Lmng-Purified, Under Turnover at pH 8, 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, Ddm/Lmng-Purified, Under Turnover at pH 8, Open-Ready State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe1001

b:12.2
occ:1.00
 FE4 G:SF41001 0.0 12.2 1.0
S2 G:SF41001 2.3 19.9 1.0
S1 G:SF41001 2.3 4.2 1.0
S3 G:SF41001 2.3 1.2 1.0
SG G:CYS108 2.3 1.7 1.0
FE1 G:SF41001 2.7 12.2 1.0
FE2 G:SF41001 2.7 7.1 1.0
FE3 G:SF41001 2.7 19.4 1.0
CB G:CYS108 3.2 4.5 1.0
S4 G:SF41001 3.9 11.9 1.0
CD G:ARG152 4.1 5.3 1.0
CB G:GLU110 4.2 17.7 1.0
NE G:ARG152 4.4 2.1 1.0
N G:GLY206 4.5 6.6 1.0
CG G:ARG152 4.6 3.1 1.0
CA G:CYS105 4.6 1.0 1.0
NE2 G:HIS101 4.6 0.9 1.0
CA G:CYS108 4.7 5.4 1.0
CA G:GLY206 4.7 6.2 1.0
N G:GLY111 4.7 13.4 1.0
SG G:CYS114 4.8 7.0 1.0
SG G:CYS105 4.8 7.3 1.0
C G:GLU110 4.9 7.9 1.0
N G:CYS105 4.9 4.3 1.0
CA G:GLU110 4.9 8.4 1.0
N G:GLU110 4.9 9.1 1.0
CZ G:ARG152 5.0 4.0 1.0
O G:ASP104 5.0 16.7 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 13:21:32 2024

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