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Iron in PDB 9efu: Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide

Enzymatic activity of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide

All present enzymatic activity of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide:
1.3.7.7;

Other elements in 9efu:

The structure of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide (pdb code 9efu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide, PDB code: 9efu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 9efu

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Iron binding site 1 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:123.2
occ:1.00
 FE1 A:SF4501 0.0 123.2 1.0
SG A:CYS29 1.6 62.6 1.0
S4 A:SF4501 2.2 115.1 1.0
S2 A:SF4501 2.2 110.8 1.0
S3 A:SF4501 2.3 114.0 1.0
FE2 A:SF4501 2.7 113.2 1.0
FE3 A:SF4501 2.7 118.7 1.0
FE4 A:SF4501 2.7 122.9 1.0
CB A:CYS29 2.8 63.4 1.0
SG A:CYS54 3.6 64.9 1.0
SG A:CYS115 3.7 60.5 1.0
S1 A:SF4501 3.8 108.4 1.0
CA A:CYS29 4.3 59.9 1.0
N A:GLY148 4.4 63.2 1.0
CG A:LEU31 4.5 53.6 1.0
CD1 A:LEU31 4.5 57.5 1.0
OD1 B:ASP36 4.7 67.9 1.0
O B:GLY35 4.7 72.7 1.0
N A:CYS29 4.7 65.5 1.0
O A:GLY146 4.8 62.2 1.0
CB A:CYS54 4.8 53.3 1.0
CA A:GLY148 4.9 67.1 1.0
C A:CYS29 4.9 57.7 1.0
CB A:LEU31 4.9 50.8 1.0
C B:GLY35 5.0 70.9 1.0

Iron binding site 2 out of 8 in 9efu

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Iron binding site 2 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:113.2
occ:1.00
 FE2 A:SF4501 0.0 113.2 1.0
S4 A:SF4501 2.2 115.1 1.0
S3 A:SF4501 2.2 114.0 1.0
S1 A:SF4501 2.2 108.4 1.0
OD1 B:ASP36 2.4 67.9 1.0
FE3 A:SF4501 2.6 118.7 1.0
FE1 A:SF4501 2.7 123.2 1.0
FE4 A:SF4501 2.7 122.9 1.0
CG B:ASP36 3.5 66.5 1.0
SG A:CYS54 3.8 64.9 1.0
S2 A:SF4501 3.8 110.8 1.0
SG A:CYS115 3.8 60.5 1.0
CG2 A:THR53 3.8 52.1 1.0
SG A:CYS29 3.9 62.6 1.0
OD2 B:ASP36 4.1 68.6 1.0
CG B:PRO33 4.1 75.5 1.0
N B:ASP36 4.5 73.8 1.0
CA B:ASP36 4.6 70.3 1.0
CB B:ASP36 4.6 67.2 1.0
C B:GLY35 4.6 70.9 1.0
O B:GLY35 4.7 72.7 1.0
CB A:THR53 4.8 50.3 1.0
CB A:CYS29 4.9 63.4 1.0
CB A:CYS115 5.0 59.2 1.0

Iron binding site 3 out of 8 in 9efu

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Iron binding site 3 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:118.7
occ:1.00
 FE3 A:SF4501 0.0 118.7 1.0
SG A:CYS54 1.2 64.9 1.0
S1 A:SF4501 2.2 108.4 1.0
S4 A:SF4501 2.3 115.1 1.0
S2 A:SF4501 2.3 110.8 1.0
FE2 A:SF4501 2.6 113.2 1.0
FE1 A:SF4501 2.7 123.2 1.0
FE4 A:SF4501 2.7 122.9 1.0
CB A:CYS54 3.0 53.3 1.0
CA A:CYS54 3.6 49.4 1.0
SG A:CYS115 3.7 60.5 1.0
S3 A:SF4501 3.8 114.0 1.0
N A:CYS54 3.9 54.3 1.0
SG A:CYS29 4.2 62.6 1.0
CD1 A:LEU31 4.4 57.5 1.0
CD A:PRO116 4.5 64.7 1.0
CB A:SER114 4.5 65.3 1.0
N A:CYS115 4.5 55.9 1.0
CB A:CYS115 4.6 59.2 1.0
C A:THR53 4.7 49.8 1.0
CG2 A:THR53 4.7 52.1 1.0
OG A:SER114 4.8 71.4 1.0
OD1 B:ASP36 4.9 67.9 1.0
CB A:THR53 5.0 50.3 1.0

Iron binding site 4 out of 8 in 9efu

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Iron binding site 4 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:122.9
occ:1.00
 FE4 A:SF4501 0.0 122.9 1.0
SG A:CYS115 1.2 60.5 1.0
S3 A:SF4501 2.2 114.0 1.0
S1 A:SF4501 2.3 108.4 1.0
S2 A:SF4501 2.3 110.8 1.0
FE2 A:SF4501 2.7 113.2 1.0
FE3 A:SF4501 2.7 118.7 1.0
FE1 A:SF4501 2.7 123.2 1.0
CB A:CYS115 2.7 59.2 1.0
N A:CYS115 3.6 55.9 1.0
CA A:CYS115 3.8 54.0 1.0
SG A:CYS54 3.8 64.9 1.0
S4 A:SF4501 3.8 115.1 1.0
N A:GLY148 3.9 63.2 1.0
CG B:PRO33 3.9 75.5 1.0
SG A:CYS29 4.1 62.6 1.0
CB B:PRO33 4.4 74.9 1.0
CB A:CYS29 4.5 63.4 1.0
OG1 B:THR96 4.5 91.7 1.0
CD A:PRO116 4.6 64.7 1.0
CA A:GLY148 4.6 67.1 1.0
CA A:SER147 4.7 52.4 1.0
OD1 B:ASP36 4.8 67.9 1.0
C A:SER147 4.8 54.8 1.0
C A:SER114 4.8 60.5 1.0
C A:CYS115 5.0 60.7 1.0

Iron binding site 5 out of 8 in 9efu

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Iron binding site 5 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:126.0
occ:1.00
 FE1 C:SF4501 0.0 126.0 1.0
SG C:CYS29 1.4 58.0 1.0
S2 C:SF4501 2.2 114.2 1.0
S4 C:SF4501 2.3 116.0 1.0
S3 C:SF4501 2.3 113.6 1.0
CB C:CYS29 2.6 64.1 1.0
FE2 C:SF4501 2.7 113.8 1.0
FE4 C:SF4501 2.7 125.7 1.0
FE3 C:SF4501 2.7 123.6 1.0
SG C:CYS54 3.7 62.5 1.0
SG C:CYS115 3.8 63.8 1.0
S1 C:SF4501 3.8 109.0 1.0
CA C:CYS29 4.0 58.3 1.0
OD1 D:ASP36 4.4 74.0 1.0
N C:CYS29 4.4 61.4 1.0
N C:GLY148 4.4 65.0 1.0
CD1 C:LEU31 4.4 56.6 1.0
CG C:LEU31 4.6 54.4 1.0
O D:GLY35 4.7 76.0 1.0
C C:CYS29 4.7 59.4 1.0
C D:GLY35 4.8 75.8 1.0
O C:GLY146 4.8 61.4 1.0
CB C:CYS54 4.9 54.2 1.0
CA C:GLY148 5.0 70.9 1.0

Iron binding site 6 out of 8 in 9efu

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Iron binding site 6 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:113.8
occ:1.00
 FE2 C:SF4501 0.0 113.8 1.0
OD1 D:ASP36 2.0 74.0 1.0
S4 C:SF4501 2.2 116.0 1.0
S3 C:SF4501 2.2 113.6 1.0
S1 C:SF4501 2.2 109.0 1.0
FE3 C:SF4501 2.7 123.6 1.0
FE1 C:SF4501 2.7 126.0 1.0
FE4 C:SF4501 2.7 125.7 1.0
CG D:ASP36 3.1 71.3 1.0
OD2 D:ASP36 3.6 74.6 1.0
S2 C:SF4501 3.8 114.2 1.0
SG C:CYS29 3.8 58.0 1.0
SG C:CYS54 3.8 62.5 1.0
SG C:CYS115 3.9 63.8 1.0
CB D:ASP36 4.2 69.9 1.0
CG2 C:THR53 4.2 53.3 1.0
N D:ASP36 4.3 77.9 1.0
CA D:ASP36 4.3 73.3 1.0
C D:GLY35 4.5 75.8 1.0
CG D:PRO33 4.5 74.4 1.0
O D:GLY35 4.5 76.0 1.0
CB C:CYS29 4.8 64.1 1.0
CB C:THR53 4.9 51.5 1.0

Iron binding site 7 out of 8 in 9efu

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Iron binding site 7 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:123.6
occ:1.00
 FE3 C:SF4501 0.0 123.6 1.0
SG C:CYS54 1.3 62.5 1.0
S1 C:SF4501 2.2 109.0 1.0
S4 C:SF4501 2.3 116.0 1.0
S2 C:SF4501 2.3 114.2 1.0
FE2 C:SF4501 2.7 113.8 1.0
FE4 C:SF4501 2.7 125.7 1.0
FE1 C:SF4501 2.7 126.0 1.0
CB C:CYS54 3.0 54.2 1.0
CA C:CYS54 3.6 52.1 1.0
SG C:CYS115 3.7 63.8 1.0
S3 C:SF4501 3.8 113.6 1.0
N C:CYS54 3.9 55.5 1.0
SG C:CYS29 3.9 58.0 1.0
CD1 C:LEU31 4.3 56.6 1.0
OD1 D:ASP36 4.5 74.0 1.0
CD C:PRO116 4.5 68.5 1.0
N C:CYS115 4.6 62.0 1.0
C C:THR53 4.7 54.6 1.0
CB C:SER114 4.7 65.6 1.0
CB C:CYS115 4.7 64.9 1.0
OG C:SER114 4.9 73.7 1.0

Iron binding site 8 out of 8 in 9efu

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Iron binding site 8 out of 8 in the Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryoem Structure of Bchn-Bchb Electron Acceptor Component Protein of Dpor with Pchlide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:125.7
occ:1.00
 FE4 C:SF4501 0.0 125.7 1.0
SG C:CYS115 1.3 63.8 1.0
S3 C:SF4501 2.2 113.6 1.0
S1 C:SF4501 2.3 109.0 1.0
S2 C:SF4501 2.3 114.2 1.0
FE2 C:SF4501 2.7 113.8 1.0
FE3 C:SF4501 2.7 123.6 1.0
FE1 C:SF4501 2.7 126.0 1.0
CB C:CYS115 2.8 64.9 1.0
N C:CYS115 3.7 62.0 1.0
S4 C:SF4501 3.8 116.0 1.0
SG C:CYS54 3.8 62.5 1.0
CA C:CYS115 3.9 60.5 1.0
N C:GLY148 4.0 65.0 1.0
SG C:CYS29 4.0 58.0 1.0
CG D:PRO33 4.1 74.4 1.0
CB C:CYS29 4.3 64.1 1.0
OG1 D:THR96 4.4 96.1 1.0
OD1 D:ASP36 4.4 74.0 1.0
CD C:PRO116 4.7 68.5 1.0
CA C:GLY148 4.7 70.9 1.0
CA C:SER147 4.7 56.7 1.0
CB D:PRO33 4.8 76.4 1.0
C C:SER147 4.9 59.0 1.0
C C:SER114 4.9 64.5 1.0

Reference:

R.Kashyap, N.Walsh, J.Deveryshetty, M.Tokmina-Lukaszewska, K.Zhao, Y.J.Gan, B.M.Hoffman, R.Sarangi, B.Bothner, B.Bennett, E.Antony. Cryo-Em Captures the Coordination of Asymmetric Electron Transfer Through A Di-Copper Site in Dpor. Nat Commun V. 16 3866 2025.
ISSN: ESSN 2041-1723
PubMed: 40274796
DOI: 10.1038/S41467-025-59158-7
Page generated: Fri Aug 8 04:08:25 2025

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