Iron in PDB 7c52: Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip

Protein crystallography data

The structure of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip, PDB code: 7c52 was solved by L.-J.Yu, Z.-Y.Wang-Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 2.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.435, 183.335, 123.857, 90, 112.58, 90
R / Rfree (%) 21.9 / 24.8

Other elements in 7c52:

The structure of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip also contains other interesting chemical elements:

Magnesium (Mg) 36 atoms
Calcium (Ca) 17 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip (pdb code 7c52). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip, PDB code: 7c52:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7c52

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Iron binding site 1 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:106.0
occ:1.00
FE C:HEM501 0.0 106.0 1.0
ND C:HEM501 1.9 105.1 1.0
NA C:HEM501 2.0 108.4 1.0
NC C:HEM501 2.1 100.8 1.0
NE2 C:HIS111 2.1 110.1 1.0
NB C:HEM501 2.1 106.7 1.0
SD C:MET94 2.3 104.2 1.0
C4D C:HEM501 2.9 105.4 1.0
CE1 C:HIS111 2.9 111.2 1.0
C1D C:HEM501 3.0 102.9 1.0
C1A C:HEM501 3.0 109.8 1.0
C4C C:HEM501 3.0 99.4 1.0
C1B C:HEM501 3.1 108.9 1.0
C4A C:HEM501 3.1 111.4 1.0
C1C C:HEM501 3.1 100.4 1.0
C4B C:HEM501 3.1 106.7 1.0
CD2 C:HIS111 3.1 111.4 1.0
CHA C:HEM501 3.3 108.2 1.0
CG C:MET94 3.4 106.6 1.0
CHD C:HEM501 3.4 99.5 1.0
CE C:MET94 3.4 104.5 1.0
CHB C:HEM501 3.4 111.8 1.0
CHC C:HEM501 3.6 103.4 1.0
ND1 C:HIS111 4.1 112.5 1.0
C2A C:HEM501 4.2 113.1 1.0
C3D C:HEM501 4.2 105.6 1.0
C2D C:HEM501 4.2 103.1 1.0
C3A C:HEM501 4.2 112.7 1.0
CB C:MET94 4.2 106.7 1.0
CG C:HIS111 4.2 114.1 1.0
C3C C:HEM501 4.3 99.8 1.0
C2B C:HEM501 4.3 108.1 1.0
C3B C:HEM501 4.3 108.7 1.0
C2C C:HEM501 4.3 99.2 1.0

Iron binding site 2 out of 9 in 7c52

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Iron binding site 2 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:86.9
occ:1.00
FE C:HEM502 0.0 86.9 1.0
ND C:HEM502 2.0 85.8 1.0
NA C:HEM502 2.0 89.3 1.0
NE2 C:HIS156 2.0 88.5 1.0
NC C:HEM502 2.1 84.2 1.0
NB C:HEM502 2.1 88.0 1.0
SD C:MET130 2.3 104.9 1.0
CE1 C:HIS156 2.7 89.9 1.0
C4D C:HEM502 2.9 86.0 1.0
C1D C:HEM502 2.9 86.3 1.0
C1A C:HEM502 3.0 87.7 1.0
C4C C:HEM502 3.0 84.8 1.0
C4A C:HEM502 3.1 94.0 1.0
C1B C:HEM502 3.1 92.6 1.0
C4B C:HEM502 3.1 87.8 1.0
C1C C:HEM502 3.1 85.1 1.0
CD2 C:HIS156 3.3 88.7 1.0
CG C:MET130 3.3 103.7 1.0
CHA C:HEM502 3.4 85.3 1.0
CHD C:HEM502 3.4 87.2 1.0
CE C:MET130 3.4 105.5 1.0
CHB C:HEM502 3.5 95.6 1.0
CHC C:HEM502 3.5 86.9 1.0
ND1 C:HIS156 3.9 89.0 1.0
C2A C:HEM502 4.1 92.4 1.0
C3A C:HEM502 4.2 94.6 1.0
C2D C:HEM502 4.2 86.7 1.0
C3D C:HEM502 4.2 88.3 1.0
CB C:MET130 4.2 99.9 1.0
CG C:HIS156 4.2 88.1 1.0
C3C C:HEM502 4.3 81.5 1.0
C2B C:HEM502 4.3 91.8 1.0
C3B C:HEM502 4.3 92.2 1.0
C2C C:HEM502 4.3 82.8 1.0
CG C:PRO162 5.0 98.0 1.0

Iron binding site 3 out of 9 in 7c52

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Iron binding site 3 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe503

b:75.1
occ:1.00
FE C:HEM503 0.0 75.1 1.0
ND C:HEM503 1.9 82.8 1.0
NA C:HEM503 2.0 77.1 1.0
NE2 C:HIS251 2.0 73.8 1.0
NC C:HEM503 2.1 77.4 1.0
NB C:HEM503 2.1 77.3 1.0
SD C:MET236 2.3 80.1 1.0
CD2 C:HIS251 2.9 72.7 1.0
C4D C:HEM503 2.9 86.0 1.0
C1D C:HEM503 2.9 84.6 1.0
C1A C:HEM503 3.0 80.4 1.0
C4C C:HEM503 3.0 81.6 1.0
C4A C:HEM503 3.0 80.1 1.0
C4B C:HEM503 3.1 80.7 1.0
C1B C:HEM503 3.1 79.8 1.0
CE1 C:HIS251 3.1 74.3 1.0
C1C C:HEM503 3.1 81.5 1.0
CE C:MET236 3.3 83.0 1.0
CG C:MET236 3.3 79.0 1.0
CHA C:HEM503 3.4 85.1 1.0
CHD C:HEM503 3.4 83.7 1.0
CHB C:HEM503 3.5 81.0 1.0
CHC C:HEM503 3.5 83.3 1.0
CG C:HIS251 4.1 74.1 1.0
ND1 C:HIS251 4.2 74.3 1.0
C2A C:HEM503 4.2 78.4 1.0
C3D C:HEM503 4.2 89.7 1.0
C2D C:HEM503 4.2 88.2 1.0
C3A C:HEM503 4.2 76.9 1.0
CB C:MET236 4.2 77.1 1.0
C3C C:HEM503 4.3 80.7 1.0
C2C C:HEM503 4.3 80.2 1.0
C2B C:HEM503 4.3 82.1 1.0
C3B C:HEM503 4.3 79.8 1.0

Iron binding site 4 out of 9 in 7c52

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Iron binding site 4 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe504

b:77.4
occ:1.00
FE C:HEM504 0.0 77.4 1.0
ND C:HEM504 1.9 77.3 1.0
NA C:HEM504 2.0 75.0 1.0
NE2 C:HIS311 2.0 80.3 1.0
NE2 C:HIS144 2.0 81.6 1.0
NC C:HEM504 2.1 77.1 1.0
NB C:HEM504 2.1 76.0 1.0
C4D C:HEM504 2.9 78.8 1.0
CE1 C:HIS144 2.9 80.7 1.0
C1D C:HEM504 2.9 79.4 1.0
C1A C:HEM504 3.0 75.8 1.0
CD2 C:HIS311 3.0 80.3 1.0
CE1 C:HIS311 3.0 79.6 1.0
C4C C:HEM504 3.0 79.6 1.0
C4A C:HEM504 3.0 79.1 1.0
C1B C:HEM504 3.1 79.2 1.0
C4B C:HEM504 3.1 78.2 1.0
C1C C:HEM504 3.1 77.9 1.0
CD2 C:HIS144 3.1 81.4 1.0
CHA C:HEM504 3.3 78.0 1.0
CHD C:HEM504 3.4 81.0 1.0
CHB C:HEM504 3.5 82.2 1.0
CHC C:HEM504 3.5 78.0 1.0
ND1 C:HIS144 4.1 81.0 1.0
ND1 C:HIS311 4.1 80.3 1.0
CG C:HIS311 4.2 79.5 1.0
C2A C:HEM504 4.2 77.4 1.0
C3D C:HEM504 4.2 82.1 1.0
C2D C:HEM504 4.2 82.5 1.0
CG C:HIS144 4.2 82.0 1.0
C3A C:HEM504 4.2 80.4 1.0
C3C C:HEM504 4.2 81.8 1.0
C2C C:HEM504 4.3 79.4 1.0
C2B C:HEM504 4.3 77.7 1.0
C3B C:HEM504 4.3 79.3 1.0
CB C:ALA272 4.5 83.5 1.0

Iron binding site 5 out of 9 in 7c52

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Iron binding site 5 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe403

b:75.6
occ:1.00
NE2 L:HIS199 2.1 82.2 1.0
NE2 M:HIS219 2.2 79.4 1.0
NE2 M:HIS266 2.2 83.9 1.0
NE2 L:HIS239 2.2 88.6 1.0
OE2 M:GLU234 2.2 86.4 1.0
OE1 M:GLU234 2.2 85.5 1.0
CD M:GLU234 2.5 85.7 1.0
CE1 M:HIS219 2.9 79.3 1.0
CE1 L:HIS199 3.1 81.5 1.0
CE1 L:HIS239 3.1 90.5 1.0
CE1 M:HIS266 3.1 83.7 1.0
CD2 M:HIS266 3.2 82.7 1.0
CD2 L:HIS199 3.2 81.1 1.0
CD2 L:HIS239 3.2 89.5 1.0
CD2 M:HIS219 3.3 78.6 1.0
CG M:GLU234 4.0 85.0 1.0
ND1 M:HIS219 4.1 79.2 1.0
ND1 L:HIS199 4.2 81.3 1.0
ND1 M:HIS266 4.2 81.7 1.0
ND1 L:HIS239 4.2 89.8 1.0
CG M:HIS266 4.3 81.6 1.0
CG L:HIS199 4.3 81.8 1.0
CG L:HIS239 4.3 87.3 1.0
CG M:HIS219 4.3 78.4 1.0
CG1 M:ILE223 4.5 74.5 1.0
CG1 L:ILE203 4.6 66.3 1.0
CB M:GLU234 4.9 87.2 1.0

Iron binding site 6 out of 9 in 7c52

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Iron binding site 6 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe101

b:162.1
occ:0.90
FE1 b:SF4101 0.0 162.1 0.9
S2 b:SF4101 2.3 195.0 0.9
S4 b:SF4101 2.3 152.5 0.9
S3 b:SF4101 2.3 157.0 0.9
FE4 b:SF4101 2.7 136.2 0.9
FE2 b:SF4101 2.7 142.8 0.9
FE3 b:SF4101 2.7 123.2 0.9
SG b:CYS43 2.8 173.2 0.9
CB b:CYS43 3.6 177.4 0.9
CA b:CYS43 3.8 178.3 0.9
S1 b:SF4101 3.9 192.8 0.9
N b:CYS43 4.6 183.1 0.9
CA b:TRP74 4.7 147.1 0.9
N b:CYS75 4.7 151.0 0.9
CB b:CYS46 4.8 164.0 0.9
CG1 b:ILE69 4.8 149.6 0.9
N b:TRP74 4.9 147.3 0.9
C b:TRP74 4.9 148.2 0.9
O b:GLY73 4.9 152.3 0.9
CE1 b:TYR19 4.9 153.6 0.9
C b:GLY73 5.0 151.5 0.9
C b:CYS43 5.0 176.6 0.9

Iron binding site 7 out of 9 in 7c52

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Iron binding site 7 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe101

b:142.8
occ:0.90
FE2 b:SF4101 0.0 142.8 0.9
S3 b:SF4101 2.3 157.0 0.9
S1 b:SF4101 2.3 192.8 0.9
S4 b:SF4101 2.3 152.5 0.9
FE4 b:SF4101 2.7 136.2 0.9
FE1 b:SF4101 2.7 162.1 0.9
FE3 b:SF4101 2.7 123.2 0.9
SG b:CYS46 2.7 153.0 0.9
CB b:CYS46 3.2 164.0 0.9
S2 b:SF4101 3.9 195.0 0.9
CB b:PHE48 4.4 148.8 0.9
CA b:TRP78 4.5 151.0 0.9
CD2 b:PHE48 4.6 137.4 0.9
O b:SER77 4.6 150.7 0.9
CD1 b:TRP78 4.7 166.8 0.9
CA b:CYS46 4.7 171.9 0.9
N b:PHE48 4.9 159.1 0.9
C b:SER77 5.0 151.5 0.9

Iron binding site 8 out of 9 in 7c52

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Iron binding site 8 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe101

b:123.2
occ:0.90
FE3 b:SF4101 0.0 123.2 0.9
S2 b:SF4101 2.3 195.0 0.9
S4 b:SF4101 2.3 152.5 0.9
S1 b:SF4101 2.3 192.8 0.9
FE4 b:SF4101 2.7 136.2 0.9
FE1 b:SF4101 2.7 162.1 0.9
FE2 b:SF4101 2.7 142.8 0.9
SG b:CYS61 2.8 138.5 0.9
CB b:CYS61 3.7 142.5 0.9
S3 b:SF4101 3.9 157.0 0.9
CB b:PHE48 4.4 148.8 0.9
CG1 b:ILE69 4.7 149.6 0.9
O b:PHE48 4.8 152.3 0.9
C b:PHE48 4.8 153.3 0.9
CE2 b:PHE64 4.8 131.3 0.9
CA b:CYS61 4.8 144.3 0.9
CD2 b:PHE64 4.9 131.8 0.9
CG b:LEU63 4.9 126.9 0.9
CD1 b:LEU63 4.9 127.8 0.9

Iron binding site 9 out of 9 in 7c52

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Iron binding site 9 out of 9 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe101

b:136.2
occ:0.90
FE4 b:SF4101 0.0 136.2 0.9
S2 b:SF4101 2.3 195.0 0.9
S3 b:SF4101 2.3 157.0 0.9
S1 b:SF4101 2.3 192.8 0.9
SG b:CYS75 2.7 142.9 0.9
FE2 b:SF4101 2.7 142.8 0.9
FE1 b:SF4101 2.7 162.1 0.9
FE3 b:SF4101 2.7 123.2 0.9
CB b:CYS75 3.6 147.6 0.9
S4 b:SF4101 3.9 152.5 0.9
N b:CYS75 3.9 151.0 0.9
CA b:CYS75 4.2 151.9 0.9
O b:CYS75 4.6 157.3 0.9
C b:CYS75 4.6 156.0 0.9
C b:TRP74 4.7 148.2 0.9
CD1 b:LEU63 4.7 127.8 0.9
CE2 b:PHE64 4.8 131.3 0.9
CD1 b:TYR19 5.0 153.8 0.9
CB b:SER77 5.0 154.9 0.9
C b:SER77 5.0 151.5 0.9

Reference:

T.Kawakami, L.J.Yu, T.Liang, K.Okazaki, M.T.Madigan, Y.Kimura, Z.Y.Wang-Otomo. Crystal Structure of A Photosynthetic LH1-Rc in Complex with Its Electron Donor Hipip. Nat Commun V. 12 1104 2021.
ISSN: ESSN 2041-1723
PubMed: 33597527
DOI: 10.1038/S41467-021-21397-9
Page generated: Sat Apr 3 15:52:43 2021

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