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Iron in PDB 8h2u: X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.

Enzymatic activity of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.

All present enzymatic activity of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.:
1.97.1.12;

Protein crystallography data

The structure of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii., PDB code: 8h2u was solved by H.Tanaka, H.Kubota-Kawai, Y.Misumi, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.74 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 194.57, 98.12, 210.13, 90, 94.56, 90
R / Rfree (%) 29.1 / 35.9

Other elements in 8h2u:

The structure of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. also contains other interesting chemical elements:

Magnesium (Mg) 211 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. (pdb code 8h2u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii., PDB code: 8h2u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 8h2u

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Iron binding site 1 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe841

b:131.5
occ:1.00
 FE1 A:SF4841 0.0 131.5 1.0
S4 A:SF4841 2.1 119.7 1.0
S2 A:SF4841 2.1 116.5 1.0
S3 A:SF4841 2.1 110.9 1.0
SG B:CYS569 2.3 141.4 1.0
CB B:CYS569 2.9 138.8 1.0
FE4 A:SF4841 3.1 116.2 1.0
FE2 A:SF4841 3.1 120.6 1.0
FE3 A:SF4841 3.1 121.6 1.0
CA B:CYS569 3.4 138.7 1.0
N B:CYS569 3.6 135.8 1.0
S1 A:SF4841 3.7 124.9 1.0
CD1 A:ILE720 4.2 145.4 1.0
CB B:CYS560 4.4 152.7 1.0
C B:THR568 4.6 143.8 1.0
SG B:CYS560 4.7 160.3 1.0
C B:CYS569 4.8 139.6 1.0
CG1 A:ILE720 4.9 147.2 1.0
SG A:CYS575 4.9 145.9 1.0
CG2 A:ILE720 4.9 151.5 1.0
N B:THR568 5.0 156.8 1.0

Iron binding site 2 out of 12 in 8h2u

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Iron binding site 2 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe841

b:120.6
occ:1.00
 FE2 A:SF4841 0.0 120.6 1.0
SG A:CYS584 2.0 157.1 1.0
S1 A:SF4841 2.1 124.9 1.0
S3 A:SF4841 2.1 110.9 1.0
S4 A:SF4841 2.1 119.7 1.0
FE4 A:SF4841 3.1 116.2 1.0
FE1 A:SF4841 3.1 131.5 1.0
FE3 A:SF4841 3.2 121.6 1.0
CB A:CYS584 3.2 147.1 1.0
SG A:CYS575 3.7 145.9 1.0
CA A:CYS584 3.7 148.7 1.0
S2 A:SF4841 3.7 116.5 1.0
N A:CYS584 4.2 154.8 1.0
CD1 B:ILE703 4.4 139.7 1.0
CB A:CYS575 4.7 146.1 1.0
CE3 B:TRP668 4.8 198.3 1.0
C A:THR583 4.9 159.8 1.0
CG1 B:ILE703 5.0 141.5 1.0

Iron binding site 3 out of 12 in 8h2u

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Iron binding site 3 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe841

b:121.6
occ:1.00
 FE3 A:SF4841 0.0 121.6 1.0
S2 A:SF4841 2.1 116.5 1.0
S1 A:SF4841 2.1 124.9 1.0
S4 A:SF4841 2.1 119.7 1.0
CB A:CYS575 3.0 146.1 1.0
SG A:CYS575 3.0 145.9 1.0
FE4 A:SF4841 3.1 116.2 1.0
FE1 A:SF4841 3.1 131.5 1.0
FE2 A:SF4841 3.2 120.6 1.0
S3 A:SF4841 3.8 110.9 1.0
N A:GLY577 4.3 177.8 1.0
CA A:CYS575 4.4 154.3 1.0
CA A:GLY577 4.4 179.3 1.0
CB B:PRO563 4.5 160.5 1.0
N B:PRO563 4.6 165.0 1.0
CD1 A:ILE720 4.6 145.4 1.0
SG B:CYS560 4.7 160.3 1.0
C A:GLY577 4.7 178.7 1.0
CA B:PRO563 4.7 162.4 1.0
C B:GLY562 4.8 160.5 1.0
O A:GLY577 4.8 179.7 1.0
N A:CYS575 4.9 157.6 1.0
SG A:CYS584 4.9 157.1 1.0
CD B:PRO563 4.9 166.6 1.0
SG B:CYS569 4.9 141.4 1.0
O B:GLY562 4.9 168.3 1.0
C A:CYS575 5.0 159.9 1.0

Iron binding site 4 out of 12 in 8h2u

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Iron binding site 4 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe841

b:116.2
occ:1.00
 FE4 A:SF4841 0.0 116.2 1.0
S3 A:SF4841 2.1 110.9 1.0
S1 A:SF4841 2.1 124.9 1.0
S2 A:SF4841 2.1 116.5 1.0
SG B:CYS560 2.2 160.3 1.0
CB B:CYS560 2.9 152.7 1.0
FE1 A:SF4841 3.1 131.5 1.0
FE2 A:SF4841 3.1 120.6 1.0
FE3 A:SF4841 3.1 121.6 1.0
S4 A:SF4841 3.6 119.7 1.0
CA B:CYS560 4.2 146.2 1.0
N B:CYS560 4.4 141.3 1.0
N A:PRO578 4.4 179.2 1.0
CD1 B:ILE703 4.5 139.7 1.0
C A:GLY577 4.6 178.7 1.0
CB A:PRO578 4.6 180.0 1.0
SG A:CYS584 4.6 157.1 1.0
C B:PRO559 4.6 144.5 1.0
CD A:PRO578 4.7 181.7 1.0
O B:PRO559 4.7 155.7 1.0
CA A:PRO578 4.7 182.1 1.0
CB B:PRO559 4.8 144.4 1.0
N B:GLY562 4.9 144.7 1.0
O A:GLY577 5.0 179.7 1.0
C B:CYS560 5.0 144.3 1.0

Iron binding site 5 out of 12 in 8h2u

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Iron binding site 5 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:158.7
occ:1.00
 FE1 C:SF41001 0.0 158.7 1.0
S3 C:SF41001 2.1 146.0 1.0
S4 C:SF41001 2.1 148.0 1.0
S2 C:SF41001 2.1 145.8 1.0
SG C:CYS51 2.6 175.8 1.0
FE4 C:SF41001 3.1 147.1 1.0
FE2 C:SF41001 3.1 147.2 1.0
FE3 C:SF41001 3.1 146.7 1.0
N C:CYS51 3.3 176.0 1.0
N C:LYS52 3.4 179.2 1.0
S1 C:SF41001 3.7 136.8 1.0
CB C:CYS51 3.8 168.6 1.0
CA C:CYS51 3.9 172.5 1.0
C C:CYS51 4.0 176.2 1.0
N C:ARG53 4.1 159.3 1.0
CD C:PRO22 4.1 152.0 1.0
N C:GLY50 4.2 183.1 1.0
C C:GLY50 4.2 174.1 1.0
CA C:LYS52 4.3 180.2 1.0
CG C:PRO22 4.4 157.3 1.0
CA C:GLY50 4.5 178.7 1.0
CG1 C:VAL49 4.5 176.5 1.0
C C:LYS52 4.7 169.9 1.0
N C:CYS54 4.9 160.9 1.0
CB C:ARG53 4.9 156.6 1.0
O C:CYS51 5.0 182.7 1.0

Iron binding site 6 out of 12 in 8h2u

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Iron binding site 6 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:147.2
occ:1.00
 FE2 C:SF41001 0.0 147.2 1.0
S4 C:SF41001 2.1 148.0 1.0
S1 C:SF41001 2.1 136.8 1.0
S3 C:SF41001 2.1 146.0 1.0
SG C:CYS21 2.4 150.2 1.0
FE1 C:SF41001 3.1 158.7 1.0
FE3 C:SF41001 3.1 146.7 1.0
FE4 C:SF41001 3.2 147.1 1.0
CB C:CYS21 3.3 144.0 1.0
S2 C:SF41001 3.7 145.8 1.0
CG2 C:VAL25 3.8 189.8 1.0
CD C:PRO22 3.8 152.0 1.0
CA C:CYS21 4.0 142.6 1.0
CB C:VAL25 4.1 186.0 1.0
N C:PRO22 4.6 149.2 1.0
C C:CYS21 4.7 146.0 1.0
CG C:PRO22 4.8 157.3 1.0
N C:LEU23 4.8 167.6 1.0
N C:VAL25 4.8 185.0 1.0

Iron binding site 7 out of 12 in 8h2u

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Iron binding site 7 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:146.7
occ:1.00
 FE3 C:SF41001 0.0 146.7 1.0
S1 C:SF41001 2.1 136.8 1.0
S2 C:SF41001 2.1 145.8 1.0
S4 C:SF41001 2.1 148.0 1.0
SG C:CYS54 2.7 178.1 1.0
CB C:CYS54 3.1 170.8 1.0
FE4 C:SF41001 3.1 147.1 1.0
FE2 C:SF41001 3.1 147.2 1.0
FE1 C:SF41001 3.1 158.7 1.0
S3 C:SF41001 3.7 146.0 1.0
CG2 C:VAL67 3.8 128.8 1.0
N C:CYS54 4.1 160.9 1.0
CA C:CYS54 4.2 167.3 1.0
N C:LYS52 4.7 179.2 1.0
CA C:LYS52 4.8 180.2 1.0
CG2 C:VAL5 4.8 172.7 1.0
N C:ARG53 4.9 159.3 1.0
CG1 C:VAL5 4.9 169.2 1.0
SG C:CYS48 5.0 180.8 1.0

Iron binding site 8 out of 12 in 8h2u

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Iron binding site 8 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:147.1
occ:1.00
 FE4 C:SF41001 0.0 147.1 1.0
S2 C:SF41001 2.1 145.8 1.0
S1 C:SF41001 2.1 136.8 1.0
S3 C:SF41001 2.1 146.0 1.0
SG C:CYS48 2.4 180.8 1.0
FE3 C:SF41001 3.1 146.7 1.0
FE1 C:SF41001 3.1 158.7 1.0
FE2 C:SF41001 3.2 147.2 1.0
CB C:CYS48 3.5 182.6 1.0
N C:GLY50 3.5 183.1 1.0
N C:VAL49 3.6 180.0 1.0
S4 C:SF41001 3.7 148.0 1.0
CA C:CYS48 3.7 183.5 1.0
CA C:GLY50 4.0 178.7 1.0
C C:CYS48 4.0 182.2 1.0
CG2 C:VAL25 4.2 189.8 1.0
CG2 C:VAL5 4.3 172.7 1.0
C C:VAL49 4.5 181.3 1.0
N C:CYS51 4.6 176.0 1.0
CA C:VAL49 4.6 180.2 1.0
C C:GLY50 4.8 174.1 1.0
CB C:VAL25 4.8 186.0 1.0
CG1 C:VAL67 4.9 144.1 1.0

Iron binding site 9 out of 12 in 8h2u

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Iron binding site 9 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1002

b:161.1
occ:1.00
 FE1 C:SF41002 0.0 161.1 1.0
S4 C:SF41002 2.1 158.0 1.0
S3 C:SF41002 2.1 147.9 1.0
S2 C:SF41002 2.1 157.3 1.0
OG C:SER64 2.9 168.8 1.0
SG C:CYS58 3.0 188.6 1.0
FE2 C:SF41002 3.1 154.8 1.0
FE4 C:SF41002 3.1 143.1 1.0
FE3 C:SF41002 3.2 149.6 1.0
CB C:CYS58 3.5 170.3 1.0
S1 C:SF41002 3.7 148.9 1.0
CD C:PRO59 4.0 177.4 1.0
CA C:CYS58 4.0 161.6 1.0
CG2 C:VAL65 4.0 152.1 1.0
CB C:SER64 4.3 157.0 1.0
OG1 C:THR60 4.3 156.5 1.0
SG C:CYS17 4.6 157.2 1.0
N C:SER64 4.6 159.2 1.0
CG2 C:THR60 4.6 161.7 1.0
N C:VAL65 4.6 148.9 1.0
C C:SER64 4.7 159.2 1.0
SG C:CYS14 4.8 194.4 1.0
CA C:SER64 4.8 158.4 1.0
N C:PRO59 4.8 172.0 1.0
C C:CYS58 4.8 162.8 1.0
SG C:CYS11 4.9 165.0 1.0
CB C:CYS17 5.0 160.2 1.0

Iron binding site 10 out of 12 in 8h2u

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Iron binding site 10 out of 12 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1002

b:154.8
occ:1.00
 FE2 C:SF41002 0.0 154.8 1.0
SG C:CYS17 1.6 157.2 1.0
S4 C:SF41002 2.1 158.0 1.0
S1 C:SF41002 2.1 148.9 1.0
S3 C:SF41002 2.1 147.9 1.0
CB C:CYS17 2.9 160.2 1.0
FE1 C:SF41002 3.1 161.1 1.0
FE3 C:SF41002 3.1 149.6 1.0
FE4 C:SF41002 3.1 143.1 1.0
S2 C:SF41002 3.7 157.3 1.0
CG2 C:VAL65 3.8 152.1 1.0
N C:CYS17 3.8 174.6 1.0
CB C:ALA40 3.9 179.6 1.0
CA C:CYS17 3.9 171.9 1.0
N C:VAL18 4.7 174.6 1.0
C C:CYS17 4.7 176.1 1.0
N C:GLN16 4.8 173.0 1.0
SG C:CYS11 4.9 165.0 1.0
N C:THR15 4.9 160.9 1.0

Reference:

C.Gerle, Y.Misumi, A.Kawamoto, H.Tanaka, H.Kawai-Kubota, R.Tokutsu, E.Kim, D.Chorev, K.Abe, C.V.Robinson, K.Mitsuoka, J.Minagawa, G.Kurisu. Three Structures of Psi-Lhci From Chlamydomonas Reinhardtii Suggest A Resting State Re-Activated By Ferredoxin. Biochim Biophys Acta 48986 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 37270022
DOI: 10.1016/J.BBABIO.2023.148986
Page generated: Sat Aug 10 05:08:07 2024

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