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Iron in PDB 4kt0: Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803

Enzymatic activity of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803

All present enzymatic activity of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803:
1.97.1.12;

Protein crystallography data

The structure of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803, PDB code: 4kt0 was solved by Y.Mazor, D.Nataf, H.Toporik, N.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.179, 173.308, 179.136, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.5

Other elements in 4kt0:

The structure of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 also contains other interesting chemical elements:

Magnesium (Mg) 92 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 (pdb code 4kt0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803, PDB code: 4kt0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4kt0

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Iron binding site 1 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:85.6
occ:1.00
 FE1 A:SF43001 0.0 85.6 1.0
SG B:CYS556 2.3 50.9 1.0
S3 A:SF43001 2.3 58.3 1.0
S2 A:SF43001 2.3 62.9 1.0
S4 A:SF43001 2.3 50.1 1.0
N A:PRO577 3.6 53.2 1.0
FE4 A:SF43001 3.7 0.4 1.0
FE2 A:SF43001 3.7 84.0 1.0
FE3 A:SF43001 3.7 0.7 1.0
CB B:CYS556 3.8 74.3 1.0
CD A:PRO577 3.8 53.0 1.0
CA A:PRO577 3.8 53.6 1.0
S1 A:SF43001 3.8 50.7 1.0
CD1 B:ILE699 3.9 55.2 1.0
C A:GLY576 3.9 63.8 1.0
CB A:PRO577 4.0 65.6 1.0
SG A:CYS583 4.3 72.2 1.0
CA A:GLY576 4.4 62.2 1.0
CG A:PRO577 4.4 53.4 1.0
O A:GLY576 4.4 71.0 1.0
SG A:CYS574 4.4 67.7 1.0
N B:GLY558 4.7 51.4 1.0
CA B:GLY558 4.7 51.6 1.0
CA B:CYS556 4.9 71.8 1.0

Iron binding site 2 out of 12 in 4kt0

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Iron binding site 2 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:84.0
occ:1.00
 FE2 A:SF43001 0.0 84.0 1.0
SG A:CYS583 2.1 72.2 1.0
S3 A:SF43001 2.3 58.3 1.0
S1 A:SF43001 2.3 50.7 1.0
S4 A:SF43001 2.3 50.1 1.0
CB A:CYS583 2.8 58.6 1.0
CA A:CYS583 3.4 63.8 1.0
CE3 B:TRP664 3.6 49.3 1.0
FE4 A:SF43001 3.7 0.4 1.0
FE1 A:SF43001 3.7 85.6 1.0
FE3 A:SF43001 3.7 0.7 1.0
S2 A:SF43001 3.8 62.9 1.0
SG A:CYS574 4.0 67.7 1.0
CZ3 B:TRP664 4.0 48.6 1.0
CB A:CYS574 4.1 69.9 1.0
N A:CYS583 4.2 78.5 1.0
NH2 A:ARG724 4.3 50.2 1.0
C A:CYS583 4.7 63.8 1.0
SG B:CYS565 4.7 64.1 1.0
CD2 B:TRP664 4.8 70.8 1.0
CD1 B:ILE699 4.8 55.2 1.0

Iron binding site 3 out of 12 in 4kt0

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Iron binding site 3 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:0.7
occ:1.00
 FE3 A:SF43001 0.0 0.7 1.0
SG B:CYS565 2.0 64.1 1.0
S1 A:SF43001 2.3 50.7 1.0
S4 A:SF43001 2.3 50.1 1.0
S2 A:SF43001 2.3 62.9 1.0
CB B:CYS565 2.7 84.8 1.0
CA B:CYS565 2.9 64.8 1.0
N B:CYS565 3.5 65.1 1.0
FE4 A:SF43001 3.7 0.4 1.0
FE1 A:SF43001 3.7 85.6 1.0
FE2 A:SF43001 3.7 84.0 1.0
S3 A:SF43001 3.9 58.3 1.0
CB B:CYS556 3.9 74.3 1.0
SG B:CYS556 4.0 50.9 1.0
C B:THR564 4.2 69.8 1.0
C B:CYS565 4.3 61.4 1.0
CZ3 B:TRP664 4.5 48.6 1.0
O B:THR564 4.5 82.0 1.0
NH1 B:ARG703 4.6 84.8 1.0
N B:ASP566 4.6 69.8 1.0
CD1 A:ILE720 4.7 48.6 1.0

Iron binding site 4 out of 12 in 4kt0

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Iron binding site 4 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:0.4
occ:1.00
 FE4 A:SF43001 0.0 0.4 1.0
SG A:CYS574 2.1 67.7 1.0
S3 A:SF43001 2.3 58.3 1.0
S2 A:SF43001 2.3 62.9 1.0
S1 A:SF43001 2.3 50.7 1.0
CD1 A:ILE720 3.6 48.6 1.0
CB B:PRO559 3.6 50.4 1.0
FE1 A:SF43001 3.7 85.6 1.0
FE2 A:SF43001 3.7 84.0 1.0
CB A:CYS574 3.7 69.9 1.0
FE3 A:SF43001 3.7 0.7 1.0
S4 A:SF43001 3.8 50.1 1.0
N B:PRO559 3.9 72.4 1.0
CA B:PRO559 4.0 61.7 1.0
CD B:PRO559 4.0 51.4 1.0
CG B:PRO559 4.1 51.2 1.0
SG B:CYS565 4.2 64.1 1.0
C B:GLY558 4.4 66.5 1.0
CB A:PRO573 4.6 53.0 1.0
N A:CYS574 4.7 59.5 1.0
CA A:CYS574 4.7 61.0 1.0
N A:GLY576 4.8 71.6 1.0
O B:GLY558 4.8 62.7 1.0
CA A:GLY576 4.9 62.2 1.0
CG1 A:ILE720 4.9 48.0 1.0
CA B:GLY558 4.9 51.6 1.0
SG B:CYS556 5.0 50.9 1.0
CG A:PRO573 5.0 51.9 1.0

Iron binding site 5 out of 12 in 4kt0

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Iron binding site 5 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.7
occ:1.00
 FE1 C:SF43002 0.0 0.7 1.0
SG C:CYS51 2.2 75.9 1.0
S3 C:SF43002 2.3 60.3 1.0
S4 C:SF43002 2.3 61.3 1.0
S2 C:SF43002 2.3 89.7 1.0
N C:CYS51 3.2 70.6 1.0
CB C:CYS51 3.4 81.2 1.0
N C:LYS52 3.4 62.8 1.0
CA C:CYS51 3.6 60.7 1.0
FE2 C:SF43002 3.7 0.7 1.0
FE3 C:SF43002 3.7 94.8 1.0
FE4 C:SF43002 3.7 88.6 1.0
S1 C:SF43002 3.8 60.6 1.0
C C:CYS51 3.9 57.9 1.0
N C:ARG53 4.1 55.5 1.0
CD C:PRO22 4.1 59.8 1.0
C C:GLY50 4.1 64.8 1.0
CG2 C:VAL49 4.2 59.9 1.0
N C:GLY50 4.2 60.2 1.0
CA C:LYS52 4.4 55.1 1.0
CA C:GLY50 4.5 58.1 1.0
CG C:PRO22 4.7 59.8 1.0
CB C:ARG53 4.7 56.3 1.0
C C:LYS52 4.8 55.0 1.0
O C:CYS51 4.9 54.8 1.0
CA C:ARG53 5.0 61.4 1.0

Iron binding site 6 out of 12 in 4kt0

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Iron binding site 6 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.7
occ:1.00
 FE2 C:SF43002 0.0 0.7 1.0
S4 C:SF43002 2.3 61.3 1.0
S1 C:SF43002 2.3 60.6 1.0
S3 C:SF43002 2.3 60.3 1.0
SG C:CYS21 2.3 0.5 1.0
CB C:CYS21 2.8 61.7 1.0
CA C:CYS21 3.4 60.8 1.0
CG2 C:VAL25 3.6 64.3 1.0
FE1 C:SF43002 3.7 0.7 1.0
FE4 C:SF43002 3.7 88.6 1.0
FE3 C:SF43002 3.7 94.8 1.0
S2 C:SF43002 3.8 89.7 1.0
CB C:VAL25 3.9 74.4 1.0
CD C:PRO22 4.1 59.8 1.0
C C:CYS21 4.1 67.1 1.0
N C:PRO22 4.2 61.9 1.0
N C:LEU23 4.4 63.3 1.0
N C:VAL25 4.5 75.2 1.0
N C:CYS21 4.7 60.5 1.0
CB C:LEU23 4.8 64.1 1.0
CA C:VAL25 4.8 71.3 1.0
CG C:LEU26 4.8 71.6 1.0
N C:ASP24 4.9 79.7 1.0
CG1 C:VAL25 4.9 64.9 1.0
CA C:LEU23 5.0 72.4 1.0
CD1 C:LEU26 5.0 61.9 1.0

Iron binding site 7 out of 12 in 4kt0

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Iron binding site 7 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:94.8
occ:1.00
 FE3 C:SF43002 0.0 94.8 1.0
SG C:CYS54 2.3 60.5 1.0
S4 C:SF43002 2.3 61.3 1.0
S1 C:SF43002 2.3 60.6 1.0
S2 C:SF43002 2.3 89.7 1.0
CB C:CYS54 2.8 72.5 1.0
N C:CYS54 3.6 56.8 1.0
FE2 C:SF43002 3.7 0.7 1.0
FE1 C:SF43002 3.7 0.7 1.0
FE4 C:SF43002 3.7 88.6 1.0
CA C:CYS54 3.8 57.3 1.0
S3 C:SF43002 3.8 60.3 1.0
CG2 C:VAL67 3.9 57.9 1.0
CA C:LYS52 4.6 55.1 1.0
N C:ARG53 4.6 55.5 1.0
CD1 C:LEU26 4.6 61.9 1.0
N C:LYS52 4.7 62.8 1.0
C C:LYS52 4.8 55.0 1.0
N C:GLU55 4.8 70.1 1.0
C C:CYS54 4.8 58.3 1.0
C C:ARG53 4.9 68.6 1.0
CD1 C:ILE65 4.9 70.2 1.0

Iron binding site 8 out of 12 in 4kt0

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Iron binding site 8 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:88.6
occ:1.00
 FE4 C:SF43002 0.0 88.6 1.0
SG C:CYS48 2.1 92.9 1.0
S3 C:SF43002 2.3 60.3 1.0
S1 C:SF43002 2.3 60.6 1.0
S2 C:SF43002 2.3 89.7 1.0
CB C:CYS48 3.1 63.1 1.0
CA C:CYS48 3.6 63.4 1.0
FE2 C:SF43002 3.7 0.7 1.0
FE1 C:SF43002 3.7 0.7 1.0
FE3 C:SF43002 3.7 94.8 1.0
N C:GLY50 3.8 60.2 1.0
S4 C:SF43002 3.8 61.3 1.0
N C:VAL49 3.9 68.6 1.0
C C:CYS48 4.1 72.1 1.0
CG2 C:VAL25 4.2 64.3 1.0
CA C:GLY50 4.2 58.1 1.0
CG2 C:VAL5 4.4 61.9 1.0
CB C:VAL25 4.6 74.4 1.0
CG1 C:VAL25 4.6 64.9 1.0
C C:VAL49 4.8 66.6 1.0
CG1 C:VAL67 4.9 58.1 1.0
CG2 C:VAL67 4.9 57.9 1.0
CA C:VAL49 4.9 60.8 1.0
N C:CYS48 4.9 65.0 1.0

Iron binding site 9 out of 12 in 4kt0

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Iron binding site 9 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3003

b:0.6
occ:1.00
 FE1 C:SF43003 0.0 0.6 1.0
S3 C:SF43003 2.3 60.1 1.0
S2 C:SF43003 2.3 61.1 1.0
S4 C:SF43003 2.3 61.2 1.0
SG C:CYS58 2.5 89.6 1.0
CB C:CYS58 3.0 57.0 1.0
CA C:CYS58 3.5 57.0 1.0
FE2 C:SF43003 3.7 81.3 1.0
CD C:PRO59 3.7 66.0 1.0
FE4 C:SF43003 3.7 0.8 1.0
FE3 C:SF43003 3.7 96.1 1.0
S1 C:SF43003 3.8 67.6 1.0
CB C:SER64 3.9 65.2 1.0
N C:PRO59 4.2 75.5 1.0
CG2 C:ILE65 4.3 58.4 1.0
C C:CYS58 4.3 56.6 1.0
N C:SER64 4.3 58.5 1.0
OG C:SER64 4.4 69.8 1.0
N C:ILE65 4.4 59.2 1.0
OG1 C:THR60 4.5 58.6 1.0
CA C:SER64 4.6 70.2 1.0
N C:CYS58 4.7 56.4 1.0
C C:SER64 4.8 70.8 1.0
CG2 C:THR60 4.8 62.0 1.0
CB C:ILE65 4.9 59.5 1.0
CG C:PRO59 4.9 59.1 1.0
N C:THR60 5.0 57.8 1.0

Iron binding site 10 out of 12 in 4kt0

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Iron binding site 10 out of 12 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3003

b:81.3
occ:1.00
 FE2 C:SF43003 0.0 81.3 1.0
SG C:CYS14 2.2 92.6 1.0
S3 C:SF43003 2.3 60.1 1.0
S4 C:SF43003 2.3 61.2 1.0
S1 C:SF43003 2.3 67.6 1.0
N C:CYS14 3.3 64.4 1.0
CB C:CYS14 3.5 91.0 1.0
N C:THR15 3.6 70.7 1.0
FE1 C:SF43003 3.7 0.6 1.0
CA C:CYS14 3.7 64.2 1.0
FE4 C:SF43003 3.7 0.8 1.0
FE3 C:SF43003 3.7 96.1 1.0
C C:CYS14 3.8 64.0 1.0
S2 C:SF43003 3.8 61.1 1.0
N C:GLN16 3.9 73.2 1.0
CD C:PRO59 3.9 66.0 1.0
CB C:GLN16 4.4 71.5 1.0
C C:GLY13 4.4 76.8 1.0
CG C:PRO59 4.5 59.1 1.0
CA C:THR15 4.5 75.2 1.0
N C:GLY13 4.5 65.2 1.0
C C:THR15 4.6 65.0 1.0
CG1 C:ILE12 4.6 62.9 1.0
O C:CYS14 4.7 63.9 1.0
CA C:GLN16 4.7 69.1 1.0
CA C:GLY13 4.7 65.9 1.0
N C:CYS17 4.7 60.5 1.0

Reference:

Y.Mazor, D.Nataf, H.Toporik, N.Nelson. Crystal Structures of Virus-Like Photosystem I Complexes From the Mesophilic Cyanobacterium Synechocystis Pcc 6803. Elife V. 3 01496 2014.
ISSN: ESSN 2050-084X
PubMed: 24473073
DOI: 10.7554/ELIFE.01496
Page generated: Mon Aug 5 05:35:50 2024

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