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Iron in PDB 1kib: Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell

Protein crystallography data

The structure of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell, PDB code: 1kib was solved by C.A.Kerfeld, M.R.Sawaya, D.Krogmann, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group I 41 3 2 3
Cell size a, b, c (Å), α, β, γ (°) 237.000, 237.000, 237.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 22.3

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell (pdb code 1kib). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell, PDB code: 1kib:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1kib

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Iron binding site 1 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe90

b:29.6
occ:1.00
FE A:HEM90 0.0 29.6 1.0
NA A:HEM90 1.9 30.1 1.0
NB A:HEM90 1.9 28.9 1.0
NC A:HEM90 1.9 29.5 1.0
ND A:HEM90 1.9 31.4 1.0
NE2 A:HIS18 2.0 30.7 1.0
SD A:MET62 2.4 22.9 1.0
C1C A:HEM90 2.9 29.3 1.0
CD2 A:HIS18 2.9 32.1 1.0
C4A A:HEM90 2.9 29.7 1.0
C1B A:HEM90 3.0 28.0 1.0
C4B A:HEM90 3.0 29.3 1.0
C1A A:HEM90 3.0 30.1 1.0
C4C A:HEM90 3.0 29.9 1.0
C1D A:HEM90 3.0 31.9 1.0
C4D A:HEM90 3.0 32.2 1.0
CE1 A:HIS18 3.0 32.1 1.0
CHC A:HEM90 3.3 29.3 1.0
CHB A:HEM90 3.3 28.2 1.0
CG A:MET62 3.3 24.1 1.0
CHD A:HEM90 3.4 30.9 1.0
CHA A:HEM90 3.4 30.2 1.0
CE A:MET62 3.5 19.4 1.0
CG A:HIS18 4.1 34.3 1.0
ND1 A:HIS18 4.1 33.4 1.0
C2C A:HEM90 4.2 29.9 1.0
C2B A:HEM90 4.2 28.7 1.0
C3A A:HEM90 4.2 30.1 1.0
C2A A:HEM90 4.2 31.1 1.0
C2D A:HEM90 4.2 32.9 1.0
C3C A:HEM90 4.2 30.9 1.0
C3B A:HEM90 4.2 29.1 1.0
C3D A:HEM90 4.2 34.0 1.0
CB A:MET62 4.2 26.7 1.0

Iron binding site 2 out of 8 in 1kib

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Iron binding site 2 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe90

b:29.6
occ:1.00
FE B:HEM90 0.0 29.6 1.0
ND B:HEM90 1.9 31.4 1.0
NA B:HEM90 1.9 30.1 1.0
NC B:HEM90 1.9 29.5 1.0
NB B:HEM90 2.0 28.9 1.0
NE2 B:HIS18 2.0 30.7 1.0
SD B:MET62 2.3 22.9 1.0
CD2 B:HIS18 2.9 32.1 1.0
C4D B:HEM90 2.9 32.2 1.0
C1A B:HEM90 2.9 30.1 1.0
C1D B:HEM90 2.9 31.9 1.0
C4A B:HEM90 3.0 29.7 1.0
C4C B:HEM90 3.0 29.9 1.0
C1C B:HEM90 3.0 29.3 1.0
CE1 B:HIS18 3.0 32.1 1.0
C1B B:HEM90 3.0 28.0 1.0
C4B B:HEM90 3.0 29.3 1.0
CHA B:HEM90 3.4 30.2 1.0
CHD B:HEM90 3.4 30.9 1.0
CG B:MET62 3.4 24.1 1.0
CHB B:HEM90 3.4 28.2 1.0
CHC B:HEM90 3.4 29.3 1.0
CE B:MET62 3.4 19.4 1.0
ND1 B:HIS18 4.1 33.4 1.0
CG B:HIS18 4.1 34.3 1.0
C2A B:HEM90 4.2 31.1 1.0
C2D B:HEM90 4.2 32.9 1.0
C2C B:HEM90 4.2 29.9 1.0
C3D B:HEM90 4.2 34.0 1.0
C3A B:HEM90 4.2 30.1 1.0
C3C B:HEM90 4.2 30.9 1.0
C2B B:HEM90 4.2 28.7 1.0
CB B:MET62 4.2 26.7 1.0
C3B B:HEM90 4.3 29.1 1.0

Iron binding site 3 out of 8 in 1kib

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Iron binding site 3 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe90

b:29.6
occ:1.00
FE C:HEM90 0.0 29.6 1.0
NA C:HEM90 1.9 30.1 1.0
ND C:HEM90 1.9 31.4 1.0
NC C:HEM90 2.0 29.5 1.0
NB C:HEM90 2.0 28.9 1.0
NE2 C:HIS18 2.0 30.7 1.0
SD C:MET62 2.4 22.9 1.0
CD2 C:HIS18 2.9 32.1 1.0
C4A C:HEM90 3.0 29.7 1.0
C1A C:HEM90 3.0 30.1 1.0
C1D C:HEM90 3.0 31.9 1.0
C4D C:HEM90 3.0 32.2 1.0
C1B C:HEM90 3.0 28.0 1.0
CE1 C:HIS18 3.0 32.1 1.0
C1C C:HEM90 3.0 29.3 1.0
C4C C:HEM90 3.0 29.9 1.0
C4B C:HEM90 3.0 29.3 1.0
CHB C:HEM90 3.4 28.2 1.0
CHA C:HEM90 3.4 30.2 1.0
CHC C:HEM90 3.4 29.3 1.0
CHD C:HEM90 3.4 30.9 1.0
CG C:MET62 3.4 24.1 1.0
CE C:MET62 3.4 19.4 1.0
ND1 C:HIS18 4.1 33.4 1.0
CG C:HIS18 4.1 34.3 1.0
C2A C:HEM90 4.2 31.1 1.0
C2C C:HEM90 4.2 29.9 1.0
C2B C:HEM90 4.2 28.7 1.0
C3A C:HEM90 4.2 30.1 1.0
C2D C:HEM90 4.2 32.9 1.0
C3D C:HEM90 4.2 34.0 1.0
C3C C:HEM90 4.2 30.9 1.0
CB C:MET62 4.2 26.7 1.0
C3B C:HEM90 4.2 29.1 1.0

Iron binding site 4 out of 8 in 1kib

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Iron binding site 4 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe90

b:29.6
occ:1.00
FE D:HEM90 0.0 29.6 1.0
NA D:HEM90 1.9 30.1 1.0
ND D:HEM90 1.9 31.4 1.0
NB D:HEM90 1.9 28.9 1.0
NC D:HEM90 1.9 29.5 1.0
NE2 D:HIS18 2.0 30.7 1.0
SD D:MET62 2.3 22.9 1.0
C4A D:HEM90 2.9 29.7 1.0
CD2 D:HIS18 3.0 32.1 1.0
C1A D:HEM90 3.0 30.1 1.0
C1C D:HEM90 3.0 29.3 1.0
C1B D:HEM90 3.0 28.0 1.0
C1D D:HEM90 3.0 31.9 1.0
C4D D:HEM90 3.0 32.2 1.0
C4C D:HEM90 3.0 29.9 1.0
C4B D:HEM90 3.0 29.3 1.0
CE1 D:HIS18 3.0 32.1 1.0
CG D:MET62 3.3 24.1 1.0
CHC D:HEM90 3.4 29.3 1.0
CHB D:HEM90 3.4 28.2 1.0
CHD D:HEM90 3.4 30.9 1.0
CHA D:HEM90 3.4 30.2 1.0
CE D:MET62 3.5 19.4 1.0
ND1 D:HIS18 4.1 33.4 1.0
CG D:HIS18 4.1 34.3 1.0
C2C D:HEM90 4.2 29.9 1.0
C2A D:HEM90 4.2 31.1 1.0
C3A D:HEM90 4.2 30.1 1.0
C2D D:HEM90 4.2 32.9 1.0
C2B D:HEM90 4.2 28.7 1.0
C3D D:HEM90 4.2 34.0 1.0
C3C D:HEM90 4.2 30.9 1.0
CB D:MET62 4.2 26.7 1.0
C3B D:HEM90 4.3 29.1 1.0

Iron binding site 5 out of 8 in 1kib

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Iron binding site 5 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe90

b:29.6
occ:1.00
FE E:HEM90 0.0 29.6 1.0
ND E:HEM90 1.9 31.4 1.0
NC E:HEM90 1.9 29.5 1.0
NA E:HEM90 1.9 30.1 1.0
NE2 E:HIS18 2.0 30.7 1.0
NB E:HEM90 2.0 28.9 1.0
SD E:MET62 2.4 22.9 1.0
CD2 E:HIS18 2.9 32.1 1.0
C1D E:HEM90 3.0 31.9 1.0
C4C E:HEM90 3.0 29.9 1.0
C1C E:HEM90 3.0 29.3 1.0
C4A E:HEM90 3.0 29.7 1.0
C4D E:HEM90 3.0 32.2 1.0
C1A E:HEM90 3.0 30.1 1.0
CE1 E:HIS18 3.0 32.1 1.0
C1B E:HEM90 3.0 28.0 1.0
C4B E:HEM90 3.0 29.3 1.0
CHD E:HEM90 3.3 30.9 1.0
CG E:MET62 3.4 24.1 1.0
CHB E:HEM90 3.4 28.2 1.0
CHC E:HEM90 3.4 29.3 1.0
CHA E:HEM90 3.4 30.2 1.0
CE E:MET62 3.5 19.4 1.0
ND1 E:HIS18 4.1 33.4 1.0
CG E:HIS18 4.1 34.3 1.0
C2C E:HEM90 4.2 29.9 1.0
C2A E:HEM90 4.2 31.1 1.0
C3A E:HEM90 4.2 30.1 1.0
C2D E:HEM90 4.2 32.9 1.0
C3C E:HEM90 4.2 30.9 1.0
C3D E:HEM90 4.2 34.0 1.0
C2B E:HEM90 4.2 28.7 1.0
CB E:MET62 4.2 26.7 1.0
C3B E:HEM90 4.3 29.1 1.0

Iron binding site 6 out of 8 in 1kib

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Iron binding site 6 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe90

b:29.6
occ:1.00
FE F:HEM90 0.0 29.6 1.0
ND F:HEM90 1.9 31.4 1.0
NC F:HEM90 1.9 29.5 1.0
NA F:HEM90 2.0 30.1 1.0
NB F:HEM90 2.0 28.9 1.0
NE2 F:HIS18 2.0 30.7 1.0
SD F:MET62 2.4 22.9 1.0
C1D F:HEM90 2.9 31.9 1.0
C4D F:HEM90 2.9 32.2 1.0
C4C F:HEM90 2.9 29.9 1.0
C1C F:HEM90 2.9 29.3 1.0
CD2 F:HIS18 3.0 32.1 1.0
C1A F:HEM90 3.0 30.1 1.0
CE1 F:HIS18 3.0 32.1 1.0
C4A F:HEM90 3.0 29.7 1.0
C1B F:HEM90 3.0 28.0 1.0
C4B F:HEM90 3.0 29.3 1.0
CHD F:HEM90 3.3 30.9 1.0
CG F:MET62 3.3 24.1 1.0
CHA F:HEM90 3.4 30.2 1.0
CHC F:HEM90 3.4 29.3 1.0
CHB F:HEM90 3.4 28.2 1.0
CE F:MET62 3.5 19.4 1.0
ND1 F:HIS18 4.1 33.4 1.0
CG F:HIS18 4.1 34.3 1.0
C2D F:HEM90 4.1 32.9 1.0
C2C F:HEM90 4.1 29.9 1.0
C3D F:HEM90 4.2 34.0 1.0
C3C F:HEM90 4.2 30.9 1.0
C2A F:HEM90 4.2 31.1 1.0
CB F:MET62 4.2 26.7 1.0
C3A F:HEM90 4.2 30.1 1.0
C2B F:HEM90 4.3 28.7 1.0
C3B F:HEM90 4.3 29.1 1.0

Iron binding site 7 out of 8 in 1kib

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Iron binding site 7 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe90

b:29.6
occ:1.00
FE G:HEM90 0.0 29.6 1.0
NC G:HEM90 1.9 29.5 1.0
ND G:HEM90 1.9 31.4 1.0
NA G:HEM90 1.9 30.1 1.0
NE2 G:HIS18 2.0 30.7 1.0
NB G:HEM90 2.0 28.9 1.0
SD G:MET62 2.4 22.9 1.0
CD2 G:HIS18 2.9 32.1 1.0
C1C G:HEM90 2.9 29.3 1.0
C4C G:HEM90 3.0 29.9 1.0
CE1 G:HIS18 3.0 32.1 1.0
C1D G:HEM90 3.0 31.9 1.0
C4A G:HEM90 3.0 29.7 1.0
C4D G:HEM90 3.0 32.2 1.0
C1B G:HEM90 3.0 28.0 1.0
C1A G:HEM90 3.0 30.1 1.0
C4B G:HEM90 3.0 29.3 1.0
CHC G:HEM90 3.3 29.3 1.0
CHD G:HEM90 3.3 30.9 1.0
CHB G:HEM90 3.4 28.2 1.0
CHA G:HEM90 3.4 30.2 1.0
CG G:MET62 3.4 24.1 1.0
CE G:MET62 3.5 19.4 1.0
ND1 G:HIS18 4.0 33.4 1.0
CG G:HIS18 4.1 34.3 1.0
C2C G:HEM90 4.1 29.9 1.0
C3C G:HEM90 4.2 30.9 1.0
C2B G:HEM90 4.2 28.7 1.0
C2A G:HEM90 4.2 31.1 1.0
C2D G:HEM90 4.2 32.9 1.0
C3A G:HEM90 4.2 30.1 1.0
C3D G:HEM90 4.2 34.0 1.0
CB G:MET62 4.2 26.7 1.0
C3B G:HEM90 4.3 29.1 1.0

Iron binding site 8 out of 8 in 1kib

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Iron binding site 8 out of 8 in the Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in the Form of An Oblate Shell within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe90

b:29.6
occ:1.00
FE H:HEM90 0.0 29.6 1.0
ND H:HEM90 1.9 31.4 1.0
NA H:HEM90 1.9 30.1 1.0
NC H:HEM90 1.9 29.5 1.0
NE2 H:HIS18 1.9 30.7 1.0
NB H:HEM90 2.0 28.9 1.0
SD H:MET62 2.4 22.9 1.0
CD2 H:HIS18 2.9 32.1 1.0
C1D H:HEM90 2.9 31.9 1.0
C1C H:HEM90 3.0 29.3 1.0
C4C H:HEM90 3.0 29.9 1.0
CE1 H:HIS18 3.0 32.1 1.0
C4D H:HEM90 3.0 32.2 1.0
C4A H:HEM90 3.0 29.7 1.0
C1A H:HEM90 3.0 30.1 1.0
C1B H:HEM90 3.0 28.0 1.0
C4B H:HEM90 3.0 29.3 1.0
CHD H:HEM90 3.3 30.9 1.0
CHC H:HEM90 3.4 29.3 1.0
CG H:MET62 3.4 24.1 1.0
CHA H:HEM90 3.4 30.2 1.0
CHB H:HEM90 3.4 28.2 1.0
CE H:MET62 3.5 19.4 1.0
ND1 H:HIS18 4.0 33.4 1.0
CG H:HIS18 4.0 34.3 1.0
C2C H:HEM90 4.1 29.9 1.0
C2A H:HEM90 4.2 31.1 1.0
C2D H:HEM90 4.2 32.9 1.0
C3A H:HEM90 4.2 30.1 1.0
C3D H:HEM90 4.2 34.0 1.0
C3C H:HEM90 4.2 30.9 1.0
C2B H:HEM90 4.2 28.7 1.0
CB H:MET62 4.2 26.7 1.0
C3B H:HEM90 4.3 29.1 1.0

Reference:

C.A.Kerfeld, M.R.Sawaya, D.W.Krogmann, T.O.Yeates. Structure of Cytochrome C6 From Arthrospira Maxima: An Assembly of 24 Subunits in A Nearly Symmetric Shell. Acta Crystallogr.,Sect.D V. 58 1104 2002.
ISSN: ISSN 0907-4449
PubMed: 12077429
DOI: 10.1107/S0907444902006534
Page generated: Sun Dec 13 14:21:07 2020

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