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Iron in PDB 2zbo: Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution, PDB code: 2zbo was solved by H.Akazaki, F.Kawai, H.Chida, Y.Matsumoto, I.Sirasaki, H.Nakade, M.Hirayama, K.Hosikawa, K.Suruga, T.Satoh, S.Yamada, S.Unzai, W.Hakamata, T.Nishio, S.-Y.Park, T.Oku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.578, 84.578, 232.911, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution (pdb code 2zbo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution, PDB code: 2zbo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2zbo

Go back to Iron Binding Sites List in 2zbo
Iron binding site 1 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe111

b:12.8
occ:1.00
FE A:HEM111 0.0 12.8 1.0
NE2 A:HIS42 1.9 10.3 1.0
NB A:HEM111 2.0 10.5 1.0
NA A:HEM111 2.0 12.3 1.0
NC A:HEM111 2.0 12.4 1.0
ND A:HEM111 2.0 12.4 1.0
SD A:MET82 2.3 13.0 1.0
CD2 A:HIS42 2.9 11.4 1.0
CE1 A:HIS42 3.0 12.5 1.0
C1B A:HEM111 3.0 11.7 1.0
C4A A:HEM111 3.0 13.5 1.0
C1C A:HEM111 3.0 11.8 1.0
C4D A:HEM111 3.0 12.0 1.0
C1A A:HEM111 3.1 11.0 1.0
C4B A:HEM111 3.1 10.7 1.0
C4C A:HEM111 3.1 12.9 1.0
C1D A:HEM111 3.1 13.0 1.0
CHB A:HEM111 3.4 13.2 1.0
CHA A:HEM111 3.4 12.9 1.0
CHD A:HEM111 3.4 12.7 1.0
CHC A:HEM111 3.4 12.0 1.0
CG A:MET82 3.4 12.2 1.0
CE A:MET82 3.5 12.5 1.0
ND1 A:HIS42 4.1 11.8 1.0
CG A:HIS42 4.1 11.5 1.0
CB A:MET82 4.2 13.7 1.0
C2B A:HEM111 4.3 11.2 1.0
C3A A:HEM111 4.3 12.4 1.0
C2C A:HEM111 4.3 13.9 1.0
C3C A:HEM111 4.3 14.7 1.0
C3B A:HEM111 4.3 11.4 1.0
C3D A:HEM111 4.3 13.4 1.0
C2A A:HEM111 4.3 12.9 1.0
C2D A:HEM111 4.3 12.6 1.0

Iron binding site 2 out of 6 in 2zbo

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Iron binding site 2 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe111

b:12.1
occ:1.00
FE C:HEM111 0.0 12.1 1.0
NE2 C:HIS42 2.0 12.4 1.0
NA C:HEM111 2.0 11.3 1.0
NB C:HEM111 2.0 12.8 1.0
NC C:HEM111 2.0 11.5 1.0
ND C:HEM111 2.1 12.3 1.0
SD C:MET82 2.3 13.2 1.0
CD2 C:HIS42 3.0 12.0 1.0
CE1 C:HIS42 3.0 12.9 1.0
C4A C:HEM111 3.0 12.4 1.0
C1C C:HEM111 3.0 12.9 1.0
C1A C:HEM111 3.0 11.5 1.0
C1B C:HEM111 3.1 11.4 1.0
C4C C:HEM111 3.1 12.9 1.0
C4B C:HEM111 3.1 11.2 1.0
C4D C:HEM111 3.1 11.8 1.0
C1D C:HEM111 3.1 11.9 1.0
CG C:MET82 3.4 14.3 1.0
CHA C:HEM111 3.4 12.2 1.0
CHC C:HEM111 3.4 12.6 1.0
CHB C:HEM111 3.4 11.8 1.0
CE C:MET82 3.4 13.3 1.0
CHD C:HEM111 3.5 13.6 1.0
ND1 C:HIS42 4.1 13.4 1.0
CG C:HIS42 4.1 12.9 1.0
CB C:MET82 4.1 14.7 1.0
C2C C:HEM111 4.3 13.8 1.0
C3A C:HEM111 4.3 12.4 1.0
C2A C:HEM111 4.3 13.4 1.0
C2B C:HEM111 4.3 12.3 1.0
C3C C:HEM111 4.3 14.4 1.0
C3B C:HEM111 4.3 13.1 1.0
C3D C:HEM111 4.3 12.5 1.0
C2D C:HEM111 4.3 13.0 1.0

Iron binding site 3 out of 6 in 2zbo

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Iron binding site 3 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe111

b:15.6
occ:1.00
FE E:HEM111 0.0 15.6 1.0
NE2 E:HIS42 1.9 15.7 1.0
NA E:HEM111 2.0 16.1 1.0
ND E:HEM111 2.0 14.8 1.0
NC E:HEM111 2.0 15.6 1.0
NB E:HEM111 2.1 14.7 1.0
SD E:MET82 2.3 16.0 1.0
CE1 E:HIS42 2.9 13.9 1.0
CD2 E:HIS42 2.9 13.8 1.0
C1A E:HEM111 3.0 16.9 1.0
C1D E:HEM111 3.0 16.4 1.0
C4D E:HEM111 3.1 16.6 1.0
C1C E:HEM111 3.1 15.0 1.0
C4C E:HEM111 3.1 16.2 1.0
C4A E:HEM111 3.1 17.6 1.0
C1B E:HEM111 3.1 16.8 1.0
C4B E:HEM111 3.1 16.2 1.0
CG E:MET82 3.4 14.8 1.0
CHA E:HEM111 3.4 17.6 1.0
CHD E:HEM111 3.4 16.3 1.0
CHB E:HEM111 3.5 16.9 1.0
CHC E:HEM111 3.5 16.1 1.0
CE E:MET82 3.5 16.2 1.0
ND1 E:HIS42 4.0 15.4 1.0
CG E:HIS42 4.1 14.7 1.0
CB E:MET82 4.1 16.3 1.0
C2A E:HEM111 4.3 17.9 1.0
C2D E:HEM111 4.3 17.0 1.0
C2C E:HEM111 4.3 16.6 1.0
C3A E:HEM111 4.3 17.1 1.0
C3D E:HEM111 4.3 17.9 1.0
C3C E:HEM111 4.3 16.3 1.0
C2B E:HEM111 4.3 16.8 1.0
C3B E:HEM111 4.3 15.5 1.0

Iron binding site 4 out of 6 in 2zbo

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Iron binding site 4 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe111

b:15.4
occ:1.00
FE G:HEM111 0.0 15.4 1.0
NE2 G:HIS42 1.9 13.6 1.0
NA G:HEM111 2.0 15.1 1.0
NB G:HEM111 2.0 15.0 1.0
NC G:HEM111 2.0 14.7 1.0
ND G:HEM111 2.1 15.5 1.0
SD G:MET82 2.3 16.7 1.0
CE1 G:HIS42 2.9 15.9 1.0
CD2 G:HIS42 2.9 14.3 1.0
C1A G:HEM111 3.0 16.1 1.0
C4A G:HEM111 3.0 15.4 1.0
C1C G:HEM111 3.0 14.1 1.0
C1B G:HEM111 3.0 14.2 1.0
C4C G:HEM111 3.1 15.3 1.0
C4B G:HEM111 3.1 14.0 1.0
C4D G:HEM111 3.1 14.3 1.0
C1D G:HEM111 3.1 14.1 1.0
CHA G:HEM111 3.4 16.4 1.0
CHB G:HEM111 3.4 15.8 1.0
CHC G:HEM111 3.4 15.0 1.0
CHD G:HEM111 3.4 15.0 1.0
CE G:MET82 3.5 17.2 1.0
CG G:MET82 3.5 16.4 1.0
ND1 G:HIS42 4.0 15.5 1.0
CG G:HIS42 4.1 15.2 1.0
CB G:MET82 4.2 16.5 1.0
C2A G:HEM111 4.2 16.8 1.0
C3A G:HEM111 4.3 16.9 1.0
C2C G:HEM111 4.3 14.8 1.0
C2B G:HEM111 4.3 15.1 1.0
C3B G:HEM111 4.3 14.7 1.0
C3C G:HEM111 4.3 15.2 1.0
C2D G:HEM111 4.3 15.8 1.0
C3D G:HEM111 4.3 15.0 1.0

Iron binding site 5 out of 6 in 2zbo

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Iron binding site 5 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe111

b:14.7
occ:1.00
FE I:HEM111 0.0 14.7 1.0
NE2 I:HIS42 1.9 13.1 1.0
NB I:HEM111 2.0 14.4 1.0
NA I:HEM111 2.0 13.3 1.0
NC I:HEM111 2.0 13.7 1.0
ND I:HEM111 2.1 14.6 1.0
SD I:MET82 2.3 16.0 1.0
CD2 I:HIS42 2.9 13.6 1.0
CE1 I:HIS42 3.0 14.4 1.0
C1C I:HEM111 3.0 13.9 1.0
C1A I:HEM111 3.0 13.5 1.0
C4A I:HEM111 3.0 14.0 1.0
C4D I:HEM111 3.1 13.1 1.0
C1B I:HEM111 3.1 13.4 1.0
C4B I:HEM111 3.1 13.4 1.0
C4C I:HEM111 3.1 12.9 1.0
C1D I:HEM111 3.1 12.9 1.0
CHC I:HEM111 3.4 13.6 1.0
CG I:MET82 3.4 16.1 1.0
CHA I:HEM111 3.4 13.8 1.0
CHB I:HEM111 3.4 14.4 1.0
CE I:MET82 3.4 16.6 1.0
CHD I:HEM111 3.5 14.3 1.0
ND1 I:HIS42 4.1 14.9 1.0
CG I:HIS42 4.1 15.0 1.0
CB I:MET82 4.1 16.2 1.0
C2C I:HEM111 4.2 14.9 1.0
C3A I:HEM111 4.3 13.9 1.0
C2A I:HEM111 4.3 13.9 1.0
C3C I:HEM111 4.3 14.4 1.0
C2B I:HEM111 4.3 15.2 1.0
C3B I:HEM111 4.3 15.2 1.0
C3D I:HEM111 4.3 13.7 1.0
C2D I:HEM111 4.3 13.2 1.0

Iron binding site 6 out of 6 in 2zbo

Go back to Iron Binding Sites List in 2zbo
Iron binding site 6 out of 6 in the Crystal Structure of Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution


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 Low-Redox-Potential Cytochrom C6 From Brown Alga Hizikia Fusiformis at 1.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe111

b:12.1
occ:1.00
FE K:HEM111 0.0 12.1 1.0
NE2 K:HIS42 1.9 11.8 1.0
NB K:HEM111 2.0 12.3 1.0
NA K:HEM111 2.0 11.9 1.0
ND K:HEM111 2.0 12.0 1.0
NC K:HEM111 2.0 12.1 1.0
SD K:MET82 2.3 15.6 1.0
CE1 K:HIS42 2.9 11.3 1.0
CD2 K:HIS42 3.0 12.0 1.0
C4A K:HEM111 3.0 12.7 1.0
C1B K:HEM111 3.0 12.1 1.0
C1A K:HEM111 3.0 12.3 1.0
C1C K:HEM111 3.0 13.3 1.0
C1D K:HEM111 3.0 12.0 1.0
C4D K:HEM111 3.0 11.6 1.0
C4B K:HEM111 3.1 13.0 1.0
C4C K:HEM111 3.1 12.9 1.0
CHB K:HEM111 3.4 12.6 1.0
CE K:MET82 3.4 15.2 1.0
CHC K:HEM111 3.4 13.9 1.0
CHA K:HEM111 3.4 12.5 1.0
CHD K:HEM111 3.4 12.4 1.0
CG K:MET82 3.4 15.1 1.0
ND1 K:HIS42 4.0 12.8 1.0
CG K:HIS42 4.1 12.7 1.0
CB K:MET82 4.1 14.5 1.0
C3A K:HEM111 4.2 13.1 1.0
C2A K:HEM111 4.2 13.4 1.0
C2B K:HEM111 4.3 12.2 1.0
C2D K:HEM111 4.3 11.9 1.0
C2C K:HEM111 4.3 13.4 1.0
C3D K:HEM111 4.3 13.3 1.0
C3C K:HEM111 4.3 13.1 1.0
C3B K:HEM111 4.3 12.5 1.0

Reference:

H.Akazaki, F.Kawai, H.Chida, Y.Matsumoto, M.Hirayama, K.Hoshikawa, S.Unzai, W.Hakamata, T.Nishio, S.-Y.Park, T.Oku. Cloning, Expression and Purification of Cytochrome C(6) From the Brown Alga Hizikia Fusiformis and Complete X-Ray Diffraction Analysis of the Structure Acta Crystallogr.,Sect.F V. 64 674 2008.
ISSN: ESSN 1744-3091
PubMed: 18678931
DOI: 10.1107/S1744309108017752
Page generated: Sun Dec 13 14:58:51 2020

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