Iron in PDB 1z1n: Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas

The structure of Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas, PDB code: 1z1n was solved by T.Santos-Silva, J.M.Dias, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.889, 90.799, 83.934, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 26

The structure of Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas (pdb code 1z1n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas, PDB code: 1z1n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe601 b:62.4 occ:1.00 FE X:HEC601 0.0 62.4 1.0 NC X:HEC601 2.0 61.7 1.0 ND X:HEC601 2.1 58.7 1.0 NB X:HEC601 2.1 63.2 1.0 NE2 X:HIS36 2.1 48.6 1.0 NE2 X:HIS54 2.1 49.9 1.0 NA X:HEC601 2.2 60.1 1.0 CE1 X:HIS36 2.7 47.5 1.0 C4C X:HEC601 3.0 60.9 1.0 C1D X:HEC601 3.0 60.2 1.0 C1C X:HEC601 3.1 62.2 1.0 CD2 X:HIS54 3.1 49.8 1.0 C4D X:HEC601 3.1 60.5 1.0 C4B X:HEC601 3.1 63.6 1.0 C1B X:HEC601 3.1 62.8 1.0 CE1 X:HIS54 3.1 50.1 1.0 C1A X:HEC601 3.1 59.0 1.0 C4A X:HEC601 3.2 59.6 1.0 CHD X:HEC601 3.3 61.2 1.0 CD2 X:HIS36 3.4 49.8 1.0 CHC X:HEC601 3.5 62.5 1.0 CHA X:HEC601 3.5 59.1 1.0 CHB X:HEC601 3.5 59.0 1.0 ND1 X:HIS36 4.0 48.1 1.0 ND1 X:HIS54 4.2 57.0 1.0 CG X:HIS54 4.3 57.5 1.0 C3C X:HEC601 4.3 63.2 1.0 C2D X:HEC601 4.3 58.1 1.0 C2C X:HEC601 4.3 62.9 1.0 CG X:HIS36 4.3 52.2 1.0 C2B X:HEC601 4.3 62.5 1.0 C3D X:HEC601 4.3 57.5 1.0 C3B X:HEC601 4.3 62.9 1.0 C2A X:HEC601 4.4 57.2 1.0 C3A X:HEC601 4.4 57.8 1.0 CBB X:HEC607 4.9 59.9 1.0 CD2 X:PHE63 5.0 57.8 1.0

Iron binding site 2 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe602 b:57.5 occ:1.00 FE X:HEC602 0.0 57.5 1.0 NC X:HEC602 1.9 48.2 1.0 ND X:HEC602 2.0 51.2 1.0 NA X:HEC602 2.1 46.8 1.0 NB X:HEC602 2.1 48.5 1.0 NE2 X:HIS89 2.2 51.9 1.0 NE2 X:HIS39 2.2 61.1 1.0 C1C X:HEC602 2.9 47.4 1.0 C4C X:HEC602 2.9 47.9 1.0 CD2 X:HIS39 3.0 61.4 1.0 C1A X:HEC602 3.0 51.5 1.0 C1D X:HEC602 3.0 53.3 1.0 C4D X:HEC602 3.0 56.2 1.0 C4B X:HEC602 3.0 46.4 1.0 CD2 X:HIS89 3.0 53.4 1.0 C4A X:HEC602 3.2 49.8 1.0 CE1 X:HIS89 3.2 51.6 1.0 CHC X:HEC602 3.3 49.5 1.0 C1B X:HEC602 3.3 48.8 1.0 CE1 X:HIS39 3.3 60.0 1.0 CHD X:HEC602 3.3 52.9 1.0 CHA X:HEC602 3.3 51.9 1.0 CHB X:HEC602 3.7 50.3 1.0 C3C X:HEC602 4.2 48.5 1.0 C2C X:HEC602 4.2 51.4 1.0 CG X:HIS39 4.2 64.4 1.0 CG X:HIS89 4.2 57.1 1.0 C2D X:HEC602 4.2 56.9 1.0 C3D X:HEC602 4.3 58.6 1.0 ND1 X:HIS89 4.3 55.8 1.0 C2A X:HEC602 4.3 51.3 1.0 ND1 X:HIS39 4.3 62.6 1.0 C3B X:HEC602 4.3 48.1 1.0 C3A X:HEC602 4.3 49.1 1.0 C2B X:HEC602 4.5 47.9 1.0 CE1 X:PHE34 4.7 57.6 1.0

Iron binding site 3 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe603 b:77.2 occ:1.00 FE X:HEC603 0.0 77.2 1.0 NC X:HEC603 2.1 74.5 1.0 NE2 X:HIS109 2.1 72.7 1.0 NE2 X:HIS82 2.1 53.4 1.0 ND X:HEC603 2.1 73.2 1.0 NA X:HEC603 2.1 74.1 1.0 NB X:HEC603 2.1 74.0 1.0 CE1 X:HIS82 2.9 53.2 1.0 CE1 X:HIS109 2.9 73.6 1.0 C4C X:HEC603 3.1 74.7 1.0 C4D X:HEC603 3.1 72.7 1.0 C1A X:HEC603 3.1 72.8 1.0 C1D X:HEC603 3.1 72.9 1.0 C1C X:HEC603 3.1 75.4 1.0 C4A X:HEC603 3.1 74.6 1.0 C4B X:HEC603 3.1 74.9 1.0 C1B X:HEC603 3.1 74.7 1.0 CD2 X:HIS82 3.1 55.1 1.0 CD2 X:HIS109 3.1 71.8 1.0 CHA X:HEC603 3.4 72.5 1.0 CHD X:HEC603 3.4 72.4 1.0 CHB X:HEC603 3.5 74.3 1.0 CHC X:HEC603 3.5 74.1 1.0 ND1 X:HIS82 4.1 57.3 1.0 ND1 X:HIS109 4.1 71.6 1.0 CG X:HIS82 4.2 55.0 1.0 CG X:HIS109 4.2 73.1 1.0 C3C X:HEC603 4.3 75.0 1.0 C2A X:HEC603 4.3 73.2 1.0 C2C X:HEC603 4.3 75.4 1.0 C3D X:HEC603 4.3 71.5 1.0 C3A X:HEC603 4.3 74.2 1.0 C2D X:HEC603 4.3 73.2 1.0 C3B X:HEC603 4.3 74.5 1.0 C2B X:HEC603 4.4 74.4 1.0

Iron binding site 4 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe604 b:54.4 occ:1.00 FE X:HEC604 0.0 54.4 1.0 NB X:HEC604 2.0 49.4 1.0 NC X:HEC604 2.0 50.5 1.0 NE2 X:HIS130 2.1 45.3 1.0 ND X:HEC604 2.1 48.0 1.0 NA X:HEC604 2.1 46.6 1.0 NE2 X:HIS153 2.1 47.0 1.0 C4B X:HEC604 2.9 48.2 1.0 C1C X:HEC604 3.0 50.6 1.0 CE1 X:HIS130 3.0 45.3 1.0 C1B X:HEC604 3.0 46.4 1.0 CD2 X:HIS153 3.1 46.8 1.0 C4C X:HEC604 3.1 51.1 1.0 C4A X:HEC604 3.1 42.5 1.0 C4D X:HEC604 3.1 49.0 1.0 CD2 X:HIS130 3.1 36.0 1.0 C1A X:HEC604 3.1 45.9 1.0 C1D X:HEC604 3.1 50.8 1.0 CE1 X:HIS153 3.2 49.0 1.0 CHC X:HEC604 3.3 48.5 1.0 CHB X:HEC604 3.4 45.4 1.0 CHA X:HEC604 3.5 45.6 1.0 CHD X:HEC604 3.5 49.7 1.0 ND1 X:HIS130 4.1 43.2 1.0 C3B X:HEC604 4.2 49.3 1.0 CG X:HIS130 4.2 39.4 1.0 C2C X:HEC604 4.2 52.5 1.0 C2B X:HEC604 4.2 48.8 1.0 CG X:HIS153 4.2 50.8 1.0 ND1 X:HIS153 4.2 47.3 1.0 C3C X:HEC604 4.3 52.1 1.0 C3A X:HEC604 4.3 43.4 1.0 C2A X:HEC604 4.3 43.4 1.0 C3D X:HEC604 4.3 47.3 1.0 C2D X:HEC604 4.4 47.8 1.0

Iron binding site 5 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe605 b:60.7 occ:1.00 FE X:HEC605 0.0 60.7 1.0 NA X:HEC605 2.0 58.2 1.0 NE2 X:HIS177 2.0 49.8 1.0 NE2 X:HIS154 2.1 58.9 1.0 ND X:HEC605 2.1 59.3 1.0 NB X:HEC605 2.1 56.6 1.0 NC X:HEC605 2.2 55.1 1.0 CE1 X:HIS177 2.9 51.4 1.0 C1A X:HEC605 2.9 59.2 1.0 C4D X:HEC605 3.0 59.6 1.0 CE1 X:HIS154 3.0 58.7 1.0 C4A X:HEC605 3.0 59.9 1.0 CD2 X:HIS154 3.1 56.5 1.0 CD2 X:HIS177 3.1 53.1 1.0 C1B X:HEC605 3.1 56.6 1.0 C4B X:HEC605 3.1 54.4 1.0 C1C X:HEC605 3.1 55.2 1.0 C1D X:HEC605 3.2 59.7 1.0 C4C X:HEC605 3.2 56.9 1.0 CHA X:HEC605 3.3 58.6 1.0 CHB X:HEC605 3.5 57.4 1.0 CHC X:HEC605 3.5 54.8 1.0 CHD X:HEC605 3.6 57.6 1.0 ND1 X:HIS177 4.0 52.1 1.0 ND1 X:HIS154 4.1 60.0 1.0 CG X:HIS177 4.2 53.0 1.0 CG X:HIS154 4.2 58.5 1.0 C2A X:HEC605 4.2 62.2 1.0 C3A X:HEC605 4.2 58.5 1.0 C3D X:HEC605 4.3 60.9 1.0 C2B X:HEC605 4.3 55.5 1.0 C3B X:HEC605 4.3 55.0 1.0 C2C X:HEC605 4.4 55.8 1.0 C2D X:HEC605 4.4 59.0 1.0 C3C X:HEC605 4.4 53.8 1.0

Iron binding site 6 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe606 b:56.5 occ:1.00 FE X:HEC606 0.0 56.5 1.0 ND X:HEC606 2.0 49.3 1.0 NB X:HEC606 2.0 45.5 1.0 NC X:HEC606 2.0 48.2 1.0 NA X:HEC606 2.1 49.2 1.0 NE2 X:HIS207 2.2 53.4 1.0 NE2 X:HIS133 2.2 47.5 1.0 C1D X:HEC606 2.9 50.9 1.0 C4C X:HEC606 2.9 46.9 1.0 CD2 X:HIS207 2.9 51.6 1.0 C1B X:HEC606 3.0 47.3 1.0 C4A X:HEC606 3.0 49.1 1.0 C4D X:HEC606 3.0 51.7 1.0 C4B X:HEC606 3.1 46.9 1.0 C1C X:HEC606 3.1 48.4 1.0 CD2 X:HIS133 3.1 50.5 1.0 C1A X:HEC606 3.2 47.7 1.0 CE1 X:HIS133 3.2 47.9 1.0 CHD X:HEC606 3.2 48.3 1.0 CE1 X:HIS207 3.3 54.4 1.0 CHB X:HEC606 3.4 48.9 1.0 CHC X:HEC606 3.5 48.0 1.0 CHA X:HEC606 3.5 49.8 1.0 C2D X:HEC606 4.2 53.1 1.0 CG X:HIS207 4.2 55.5 1.0 C3C X:HEC606 4.2 45.9 1.0 C3D X:HEC606 4.2 53.6 1.0 C2B X:HEC606 4.2 47.2 1.0 C3B X:HEC606 4.3 47.5 1.0 CG X:HIS133 4.3 48.2 1.0 C2C X:HEC606 4.3 47.0 1.0 ND1 X:HIS133 4.3 49.1 1.0 C3A X:HEC606 4.3 46.7 1.0 ND1 X:HIS207 4.3 56.1 1.0 C2A X:HEC606 4.4 46.4 1.0 CA X:GLY218 4.8 64.3 1.0

Iron binding site 7 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe607 b:59.5 occ:1.00 FE X:HEC607 0.0 59.5 1.0 NC X:HEC607 2.0 55.7 1.0 NA X:HEC607 2.0 53.1 1.0 ND X:HEC607 2.1 54.2 1.0 NE2 X:HIS226 2.1 57.0 1.0 NB X:HEC607 2.2 56.4 1.0 NE2 X:HIS200 2.2 42.9 1.0 C4C X:HEC607 3.0 56.6 1.0 CE1 X:HIS226 3.0 57.1 1.0 C1A X:HEC607 3.0 55.1 1.0 C1C X:HEC607 3.0 57.1 1.0 C1D X:HEC607 3.0 52.8 1.0 C4A X:HEC607 3.0 54.0 1.0 CD2 X:HIS200 3.1 44.9 1.0 C4D X:HEC607 3.1 54.0 1.0 C4B X:HEC607 3.1 55.9 1.0 C1B X:HEC607 3.2 53.9 1.0 CE1 X:HIS200 3.2 44.0 1.0 CD2 X:HIS226 3.2 60.1 1.0 CHD X:HEC607 3.4 53.9 1.0 CHC X:HEC607 3.4 57.1 1.0 CHA X:HEC607 3.4 51.6 1.0 CHB X:HEC607 3.5 55.3 1.0 ND1 X:HIS226 4.1 57.8 1.0 C3C X:HEC607 4.2 57.8 1.0 C2C X:HEC607 4.2 57.4 1.0 C2A X:HEC607 4.2 53.1 1.0 C3A X:HEC607 4.2 52.0 1.0 CG X:HIS200 4.3 45.6 1.0 CG X:HIS226 4.3 58.0 1.0 ND1 X:HIS200 4.3 47.8 1.0 C2D X:HEC607 4.3 52.1 1.0 C3D X:HEC607 4.3 51.5 1.0 C3B X:HEC607 4.3 56.4 1.0 C2B X:HEC607 4.4 55.7 1.0

Iron binding site 8 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe608 b:38.8 occ:1.00 FE X:HEC608 0.0 38.8 1.0 NC X:HEC608 2.0 32.4 1.0 NE2 X:HIS294 2.0 33.6 1.0 ND X:HEC608 2.0 37.1 1.0 NB X:HEC608 2.1 33.0 1.0 NA X:HEC608 2.2 36.3 1.0 NE2 X:HIS280 2.2 31.6 1.0 CE1 X:HIS294 2.9 37.0 1.0 C4C X:HEC608 2.9 31.9 1.0 C1D X:HEC608 3.0 38.3 1.0 C1C X:HEC608 3.0 32.0 1.0 CD2 X:HIS280 3.1 28.2 1.0 C1B X:HEC608 3.1 37.1 1.0 C4D X:HEC608 3.1 41.0 1.0 C4A X:HEC608 3.1 38.6 1.0 CD2 X:HIS294 3.1 34.0 1.0 C4B X:HEC608 3.1 35.4 1.0 C1A X:HEC608 3.2 37.9 1.0 CE1 X:HIS280 3.2 31.1 1.0 CHD X:HEC608 3.2 32.8 1.0 CHB X:HEC608 3.4 34.6 1.0 CHC X:HEC608 3.5 30.9 1.0 CHA X:HEC608 3.5 34.8 1.0 ND1 X:HIS294 4.0 35.9 1.0 C3C X:HEC608 4.2 32.3 1.0 CG X:HIS294 4.2 36.5 1.0 C2C X:HEC608 4.2 33.2 1.0 CG X:HIS280 4.2 28.5 1.0 ND1 X:HIS280 4.3 34.4 1.0 C2D X:HEC608 4.3 37.7 1.0 C3D X:HEC608 4.3 39.0 1.0 C2B X:HEC608 4.3 31.9 1.0 C3B X:HEC608 4.4 33.9 1.0 C2A X:HEC608 4.4 39.7 1.0 C3A X:HEC608 4.4 37.2 1.0 CB X:GLN247 4.8 35.5 1.0

Iron binding site 9 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe609 b:52.4 occ:1.00 FE X:HEC609 0.0 52.4 1.0 NC X:HEC609 2.0 50.1 1.0 NE2 X:HIS295 2.1 46.4 1.0 NA X:HEC609 2.1 45.6 1.0 NB X:HEC609 2.1 46.9 1.0 ND X:HEC609 2.1 51.8 1.0 NE2 X:HIS311 2.2 46.4 1.0 CE1 X:HIS295 2.7 47.2 1.0 CE1 X:HIS311 3.0 50.5 1.0 C4C X:HEC609 3.0 52.6 1.0 C1D X:HEC609 3.0 52.6 1.0 C1B X:HEC609 3.1 46.6 1.0 C4A X:HEC609 3.1 44.6 1.0 C1C X:HEC609 3.1 50.9 1.0 C1A X:HEC609 3.1 47.3 1.0 C4B X:HEC609 3.1 48.1 1.0 C4D X:HEC609 3.2 52.0 1.0 CD2 X:HIS295 3.3 44.8 1.0 CHD X:HEC609 3.3 50.3 1.0 CHB X:HEC609 3.4 46.1 1.0 CD2 X:HIS311 3.4 48.3 1.0 CHA X:HEC609 3.5 50.1 1.0 CHC X:HEC609 3.5 48.3 1.0 ND1 X:HIS295 4.0 45.8 1.0 ND1 X:HIS311 4.2 50.9 1.0 C3C X:HEC609 4.2 52.8 1.0 CG X:HIS295 4.3 45.9 1.0 C2D X:HEC609 4.3 53.3 1.0 C2B X:HEC609 4.3 48.9 1.0 C2C X:HEC609 4.3 50.5 1.0 C3A X:HEC609 4.3 44.5 1.0 C2A X:HEC609 4.3 48.2 1.0 C3B X:HEC609 4.4 44.1 1.0 C3D X:HEC609 4.4 51.5 1.0 CG X:HIS311 4.4 51.2 1.0

Iron binding site 10 out of 16 in the Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas


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 the Sixteen Heme Cytochrome From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe610 b:35.2 occ:1.00 FE X:HEC610 0.0 35.2 1.0 NA X:HEC610 1.9 23.4 1.0 NC X:HEC610 1.9 26.3 1.0 NB X:HEC610 2.0 26.0 1.0 ND X:HEC610 2.1 27.3 1.0 NE2 X:HIS341 2.1 26.3 1.0 NE2 X:HIS283 2.2 23.2 1.0 C4A X:HEC610 2.9 26.8 1.0 C1C X:HEC610 2.9 30.0 1.0 C4B X:HEC610 2.9 20.2 1.0 C1A X:HEC610 3.0 25.0 1.0 C4C X:HEC610 3.0 26.4 1.0 C1D X:HEC610 3.0 24.7 1.0 C1B X:HEC610 3.1 22.3 1.0 CE1 X:HIS283 3.1 33.0 1.0 CD2 X:HIS341 3.1 33.7 1.0 C4D X:HEC610 3.1 21.0 1.0 CE1 X:HIS341 3.1 31.3 1.0 CD2 X:HIS283 3.2 26.0 1.0 CHC X:HEC610 3.3 28.4 1.0 CHD X:HEC610 3.4 30.1 1.0 CHB X:HEC610 3.4 26.4 1.0 CHA X:HEC610 3.5 26.0 1.0 C3A X:HEC610 4.1 23.6 1.0 C2C X:HEC610 4.2 26.7 1.0 C2A X:HEC610 4.2 24.1 1.0 C3C X:HEC610 4.2 23.2 1.0 ND1 X:HIS283 4.2 26.1 1.0 C3B X:HEC610 4.2 25.7 1.0 ND1 X:HIS341 4.2 32.5 1.0 CG X:HIS341 4.2 32.7 1.0 C2B X:HEC610 4.3 26.7 1.0 CG X:HIS283 4.3 29.5 1.0 C2D X:HEC610 4.3 20.8 1.0 C3D X:HEC610 4.4 22.9 1.0

T.Santos-Silva, J.M.Dias, M.J.Romao. Crystal Structure of the Sixteen Heme Cytochrome From Desulfovibrio Gigas To Be Published.