Iron in PDB 5ze8: Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum

The structure of Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum, PDB code: 5ze8 was solved by L.-J.Yu, J.-H.Chen, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.28 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.700, 39.100, 68.650, 90.00, 109.31, 90.00
R / Rfree (%)	15.8 / 19.1

The binding sites of Iron atom in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum (pdb code 5ze8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum, PDB code: 5ze8:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum


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 Penta-Heme Cytochrome C552 From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:13.5 occ:1.00 FE A:HEC501 0.0 13.5 1.0 ND A:HEC501 1.9 14.8 1.0 NA A:HEC501 2.0 13.4 1.0 NC A:HEC501 2.1 13.3 1.0 NB A:HEC501 2.1 13.0 1.0 NE2 A:HIS49 2.1 15.9 1.0 NE2 A:HIS195 2.1 14.0 1.0 C4D A:HEC501 2.9 14.3 1.0 C1D A:HEC501 3.0 15.8 1.0 CE1 A:HIS49 3.0 14.2 1.0 C1A A:HEC501 3.0 14.1 1.0 C4B A:HEC501 3.0 12.9 1.0 C1B A:HEC501 3.1 13.5 1.0 C4A A:HEC501 3.1 14.1 1.0 CD2 A:HIS195 3.1 12.9 1.0 C1C A:HEC501 3.1 14.4 1.0 CE1 A:HIS195 3.1 12.6 1.0 C4C A:HEC501 3.1 15.0 1.0 CD2 A:HIS49 3.1 13.3 1.0 CHD A:HEC501 3.4 14.1 1.0 CHB A:HEC501 3.4 13.9 1.0 CHA A:HEC501 3.4 13.4 1.0 CHC A:HEC501 3.4 14.0 1.0 ND1 A:HIS49 4.2 14.3 1.0 C2D A:HEC501 4.2 16.7 1.0 ND1 A:HIS195 4.2 14.3 1.0 C3D A:HEC501 4.2 16.1 1.0 CG A:HIS195 4.2 13.1 1.0 CG A:HIS49 4.2 13.3 1.0 C2A A:HEC501 4.3 15.1 1.0 C2B A:HEC501 4.3 11.7 1.0 C3A A:HEC501 4.3 13.9 1.0 C2C A:HEC501 4.3 14.8 1.0 C3C A:HEC501 4.3 15.5 1.0 C3B A:HEC501 4.3 12.8 1.0 CE A:MET212 4.9 14.2 1.0

Iron binding site 2 out of 5 in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum


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 Penta-Heme Cytochrome C552 From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:10.5 occ:1.00 FE A:HEC502 0.0 10.5 1.0 ND A:HEC502 2.0 10.3 1.0 NA A:HEC502 2.0 12.3 1.0 NC A:HEC502 2.0 11.4 1.0 NB A:HEC502 2.0 10.9 1.0 NE2 A:HIS103 2.1 10.2 1.0 C1D A:HEC502 3.0 10.2 1.0 C4D A:HEC502 3.0 12.3 1.0 C4B A:HEC502 3.0 13.0 1.0 C4C A:HEC502 3.0 9.1 1.0 C1B A:HEC502 3.0 12.9 1.0 C1A A:HEC502 3.0 11.3 1.0 C4A A:HEC502 3.0 12.7 1.0 C1C A:HEC502 3.1 10.0 1.0 CE1 A:HIS103 3.1 10.2 1.0 CD2 A:HIS103 3.1 9.0 1.0 CHC A:HEC502 3.3 11.4 1.0 CHD A:HEC502 3.4 9.9 1.0 CHB A:HEC502 3.4 13.0 1.0 CHA A:HEC502 3.4 11.4 1.0 C2D A:HEC502 4.2 11.6 1.0 C2B A:HEC502 4.2 12.3 1.0 C3D A:HEC502 4.3 11.3 1.0 C3A A:HEC502 4.3 13.5 1.0 C2A A:HEC502 4.3 13.5 1.0 ND1 A:HIS103 4.3 9.1 1.0 C2C A:HEC502 4.3 9.8 1.0 C3C A:HEC502 4.3 9.9 1.0 C3B A:HEC502 4.3 12.7 1.0 CG A:HIS103 4.3 9.9 1.0 NH2 A:ARG232 4.5 37.8 1.0 ND1 A:HIS72 4.6 11.4 1.0 CE1 A:HIS72 4.9 11.8 1.0

Iron binding site 3 out of 5 in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum


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 Penta-Heme Cytochrome C552 From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:10.1 occ:1.00 FE A:HEC503 0.0 10.1 1.0 ND A:HEC503 1.9 9.3 1.0 NA A:HEC503 2.0 9.8 1.0 NC A:HEC503 2.0 8.6 1.0 NB A:HEC503 2.0 9.2 1.0 NE2 A:HIS131 2.1 10.4 1.0 NE2 A:HIS270 2.1 10.1 1.0 C1B A:HEC503 3.0 9.7 1.0 CE1 A:HIS131 3.0 10.2 1.0 C1D A:HEC503 3.0 9.2 1.0 C4A A:HEC503 3.0 10.1 1.0 C4C A:HEC503 3.0 8.7 1.0 C4D A:HEC503 3.0 10.0 1.0 C1A A:HEC503 3.0 11.0 1.0 CD2 A:HIS270 3.0 9.7 1.0 C1C A:HEC503 3.1 9.8 1.0 C4B A:HEC503 3.1 9.9 1.0 CE1 A:HIS270 3.1 9.6 1.0 CD2 A:HIS131 3.1 9.8 1.0 CHB A:HEC503 3.4 10.2 1.0 CHD A:HEC503 3.4 8.5 1.0 CHA A:HEC503 3.5 10.4 1.0 CHC A:HEC503 3.5 9.3 1.0 ND1 A:HIS131 4.2 10.0 1.0 CG A:HIS270 4.2 9.5 1.0 C2B A:HEC503 4.2 10.4 1.0 ND1 A:HIS270 4.2 9.0 1.0 C3A A:HEC503 4.2 10.8 1.0 C2A A:HEC503 4.2 10.2 1.0 CG A:HIS131 4.2 8.9 1.0 C2C A:HEC503 4.3 8.9 1.0 C3D A:HEC503 4.3 10.4 1.0 C2D A:HEC503 4.3 10.5 1.0 C3C A:HEC503 4.3 9.4 1.0 C3B A:HEC503 4.3 9.4 1.0 CE A:MET261 4.7 12.1 1.0

Iron binding site 4 out of 5 in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum


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 Penta-Heme Cytochrome C552 From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:9.2 occ:1.00 FE A:HEC504 0.0 9.2 1.0 ND A:HEC504 2.0 8.0 1.0 NC A:HEC504 2.0 8.5 1.0 NA A:HEC504 2.0 9.1 1.0 NB A:HEC504 2.0 8.4 1.0 NE2 A:HIS61 2.1 8.5 1.0 NE2 A:HIS229 2.1 10.0 1.0 C4D A:HEC504 3.0 10.0 1.0 C1C A:HEC504 3.0 7.6 1.0 CE1 A:HIS61 3.0 7.8 1.0 C4A A:HEC504 3.0 9.1 1.0 C1D A:HEC504 3.0 9.1 1.0 C4B A:HEC504 3.0 8.6 1.0 CD2 A:HIS61 3.1 8.2 1.0 C1B A:HEC504 3.1 10.1 1.0 C1A A:HEC504 3.1 9.3 1.0 C4C A:HEC504 3.1 8.9 1.0 CD2 A:HIS229 3.1 9.9 1.0 CE1 A:HIS229 3.1 10.8 1.0 CHA A:HEC504 3.4 10.2 1.0 CHC A:HEC504 3.4 8.8 1.0 CHB A:HEC504 3.4 9.6 1.0 CHD A:HEC504 3.5 8.3 1.0 ND1 A:HIS61 4.2 8.6 1.0 CG A:HIS61 4.2 8.2 1.0 CG A:HIS229 4.2 9.4 1.0 C3A A:HEC504 4.2 9.1 1.0 ND1 A:HIS229 4.2 9.8 1.0 C2D A:HEC504 4.3 9.4 1.0 C2B A:HEC504 4.3 9.6 1.0 C3D A:HEC504 4.3 9.9 1.0 C3B A:HEC504 4.3 9.6 1.0 C3C A:HEC504 4.3 8.6 1.0 C2A A:HEC504 4.3 9.5 1.0 C2C A:HEC504 4.3 8.3 1.0 O A:HOH833 5.0 12.9 1.0 CMD A:HEC502 5.0 11.4 1.0

Iron binding site 5 out of 5 in the Crystal Structure of A Penta-Heme Cytochrome C552 From Thermochromatium Tepidum


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 Penta-Heme Cytochrome C552 From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:10.9 occ:1.00 FE A:HEC505 0.0 10.9 1.0 ND A:HEC505 1.9 11.6 1.0 NA A:HEC505 2.0 9.9 1.0 NC A:HEC505 2.0 10.3 1.0 NB A:HEC505 2.0 11.4 1.0 NE2 A:HIS310 2.1 10.2 1.0 NE2 A:HIS260 2.1 10.3 1.0 C4D A:HEC505 3.0 10.5 1.0 C1A A:HEC505 3.0 10.3 1.0 C1D A:HEC505 3.0 11.9 1.0 C1B A:HEC505 3.0 11.3 1.0 C1C A:HEC505 3.0 11.7 1.0 CE1 A:HIS260 3.0 10.1 1.0 CE1 A:HIS310 3.0 11.0 1.0 C4A A:HEC505 3.0 12.9 1.0 C4C A:HEC505 3.0 11.2 1.0 CD2 A:HIS310 3.1 10.2 1.0 C4B A:HEC505 3.1 10.6 1.0 CD2 A:HIS260 3.1 9.6 1.0 CHA A:HEC505 3.3 10.7 1.0 CHB A:HEC505 3.4 11.6 1.0 CHD A:HEC505 3.4 11.4 1.0 CHC A:HEC505 3.4 11.1 1.0 ND1 A:HIS260 4.2 10.3 1.0 ND1 A:HIS310 4.2 10.8 1.0 CG A:HIS260 4.2 10.9 1.0 CG A:HIS310 4.2 10.9 1.0 C3A A:HEC505 4.2 12.1 1.0 C2C A:HEC505 4.2 10.8 1.0 C2A A:HEC505 4.2 10.6 1.0 C2B A:HEC505 4.2 10.6 1.0 C3C A:HEC505 4.3 11.9 1.0 C2D A:HEC505 4.3 11.4 1.0 C3D A:HEC505 4.3 11.4 1.0 C3B A:HEC505 4.3 11.8 1.0

J.H.Chen, L.J.Yu, A.Boussac, Z.Y.Wang-Otomo, T.Kuang, J.R.Shen. Properties and Structure of A Low-Potential, Penta-Heme Cytochrome C552FROM A Thermophilic Purple Sulfur Photosynthetic Bacterium Thermochromatium Tepidum. Photosyn. Res. V. 139 281 2019.
ISSN: ISSN 1573-5079
PubMed: 29691716
DOI: 10.1007/S11120-018-0507-Y