Iron in PDB 1ynr: Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution

The structure of Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution, PDB code: 1ynr was solved by C.Travaglini-Allocatelli, S.Gianni, V.K.Dubey, A.Borgia, A.Di Matteo, D.Bonivento, F.Cutruzzola, K.L.Bren, M.Brunori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.712, 56.712, 220.179, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.8

The binding sites of Iron atom in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution (pdb code 1ynr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution, PDB code: 1ynr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 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 the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe81 b:2.0 occ:1.00 FE A:HEC81 0.0 2.0 1.0 NA A:HEC81 2.0 2.0 1.0 NB A:HEC81 2.0 2.0 1.0 ND A:HEC81 2.0 2.0 1.0 NC A:HEC81 2.0 2.0 1.0 NE2 A:HIS14 2.1 8.4 1.0 SD A:MET59 2.4 8.9 1.0 C4D A:HEC81 3.0 2.0 1.0 C1A A:HEC81 3.0 2.0 1.0 C4B A:HEC81 3.0 2.0 1.0 CE1 A:HIS14 3.0 7.6 1.0 C1C A:HEC81 3.1 2.0 1.0 C1B A:HEC81 3.1 2.0 1.0 C4A A:HEC81 3.1 2.0 1.0 C4C A:HEC81 3.1 2.0 1.0 C1D A:HEC81 3.1 2.0 1.0 CD2 A:HIS14 3.1 10.8 1.0 CE A:MET59 3.3 8.1 1.0 CHA A:HEC81 3.3 2.0 1.0 CG A:MET59 3.4 9.6 1.0 CHC A:HEC81 3.4 2.0 1.0 CHB A:HEC81 3.5 2.0 1.0 CHD A:HEC81 3.5 2.0 1.0 ND1 A:HIS14 4.2 7.3 1.0 CB A:MET59 4.2 8.8 1.0 C3B A:HEC81 4.2 2.0 1.0 CG A:HIS14 4.2 7.2 1.0 C2A A:HEC81 4.2 2.0 1.0 C2B A:HEC81 4.2 2.0 1.0 C3D A:HEC81 4.3 2.0 1.0 C3A A:HEC81 4.3 2.0 1.0 C2C A:HEC81 4.3 2.0 1.0 C3C A:HEC81 4.3 2.0 1.0 C2D A:HEC81 4.3 2.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 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 the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe81 b:2.0 occ:1.00 FE B:HEC81 0.0 2.0 1.0 NB B:HEC81 2.0 2.0 1.0 ND B:HEC81 2.0 2.0 1.0 NE2 B:HIS14 2.1 10.3 1.0 NA B:HEC81 2.1 2.0 1.0 NC B:HEC81 2.1 2.0 1.0 SD B:MET59 2.3 8.1 1.0 CE1 B:HIS14 3.0 6.2 1.0 C1B B:HEC81 3.0 2.0 1.0 C4D B:HEC81 3.0 2.0 1.0 C4B B:HEC81 3.1 2.0 1.0 C1D B:HEC81 3.1 2.0 1.0 C4A B:HEC81 3.1 2.0 1.0 C1A B:HEC81 3.1 2.0 1.0 C4C B:HEC81 3.1 2.0 1.0 CD2 B:HIS14 3.1 6.0 1.0 C1C B:HEC81 3.1 2.0 1.0 CE B:MET59 3.3 8.0 1.0 CG B:MET59 3.4 6.9 1.0 CHB B:HEC81 3.4 2.0 1.0 CHA B:HEC81 3.4 2.0 1.0 CHD B:HEC81 3.4 2.0 1.0 CHC B:HEC81 3.5 2.0 1.0 CB B:MET59 4.1 8.1 1.0 ND1 B:HIS14 4.1 5.9 1.0 CG B:HIS14 4.2 6.3 1.0 C2B B:HEC81 4.3 2.0 1.0 C3B B:HEC81 4.3 2.0 1.0 C3D B:HEC81 4.3 2.0 1.0 C2D B:HEC81 4.3 2.0 1.0 C3A B:HEC81 4.3 2.0 1.0 C2A B:HEC81 4.3 2.0 1.0 C3C B:HEC81 4.3 2.0 1.0 C2C B:HEC81 4.3 2.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 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 the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe81 b:2.2 occ:1.00 FE C:HEC81 0.0 2.2 1.0 NC C:HEC81 2.0 2.0 1.0 NA C:HEC81 2.0 2.3 1.0 NE2 C:HIS14 2.1 6.5 1.0 NB C:HEC81 2.1 2.0 1.0 ND C:HEC81 2.1 2.0 1.0 SD C:MET59 2.3 9.2 1.0 C1A C:HEC81 3.0 2.3 1.0 CD2 C:HIS14 3.0 6.6 1.0 C4C C:HEC81 3.0 2.0 1.0 C1C C:HEC81 3.0 2.0 1.0 CE1 C:HIS14 3.1 8.6 1.0 C4A C:HEC81 3.1 4.5 1.0 C4B C:HEC81 3.1 2.0 1.0 C4D C:HEC81 3.1 2.0 1.0 C1B C:HEC81 3.1 2.0 1.0 C1D C:HEC81 3.1 2.0 1.0 CG C:MET59 3.4 6.5 1.0 CHC C:HEC81 3.4 2.0 1.0 CHA C:HEC81 3.4 2.0 1.0 CE C:MET59 3.4 6.4 1.0 CHD C:HEC81 3.4 2.0 1.0 CHB C:HEC81 3.5 2.0 1.0 CB C:MET59 4.2 8.7 1.0 ND1 C:HIS14 4.2 5.1 1.0 CG C:HIS14 4.2 6.7 1.0 C2A C:HEC81 4.2 2.6 1.0 C3C C:HEC81 4.3 2.0 1.0 C2C C:HEC81 4.3 2.0 1.0 C3A C:HEC81 4.3 3.0 1.0 C2B C:HEC81 4.3 2.0 1.0 C3B C:HEC81 4.3 2.0 1.0 C3D C:HEC81 4.4 2.0 1.0 C2D C:HEC81 4.4 2.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 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 the Cytochrome C-552 From Hydrogenobacter Thermophilus at 2.0 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe81 b:2.0 occ:1.00 FE D:HEC81 0.0 2.0 1.0 NA D:HEC81 2.0 2.0 1.0 NE2 D:HIS14 2.0 5.3 1.0 NC D:HEC81 2.0 2.0 1.0 ND D:HEC81 2.1 2.0 1.0 NB D:HEC81 2.1 2.0 1.0 SD D:MET59 2.3 6.6 1.0 CE1 D:HIS14 3.0 5.7 1.0 C4A D:HEC81 3.0 2.0 1.0 C4C D:HEC81 3.1 2.0 1.0 C1D D:HEC81 3.1 2.0 1.0 C1A D:HEC81 3.1 2.0 1.0 C1C D:HEC81 3.1 2.0 1.0 C1B D:HEC81 3.1 2.0 1.0 CD2 D:HIS14 3.1 5.7 1.0 C4D D:HEC81 3.1 2.0 1.0 C4B D:HEC81 3.1 2.0 1.0 CG D:MET59 3.4 4.8 1.0 CHB D:HEC81 3.4 2.0 1.0 CHD D:HEC81 3.4 2.0 1.0 CE D:MET59 3.4 9.4 1.0 CHA D:HEC81 3.5 2.0 1.0 CHC D:HEC81 3.5 2.0 1.0 ND1 D:HIS14 4.1 5.2 1.0 CB D:MET59 4.1 7.1 1.0 CG D:HIS14 4.2 4.4 1.0 C3A D:HEC81 4.2 2.0 1.0 C2A D:HEC81 4.3 2.0 1.0 C3C D:HEC81 4.3 2.0 1.0 C2C D:HEC81 4.3 2.0 1.0 C2D D:HEC81 4.3 2.0 1.0 C3D D:HEC81 4.3 2.0 1.0 C2B D:HEC81 4.3 2.0 1.0 C3B D:HEC81 4.4 2.0 1.0

C.Travaglini-Allocatelli, S.Gianni, V.K.Dubey, A.Borgia, A.Di Matteo, D.Bonivento, F.Cutruzzola, K.L.Bren, M.Brunori. An Obligatory Intermediate in the Folding Pathway of Cytochrome C552 From Hydrogenobacter Thermophilus J.Biol.Chem. V. 280 25729 2005.
ISSN: ISSN 0021-9258
PubMed: 15883159
DOI: 10.1074/JBC.M502628200