Iron in PDB 2d0w: Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans

The structure of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans, PDB code: 2d0w was solved by M.Nojiri, D.Hira, K.Yamaguchi, S.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.24 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.779, 57.283, 67.007, 90.00, 101.55, 90.00
R / Rfree (%)	18.5 / 19.1

The structure of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans also contains other interesting chemical elements:

Zinc

(Zn)

10 atoms

The binding sites of Iron atom in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans (pdb code 2d0w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans, PDB code: 2d0w:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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 Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:14.2 occ:1.00 FE A:HEM200 0.0 14.2 1.0 NE2 A:HIS63 1.9 12.4 1.0 NB A:HEM200 2.1 11.5 1.0 NC A:HEM200 2.1 15.5 1.0 NA A:HEM200 2.1 13.9 1.0 ND A:HEM200 2.2 12.1 1.0 SD A:MET103 2.4 14.6 1.0 CE1 A:HIS63 2.8 10.1 1.0 CD2 A:HIS63 2.9 13.0 1.0 C1B A:HEM200 3.0 14.3 1.0 C4A A:HEM200 3.0 13.6 1.0 C4C A:HEM200 3.0 13.1 1.0 C4B A:HEM200 3.1 12.7 1.0 C1D A:HEM200 3.1 11.5 1.0 C1C A:HEM200 3.1 14.1 1.0 C1A A:HEM200 3.2 13.4 1.0 C4D A:HEM200 3.2 11.9 1.0 CHB A:HEM200 3.3 11.3 1.0 CHD A:HEM200 3.4 12.1 1.0 CE A:MET103 3.4 13.9 1.0 CHC A:HEM200 3.5 11.1 1.0 CHA A:HEM200 3.5 11.4 1.0 CG A:MET103 3.6 15.8 1.0 ND1 A:HIS63 3.9 6.6 1.0 CG A:HIS63 4.0 11.4 1.0 CB A:MET103 4.1 16.3 1.0 C2B A:HEM200 4.2 13.2 1.0 C3B A:HEM200 4.3 11.9 1.0 C3A A:HEM200 4.3 12.2 1.0 C3C A:HEM200 4.3 15.4 1.0 C2C A:HEM200 4.3 13.0 1.0 C2A A:HEM200 4.3 10.3 1.0 C2D A:HEM200 4.4 14.7 1.0 C3D A:HEM200 4.4 11.9 1.0 CA A:MET103 4.7 16.0 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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 Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:14.3 occ:1.00 FE B:HEM201 0.0 14.3 1.0 NA B:HEM201 2.0 14.9 1.0 NC B:HEM201 2.1 17.6 1.0 NB B:HEM201 2.1 17.3 1.0 NE2 B:HIS63 2.2 17.0 1.0 ND B:HEM201 2.2 13.9 1.0 SD B:MET103 2.2 16.6 1.0 C4A B:HEM201 3.0 15.1 1.0 C1C B:HEM201 3.0 17.1 1.0 C1A B:HEM201 3.0 15.3 1.0 C1B B:HEM201 3.1 15.9 1.0 C4B B:HEM201 3.1 16.1 1.0 CE1 B:HIS63 3.1 14.2 1.0 C4C B:HEM201 3.1 17.4 1.0 C4D B:HEM201 3.1 16.1 1.0 CD2 B:HIS63 3.2 15.3 1.0 C1D B:HEM201 3.2 17.4 1.0 CE B:MET103 3.3 14.7 1.0 CHB B:HEM201 3.4 14.8 1.0 CHC B:HEM201 3.4 15.9 1.0 CHA B:HEM201 3.4 14.3 1.0 CG B:MET103 3.5 17.6 1.0 CHD B:HEM201 3.5 17.6 1.0 CB B:MET103 4.1 20.3 1.0 C3A B:HEM201 4.2 14.6 1.0 ND1 B:HIS63 4.2 13.8 1.0 C2A B:HEM201 4.2 15.6 1.0 C2C B:HEM201 4.3 16.7 1.0 C2B B:HEM201 4.3 16.4 1.0 CG B:HIS63 4.3 13.1 1.0 C3C B:HEM201 4.3 17.4 1.0 C3B B:HEM201 4.3 16.8 1.0 C3D B:HEM201 4.4 16.5 1.0 C2D B:HEM201 4.4 16.0 1.0 CA B:MET103 4.7 21.3 1.0

M.Nojiri, D.Hira, K.Yamaguchi, T.Okajima, K.Tanizawa, S.Suzuki. Crystal Structures of Cytochrome C(L) and Methanol Dehydrogenase From Hyphomicrobium Denitrificans: Structural and Mechanistic Insights Into Interactions Between the Two Proteins Biochemistry V. 45 3481 2006.
ISSN: ISSN 0006-2960
PubMed: 16533029
DOI: 10.1021/BI051877J