Iron in PDB 2dc3: Crystal Structure of Human Cytoglobin at 1.68 Angstroms Resolution

The structure of Crystal Structure of Human Cytoglobin at 1.68 Angstroms Resolution, PDB code: 2dc3 was solved by M.Makino, H.Sugimoto, H.Sawai, N.Kawada, K.Yoshizato, Y.Shiro, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.530, 52.760, 83.440, 90.00, 87.75, 90.00
R / Rfree (%)	14 / 18.1

The binding sites of Iron atom in the Crystal Structure of Human Cytoglobin at 1.68 Angstroms Resolution (pdb code 2dc3). 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 Human Cytoglobin at 1.68 Angstroms Resolution, PDB code: 2dc3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Human Cytoglobin at 1.68 Angstroms 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 Human Cytoglobin at 1.68 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe191 b:7.4 occ:1.00 FE A:HEM191 0.0 7.4 1.0 ND A:HEM191 2.0 6.2 1.0 NB A:HEM191 2.0 6.2 1.0 NA A:HEM191 2.0 7.7 1.0 NC A:HEM191 2.0 6.8 1.0 NE2 A:HIS81 2.1 6.2 1.0 NE2 A:HIS113 2.1 7.1 1.0 C4D A:HEM191 3.0 7.9 1.0 CE1 A:HIS81 3.0 8.5 1.0 CE1 A:HIS113 3.0 7.9 1.0 C1A A:HEM191 3.0 9.3 1.0 C1C A:HEM191 3.1 8.4 1.0 C1D A:HEM191 3.1 7.7 1.0 C4B A:HEM191 3.1 6.3 1.0 C4C A:HEM191 3.1 7.8 1.0 CD2 A:HIS81 3.1 7.4 1.0 C4A A:HEM191 3.1 6.5 1.0 C1B A:HEM191 3.1 5.6 1.0 CD2 A:HIS113 3.1 7.1 1.0 CHA A:HEM191 3.4 7.7 1.0 CHC A:HEM191 3.4 8.2 1.0 CHD A:HEM191 3.4 7.4 1.0 CHB A:HEM191 3.4 7.0 1.0 ND1 A:HIS81 4.2 9.1 1.0 ND1 A:HIS113 4.2 8.0 1.0 CG A:HIS81 4.2 7.6 1.0 CG A:HIS113 4.2 6.5 1.0 C3D A:HEM191 4.2 8.4 1.0 C2D A:HEM191 4.3 7.5 1.0 C3B A:HEM191 4.3 7.6 1.0 C2C A:HEM191 4.3 6.6 1.0 C3C A:HEM191 4.3 8.5 1.0 C2A A:HEM191 4.3 8.1 1.0 C2B A:HEM191 4.3 6.9 1.0 C3A A:HEM191 4.3 7.6 1.0 CG2 A:VAL85 4.7 6.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Human Cytoglobin at 1.68 Angstroms 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 Human Cytoglobin at 1.68 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe191 b:8.3 occ:1.00 FE B:HEM191 0.0 8.3 1.0 ND B:HEM191 2.0 7.1 1.0 NC B:HEM191 2.0 7.0 1.0 NA B:HEM191 2.0 7.3 1.0 NB B:HEM191 2.0 6.8 1.0 NE2 B:HIS113 2.1 6.7 1.0 NE2 B:HIS81 2.1 5.7 1.0 C4D B:HEM191 3.0 7.9 1.0 CE1 B:HIS113 3.0 7.3 1.0 CD2 B:HIS81 3.0 8.1 1.0 C1D B:HEM191 3.0 8.0 1.0 C1A B:HEM191 3.0 8.9 1.0 C4A B:HEM191 3.1 8.8 1.0 C4C B:HEM191 3.1 8.7 1.0 C1B B:HEM191 3.1 6.8 1.0 C1C B:HEM191 3.1 8.6 1.0 C4B B:HEM191 3.1 8.1 1.0 CD2 B:HIS113 3.1 7.6 1.0 CE1 B:HIS81 3.1 6.5 1.0 CHA B:HEM191 3.4 9.8 1.0 CHB B:HEM191 3.4 8.9 1.0 CHD B:HEM191 3.4 9.5 1.0 CHC B:HEM191 3.4 9.0 1.0 ND1 B:HIS113 4.1 9.1 1.0 CG B:HIS81 4.2 7.5 1.0 ND1 B:HIS81 4.2 7.9 1.0 CG B:HIS113 4.2 6.2 1.0 C2D B:HEM191 4.2 8.3 1.0 C3D B:HEM191 4.2 8.3 1.0 C2A B:HEM191 4.3 8.7 1.0 C3C B:HEM191 4.3 8.4 1.0 C3A B:HEM191 4.3 9.7 1.0 C2C B:HEM191 4.3 7.7 1.0 C2B B:HEM191 4.3 8.0 1.0 C3B B:HEM191 4.3 8.5 1.0 CG2 B:VAL85 4.7 7.7 1.0

M.Makino, H.Sugimoto, H.Sawai, N.Kawada, K.Yoshizato, Y.Shiro. High-Resolution Structure of Human Cytoglobin: Identification of Extra N- and C-Termini and A New Dimerization Mode. Acta Crystallogr.,Sect.D V. 62 671 2006.
ISSN: ISSN 0907-4449
PubMed: 16699195
DOI: 10.1107/S0907444906013813