Iron in PDB 1ury: Cytoglobin Cavities

The structure of Cytoglobin Cavities, PDB code: 1ury was solved by D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.4
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.848, 70.524, 98.728, 90.00, 90.00, 90.00
R / Rfree (%)	19.702 / 25.442

The structure of Cytoglobin Cavities also contains other interesting chemical elements:

Xenon

(Xe)

7 atoms

The binding sites of Iron atom in the Cytoglobin Cavities (pdb code 1ury). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytoglobin Cavities, PDB code: 1ury:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe700 b:17.9 occ:1.00 FE A:HEM700 0.0 17.9 1.0 NB A:HEM700 2.0 15.0 1.0 NA A:HEM700 2.0 17.4 1.0 NC A:HEM700 2.1 18.3 1.0 NE2 A:HIS81 2.1 31.8 1.0 NE2 A:HIS113 2.1 23.1 1.0 ND A:HEM700 2.2 19.2 1.0 CE1 A:HIS81 2.7 32.3 1.0 CE1 A:HIS113 2.9 22.5 1.0 C1B A:HEM700 3.0 15.7 1.0 C4A A:HEM700 3.0 16.8 1.0 C4B A:HEM700 3.0 19.1 1.0 C1A A:HEM700 3.1 18.9 1.0 C4C A:HEM700 3.1 19.3 1.0 C1C A:HEM700 3.1 19.4 1.0 C1D A:HEM700 3.1 19.1 1.0 C4D A:HEM700 3.2 19.1 1.0 CD2 A:HIS113 3.2 26.2 1.0 CD2 A:HIS81 3.3 31.7 1.0 CHB A:HEM700 3.4 16.3 1.0 CHC A:HEM700 3.5 20.2 1.0 CHD A:HEM700 3.5 20.4 1.0 CHA A:HEM700 3.5 18.5 1.0 ND1 A:HIS81 3.8 32.9 1.0 ND1 A:HIS113 4.0 23.7 1.0 CG A:HIS81 4.2 26.2 1.0 C2B A:HEM700 4.2 16.8 1.0 C3A A:HEM700 4.2 19.6 1.0 CG A:HIS113 4.2 21.9 1.0 C3B A:HEM700 4.2 18.6 1.0 C2A A:HEM700 4.3 21.3 1.0 C3C A:HEM700 4.3 18.7 1.0 C2C A:HEM700 4.3 19.5 1.0 C3D A:HEM700 4.4 21.0 1.0 C2D A:HEM700 4.4 21.1 1.0 CG2 A:VAL85 4.7 21.0 1.0

Iron binding site 2 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1175 b:26.2 occ:0.50 FE2 A:FC61175 0.0 26.2 0.5 C11 A:FC61175 1.8 25.2 0.5 C23 A:FC61175 1.8 25.3 0.5 C21 A:FC61175 1.8 26.8 0.5 C22 A:FC61175 1.8 23.5 0.5 C24 A:FC61175 1.8 25.1 0.5 C26 A:FC61175 1.8 27.9 0.5 N11 A:FC61175 3.0 24.8 0.5 N23 A:FC61175 3.0 25.1 0.5 N22 A:FC61175 3.0 14.2 1.0 N25 A:FC61175 3.0 28.2 0.5 N24 A:FC61175 3.0 21.4 0.5 N21 A:FC61175 3.0 30.0 0.5 CD A:LYS125 4.3 23.5 1.0 CB B:SER55 4.5 20.4 1.0 NE A:ARG155 4.5 25.4 1.0 CD A:ARG155 4.6 25.8 1.0 CD2 A:TYR159 4.7 26.6 1.0 OG B:SER55 4.7 21.8 1.0 N B:SER55 4.8 19.9 1.0 NZ A:LYS125 4.9 28.7 1.0 CZ A:ARG155 5.0 21.8 1.0

Iron binding site 3 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe700 b:18.0 occ:1.00 FE B:HEM700 0.0 18.0 1.0 NC B:HEM700 1.9 17.7 1.0 NE2 B:HIS113 2.0 20.9 1.0 NA B:HEM700 2.0 15.9 1.0 ND B:HEM700 2.0 18.5 1.0 NB B:HEM700 2.0 17.1 1.0 NE2 B:HIS81 2.1 24.2 1.0 CE1 B:HIS81 2.9 26.0 1.0 C4C B:HEM700 2.9 16.9 1.0 CE1 B:HIS113 2.9 20.2 1.0 C1D B:HEM700 3.0 18.1 1.0 C1C B:HEM700 3.0 18.8 1.0 CD2 B:HIS113 3.0 22.9 1.0 C4A B:HEM700 3.0 15.5 1.0 C1A B:HEM700 3.1 16.0 1.0 C1B B:HEM700 3.1 17.9 1.0 C4B B:HEM700 3.1 20.1 1.0 C4D B:HEM700 3.1 16.0 1.0 CD2 B:HIS81 3.2 24.9 1.0 CHD B:HEM700 3.3 18.5 1.0 CHC B:HEM700 3.4 20.8 1.0 CHB B:HEM700 3.4 16.5 1.0 CHA B:HEM700 3.5 14.0 1.0 ND1 B:HIS81 4.0 27.4 1.0 ND1 B:HIS113 4.1 20.9 1.0 CG B:HIS113 4.1 22.5 1.0 C3C B:HEM700 4.2 17.1 1.0 C2C B:HEM700 4.2 18.1 1.0 C2D B:HEM700 4.2 18.9 1.0 CG B:HIS81 4.3 23.0 1.0 C3A B:HEM700 4.3 16.4 1.0 C2A B:HEM700 4.3 17.2 1.0 C3D B:HEM700 4.3 18.6 1.0 C3B B:HEM700 4.3 19.2 1.0 C2B B:HEM700 4.3 17.2 1.0 CG2 B:VAL85 4.7 24.5 1.0 CD2 B:HIS117 4.9 22.3 1.0

Iron binding site 4 out of 4 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1175 b:48.8 occ:1.00 FE2 B:FC61175 0.0 48.8 1.0 C21 B:FC61175 1.8 46.0 1.0 C23 B:FC61175 1.8 47.2 1.0 C22 B:FC61175 1.8 48.6 1.0 C26 B:FC61175 1.8 44.8 1.0 C11 B:FC61175 1.8 48.0 1.0 C24 B:FC61175 1.8 49.0 1.0 N25 B:FC61175 3.0 44.9 1.0 N23 B:FC61175 3.0 47.8 1.0 N21 B:FC61175 3.0 34.8 1.0 N22 B:FC61175 3.0 49.3 1.0 N11 B:FC61175 3.0 43.6 1.0 N24 B:FC61175 3.0 48.3 1.0 CE B:LYS125 4.3 25.4 1.0 NE B:ARG155 4.3 26.9 1.0 CB A:SER55 4.4 20.1 1.0 CD1 B:TYR159 4.5 25.1 1.0 CD B:ARG155 4.6 26.1 1.0 OG A:SER55 4.6 20.8 1.0 N A:SER55 4.8 19.9 1.0 CZ B:ARG155 4.8 26.5 1.0 CG A:PRO54 4.9 19.1 1.0

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Cytoglobin Cavities Biochem.Biophys.Res.Commun. V. 316 1217 2004.
ISSN: ISSN 0006-291X
PubMed: 15044115
DOI: 10.1016/J.BBRC.2004.03.007