Iron in PDB 1ux9: Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9 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)	29.8 / 2.4
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.840, 70.520, 98.730, 90.00, 90.00, 90.00
R / Rfree (%)	19.163 / 23.804

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation also contains other interesting chemical elements:

Xenon

(Xe)

7 atoms

The binding sites of Iron atom in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation (pdb code 1ux9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1172 b:20.1 occ:1.00 FE A:HEM1172 0.0 20.1 1.0 NA A:HEM1172 2.0 19.0 1.0 NB A:HEM1172 2.0 18.0 1.0 NC A:HEM1172 2.0 19.8 1.0 NE2 A:HIS81 2.1 34.8 1.0 NE2 A:HIS113 2.1 22.5 1.0 ND A:HEM1172 2.2 21.0 1.0 CE1 A:HIS81 2.6 35.4 1.0 CE1 A:HIS113 2.9 21.3 1.0 C4A A:HEM1172 3.0 18.7 1.0 C1B A:HEM1172 3.0 17.7 1.0 C4B A:HEM1172 3.1 21.5 1.0 C4C A:HEM1172 3.1 21.5 1.0 C1A A:HEM1172 3.1 20.2 1.0 C1C A:HEM1172 3.1 22.0 1.0 C1D A:HEM1172 3.2 20.5 1.0 C4D A:HEM1172 3.2 19.7 1.0 CD2 A:HIS113 3.2 25.2 1.0 CD2 A:HIS81 3.3 34.6 1.0 CHB A:HEM1172 3.4 18.0 1.0 CHC A:HEM1172 3.4 23.0 1.0 CHD A:HEM1172 3.5 21.9 1.0 CHA A:HEM1172 3.5 19.2 1.0 ND1 A:HIS81 3.8 36.3 1.0 ND1 A:HIS113 4.0 23.0 1.0 CG A:HIS81 4.2 28.8 1.0 CG A:HIS113 4.2 21.2 1.0 C3A A:HEM1172 4.2 20.4 1.0 C2A A:HEM1172 4.2 21.5 1.0 C2B A:HEM1172 4.3 19.3 1.0 C3B A:HEM1172 4.3 21.8 1.0 C3C A:HEM1172 4.3 20.8 1.0 C2C A:HEM1172 4.3 21.4 1.0 C3D A:HEM1172 4.4 22.0 1.0 C2D A:HEM1172 4.4 22.4 1.0 CG2 A:VAL85 4.8 22.9 1.0

Iron binding site 2 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1176 b:31.2 occ:0.50 FE2 A:FC61176 0.0 31.2 0.5 C24 A:FC61176 1.8 30.2 0.5 C11 A:FC61176 1.8 30.0 0.5 C22 A:FC61176 1.8 31.5 0.5 C26 A:FC61176 1.8 28.4 0.5 C23 A:FC61176 1.8 33.0 0.5 C21 A:FC61176 1.8 30.3 0.5 N24 A:FC61176 3.0 29.9 0.5 N11 A:FC61176 3.0 29.8 0.5 N21 A:FC61176 3.0 19.3 1.0 N22 A:FC61176 3.0 32.3 0.5 N23 A:FC61176 3.0 35.5 0.5 N25 A:FC61176 3.0 26.6 0.5 CD A:LYS125 4.3 23.4 1.0 CB B:SER55 4.4 21.6 1.0 NE A:ARG155 4.5 28.9 1.0 CD A:ARG155 4.6 28.8 1.0 CD2 A:TYR159 4.7 26.8 1.0 OG B:SER55 4.8 22.9 1.0 NZ A:LYS125 4.8 28.0 1.0 N B:SER55 4.8 21.1 1.0 CZ A:ARG155 5.0 25.9 1.0

Iron binding site 3 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1172 b:20.0 occ:1.00 FE B:HEM1172 0.0 20.0 1.0 NC B:HEM1172 1.9 19.8 1.0 NE2 B:HIS113 2.0 21.8 1.0 NA B:HEM1172 2.0 17.4 1.0 NB B:HEM1172 2.0 19.0 1.0 ND B:HEM1172 2.0 19.9 1.0 NE2 B:HIS81 2.1 28.4 1.0 CE1 B:HIS81 2.8 30.1 1.0 CE1 B:HIS113 2.9 21.3 1.0 C4C B:HEM1172 2.9 18.6 1.0 C1D B:HEM1172 3.0 19.5 1.0 C1C B:HEM1172 3.0 20.9 1.0 CD2 B:HIS113 3.0 22.9 1.0 C4A B:HEM1172 3.0 17.0 1.0 C1B B:HEM1172 3.0 20.1 1.0 C1A B:HEM1172 3.1 17.6 1.0 C4B B:HEM1172 3.1 21.9 1.0 C4D B:HEM1172 3.1 17.5 1.0 CD2 B:HIS81 3.3 29.0 1.0 CHD B:HEM1172 3.3 19.9 1.0 CHB B:HEM1172 3.4 18.4 1.0 CHC B:HEM1172 3.4 23.3 1.0 CHA B:HEM1172 3.5 14.8 1.0 ND1 B:HIS81 4.0 31.7 1.0 ND1 B:HIS113 4.0 22.2 1.0 CG B:HIS113 4.1 22.5 1.0 C3C B:HEM1172 4.2 19.2 1.0 C2C B:HEM1172 4.2 19.7 1.0 C3A B:HEM1172 4.2 18.0 1.0 C2D B:HEM1172 4.2 19.9 1.0 CG B:HIS81 4.3 26.9 1.0 C2A B:HEM1172 4.3 18.5 1.0 C2B B:HEM1172 4.3 19.8 1.0 C3B B:HEM1172 4.3 21.2 1.0 C3D B:HEM1172 4.3 19.4 1.0 CG2 B:VAL85 4.7 26.8 1.0 CD2 B:HIS117 4.9 22.4 1.0

Iron binding site 4 out of 4 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1176 b:54.4 occ:1.00 FE2 B:FC61176 0.0 54.4 1.0 C22 B:FC61176 1.8 51.5 1.0 C11 B:FC61176 1.8 52.5 1.0 C26 B:FC61176 1.8 54.0 1.0 C21 B:FC61176 1.9 54.5 1.0 C23 B:FC61176 1.9 50.2 1.0 C24 B:FC61176 1.9 53.2 1.0 N22 B:FC61176 3.0 50.2 1.0 N11 B:FC61176 3.0 53.0 1.0 N21 B:FC61176 3.0 54.8 1.0 N23 B:FC61176 3.0 40.0 1.0 N25 B:FC61176 3.0 53.6 1.0 N24 B:FC61176 3.0 48.3 1.0 CE B:LYS125 4.3 25.7 1.0 CB A:SER55 4.3 20.8 1.0 NE B:ARG155 4.4 28.7 1.0 CD1 B:TYR159 4.5 25.6 1.0 CD B:ARG155 4.6 27.7 1.0 OG A:SER55 4.6 21.0 1.0 N A:SER55 4.8 20.5 1.0 CZ B:ARG155 4.8 27.9 1.0 CG A:PRO54 5.0 19.5 1.0

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