Iron in PDB 8oup: Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima

The structure of Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima, PDB code: 8oup was solved by M.Nardini, A.Pesce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.219, 50.684, 74.165, 75.65, 88.09, 85.3
R / Rfree (%)	15 / 19.7

The binding sites of Iron atom in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima (pdb code 8oup). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima, PDB code: 8oup:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.8 occ:1.00 FE A:HEM201 0.0 12.8 1.0 ND A:HEM201 1.9 13.3 1.0 NA A:HEM201 1.9 13.0 1.0 NE2 A:HIS103 2.0 13.9 1.0 NE2 A:HIS71 2.0 11.7 1.0 NB A:HEM201 2.1 12.3 1.0 NC A:HEM201 2.1 12.8 1.0 C4D A:HEM201 3.0 14.0 1.0 CE1 A:HIS103 3.0 16.7 1.0 C1A A:HEM201 3.0 15.1 1.0 C1D A:HEM201 3.0 12.3 1.0 C4B A:HEM201 3.0 12.7 1.0 C4A A:HEM201 3.0 13.7 1.0 CD2 A:HIS71 3.0 12.7 1.0 CE1 A:HIS71 3.0 13.1 1.0 C1B A:HEM201 3.1 12.4 1.0 C4C A:HEM201 3.1 12.5 1.0 CD2 A:HIS103 3.1 15.5 1.0 C1C A:HEM201 3.1 14.7 1.0 CHA A:HEM201 3.4 13.4 1.0 CHC A:HEM201 3.4 11.8 1.0 CHB A:HEM201 3.4 12.7 1.0 CHD A:HEM201 3.4 13.5 1.0 ND1 A:HIS103 4.1 17.4 1.0 ND1 A:HIS71 4.2 12.4 1.0 C2A A:HEM201 4.2 16.6 1.0 C3A A:HEM201 4.2 16.3 1.0 CG A:HIS103 4.2 15.4 1.0 CG A:HIS71 4.2 11.9 1.0 C3D A:HEM201 4.2 16.6 1.0 C2D A:HEM201 4.2 15.0 1.0 C3C A:HEM201 4.3 15.1 1.0 C2C A:HEM201 4.3 14.2 1.0 C3B A:HEM201 4.3 14.5 1.0 C2B A:HEM201 4.3 13.3 1.0 NH1 A:ARG106 4.8 22.1 0.5

Iron binding site 2 out of 4 in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.6 occ:1.00 FE B:HEM201 0.0 9.6 1.0 NA B:HEM201 2.0 11.5 1.0 ND B:HEM201 2.0 10.5 1.0 NC B:HEM201 2.0 10.6 1.0 NB B:HEM201 2.0 9.8 1.0 NE2 B:HIS71 2.1 8.3 1.0 NE2 B:HIS103 2.1 9.7 1.0 C4D B:HEM201 3.0 13.2 1.0 C1A B:HEM201 3.0 13.3 1.0 C1D B:HEM201 3.0 11.9 1.0 C4B B:HEM201 3.0 11.1 1.0 C1B B:HEM201 3.0 11.3 1.0 C4C B:HEM201 3.0 11.9 1.0 CE1 B:HIS103 3.0 12.2 1.0 C4A B:HEM201 3.0 11.1 1.0 CE1 B:HIS71 3.0 9.1 1.0 CD2 B:HIS103 3.1 9.8 1.0 CD2 B:HIS71 3.1 8.7 1.0 C1C B:HEM201 3.1 11.5 1.0 CHA B:HEM201 3.4 13.6 1.0 CHD B:HEM201 3.4 12.0 1.0 CHB B:HEM201 3.4 10.4 1.0 CHC B:HEM201 3.5 10.7 1.0 ND1 B:HIS103 4.2 11.5 1.0 ND1 B:HIS71 4.2 8.8 1.0 C2A B:HEM201 4.2 14.2 1.0 C3A B:HEM201 4.2 12.5 1.0 C3C B:HEM201 4.2 13.1 1.0 CG B:HIS103 4.2 10.5 1.0 CG B:HIS71 4.2 9.0 1.0 C3B B:HEM201 4.2 12.5 1.0 C2B B:HEM201 4.2 11.6 1.0 C2D B:HEM201 4.2 12.4 1.0 C3D B:HEM201 4.2 13.2 1.0 C2C B:HEM201 4.3 11.9 1.0 NH1 B:ARG106 4.8 14.6 0.5

Iron binding site 3 out of 4 in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:11.9 occ:1.00 FE C:HEM200 0.0 11.9 1.0 ND C:HEM200 1.9 13.0 1.0 NA C:HEM200 2.0 12.8 1.0 NE2 C:HIS71 2.0 13.1 1.0 NB C:HEM200 2.0 12.8 1.0 NE2 C:HIS103 2.1 13.4 1.0 NC C:HEM200 2.1 13.3 1.0 C1D C:HEM200 2.9 13.1 1.0 C4D C:HEM200 3.0 13.8 1.0 C1A C:HEM200 3.0 13.6 1.0 CE1 C:HIS103 3.0 14.2 1.0 C1B C:HEM200 3.0 11.7 1.0 C4C C:HEM200 3.0 12.8 1.0 CD2 C:HIS71 3.1 11.5 1.0 CE1 C:HIS71 3.1 12.8 1.0 C4A C:HEM200 3.1 12.0 1.0 C4B C:HEM200 3.1 13.7 1.0 C1C C:HEM200 3.1 14.1 1.0 CD2 C:HIS103 3.1 12.6 1.0 CHD C:HEM200 3.4 12.9 1.0 CHA C:HEM200 3.4 13.5 1.0 CHB C:HEM200 3.4 11.2 1.0 CHC C:HEM200 3.4 12.7 1.0 ND1 C:HIS103 4.2 14.1 1.0 ND1 C:HIS71 4.2 11.8 1.0 CG C:HIS71 4.2 11.8 1.0 C3D C:HEM200 4.2 16.0 1.0 C3A C:HEM200 4.2 13.1 1.0 C2D C:HEM200 4.2 15.0 1.0 CG C:HIS103 4.2 12.9 1.0 C2B C:HEM200 4.2 14.2 1.0 C2A C:HEM200 4.3 15.2 1.0 C3C C:HEM200 4.3 15.1 1.0 C3B C:HEM200 4.3 14.2 1.0 C2C C:HEM200 4.3 14.7 1.0 NH1 C:ARG106 4.9 28.3 1.0

Iron binding site 4 out of 4 in the Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Characterization of the Hexa-Coordinated Globin From Spisula Solidissima within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:11.4 occ:1.00 FE D:HEM200 0.0 11.4 1.0 ND D:HEM200 1.9 12.8 1.0 NA D:HEM200 2.0 12.7 1.0 NE2 D:HIS71 2.1 9.0 1.0 NB D:HEM200 2.1 12.1 1.0 NC D:HEM200 2.1 12.0 1.0 NE2 D:HIS103 2.1 11.0 1.0 C1D D:HEM200 3.0 11.9 1.0 C1A D:HEM200 3.0 13.8 1.0 C4D D:HEM200 3.0 13.1 1.0 C4A D:HEM200 3.0 12.9 1.0 C1B D:HEM200 3.0 12.2 1.0 C4B D:HEM200 3.0 12.7 1.0 CE1 D:HIS71 3.1 9.3 1.0 C4C D:HEM200 3.1 12.6 1.0 CD2 D:HIS71 3.1 9.2 1.0 CE1 D:HIS103 3.1 14.0 1.0 C1C D:HEM200 3.1 12.9 1.0 CD2 D:HIS103 3.1 12.5 1.0 CHD D:HEM200 3.4 12.8 1.0 CHA D:HEM200 3.4 12.6 1.0 CHB D:HEM200 3.4 12.5 1.0 CHC D:HEM200 3.4 11.9 1.0 C2A D:HEM200 4.2 15.3 1.0 ND1 D:HIS71 4.2 9.7 1.0 C3A D:HEM200 4.2 14.8 1.0 C2D D:HEM200 4.2 13.8 1.0 CG D:HIS71 4.2 8.8 1.0 ND1 D:HIS103 4.2 13.0 1.0 CG D:HIS103 4.3 13.3 1.0 C3D D:HEM200 4.3 13.7 1.0 C2B D:HEM200 4.3 13.4 1.0 C3B D:HEM200 4.3 14.4 1.0 C3C D:HEM200 4.3 13.7 1.0 C2C D:HEM200 4.3 13.0 1.0

A.Pesce, K.Barmpidi, S.Dewilde, C.Estarellas, L.Moens, M.Bolognesi, F.J.Luque, M.Nardini. Structural and Dynamic Characterization of the Hexa-Coordinated Globin From Spisula Solidissima. J.Inorg.Biochem. V. 246 12289 2023.
ISSN: ISSN 0162-0134
PubMed: 37354606
DOI: 10.1016/J.JINORGBIO.2023.112289