Iron in PDB 4k8f: Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum

The structure of Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum, PDB code: 4k8f was solved by M.Kuchinskas, H.Li, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 2.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	71.230, 71.230, 143.733, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 26.3

The binding sites of Iron atom in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum (pdb code 4k8f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum, PDB code: 4k8f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:57.0 occ:1.00 FE A:HEM300 0.0 57.0 1.0 NC A:HEM300 1.9 59.2 1.0 NE2 A:HIS77 2.1 54.2 1.0 NB A:HEM300 2.1 59.0 1.0 ND A:HEM300 2.1 60.9 1.0 NA A:HEM300 2.1 57.8 1.0 N B:PRO2 2.2 58.8 1.0 CE1 A:HIS77 2.9 53.7 1.0 C1C A:HEM300 2.9 62.7 1.0 C4C A:HEM300 3.0 63.5 1.0 CA B:PRO2 3.0 62.3 1.0 C4B A:HEM300 3.0 58.7 1.0 C1D A:HEM300 3.1 63.5 1.0 C4D A:HEM300 3.1 63.1 1.0 C1A A:HEM300 3.1 60.8 1.0 C1B A:HEM300 3.2 54.8 1.0 C4A A:HEM300 3.2 55.7 1.0 CD2 A:HIS77 3.2 54.0 1.0 CD B:PRO2 3.3 56.7 1.0 CHC A:HEM300 3.3 58.3 1.0 CHD A:HEM300 3.4 61.3 1.0 CHA A:HEM300 3.5 58.8 1.0 CHB A:HEM300 3.6 55.6 1.0 C B:PRO2 3.7 61.3 1.0 O B:PRO2 3.9 63.7 1.0 ND1 A:HIS77 4.1 54.8 1.0 C2C A:HEM300 4.1 66.9 1.0 C3C A:HEM300 4.1 64.7 1.0 CB B:PRO2 4.2 57.5 1.0 CG A:HIS77 4.3 56.5 1.0 C3B A:HEM300 4.3 62.8 1.0 C2D A:HEM300 4.3 68.0 1.0 C3D A:HEM300 4.3 71.5 1.0 C2B A:HEM300 4.3 61.8 1.0 C2A A:HEM300 4.3 67.0 1.0 C3A A:HEM300 4.4 58.5 1.0 CG B:PRO2 4.4 57.4 1.0 N B:PRO3 4.7 62.1 1.0 SG A:CYS75 4.8 56.2 1.0

Iron binding site 2 out of 4 in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:54.0 occ:1.00 FE B:HEM300 0.0 54.0 1.0 NC B:HEM300 2.0 56.5 1.0 NB B:HEM300 2.0 59.9 1.0 NA B:HEM300 2.0 61.1 1.0 NE2 B:HIS77 2.1 61.8 1.0 ND B:HEM300 2.1 56.1 1.0 N A:PRO2 2.3 57.5 1.0 CE1 B:HIS77 3.0 59.9 1.0 C4C B:HEM300 3.0 60.3 1.0 C1C B:HEM300 3.0 59.8 1.0 C1B B:HEM300 3.0 57.3 1.0 C4A B:HEM300 3.1 63.3 1.0 C4B B:HEM300 3.1 55.8 1.0 C1A B:HEM300 3.1 65.7 1.0 C1D B:HEM300 3.1 57.3 1.0 C4D B:HEM300 3.1 58.5 1.0 CA A:PRO2 3.1 58.5 1.0 CD2 B:HIS77 3.2 60.5 1.0 CD A:PRO2 3.3 54.6 1.0 CHD B:HEM300 3.4 58.3 1.0 CHB B:HEM300 3.4 57.2 1.0 CHC B:HEM300 3.4 56.4 1.0 CHA B:HEM300 3.5 62.3 1.0 C A:PRO2 4.0 59.7 1.0 ND1 B:HIS77 4.1 61.4 1.0 C3C B:HEM300 4.2 63.5 1.0 C2C B:HEM300 4.2 60.8 1.0 O A:PRO2 4.2 62.6 1.0 CG B:HIS77 4.3 62.9 1.0 C2B B:HEM300 4.3 59.6 1.0 C3B B:HEM300 4.3 58.1 1.0 C3A B:HEM300 4.3 64.5 1.0 C2A B:HEM300 4.3 67.2 1.0 C3D B:HEM300 4.4 61.3 1.0 C2D B:HEM300 4.4 59.0 1.0 CB A:PRO2 4.4 58.7 1.0 CG A:PRO2 4.5 57.0 1.0 SG B:CYS75 4.8 60.7 1.0 N A:PRO3 4.8 60.1 1.0

Iron binding site 3 out of 4 in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe300 b:57.7 occ:1.00 FE C:HEM300 0.0 57.7 1.0 NC C:HEM300 2.0 53.1 1.0 NA C:HEM300 2.0 55.4 1.0 NB C:HEM300 2.1 59.2 1.0 ND C:HEM300 2.1 55.0 1.0 NE2 C:HIS77 2.1 56.1 1.0 N D:PRO2 2.4 62.2 1.0 C4C C:HEM300 3.0 59.2 1.0 CA D:PRO2 3.0 60.7 1.0 C1C C:HEM300 3.0 55.7 1.0 C1A C:HEM300 3.0 61.2 1.0 C4A C:HEM300 3.1 54.6 1.0 C1B C:HEM300 3.1 58.0 1.0 C4D C:HEM300 3.1 58.5 1.0 CE1 C:HIS77 3.1 50.8 1.0 CD2 C:HIS77 3.1 52.1 1.0 C1D C:HEM300 3.1 57.4 1.0 C4B C:HEM300 3.1 55.9 1.0 CHD C:HEM300 3.4 55.5 1.0 CHA C:HEM300 3.4 60.8 1.0 CHC C:HEM300 3.4 57.2 1.0 CHB C:HEM300 3.5 55.3 1.0 CD D:PRO2 3.6 57.8 1.0 C D:PRO2 3.8 60.8 1.0 O D:PRO2 4.1 67.4 1.0 C3C C:HEM300 4.2 62.9 1.0 ND1 C:HIS77 4.2 58.5 1.0 C2C C:HEM300 4.2 61.3 1.0 CG C:HIS77 4.2 55.9 1.0 C2A C:HEM300 4.3 62.0 1.0 CB D:PRO2 4.3 57.8 1.0 C3A C:HEM300 4.3 62.3 1.0 C2B C:HEM300 4.3 56.0 1.0 C3B C:HEM300 4.3 57.6 1.0 C3D C:HEM300 4.3 65.1 1.0 C2D C:HEM300 4.3 64.2 1.0 N D:PRO3 4.6 59.0 1.0 CG D:PRO2 4.6 63.2 1.0 CD D:PRO3 5.0 57.0 1.0

Iron binding site 4 out of 4 in the Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Heme Domain of Cooa From Rhodospirillum Rubrum within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe300 b:58.9 occ:1.00 FE D:HEM300 0.0 58.9 1.0 NC D:HEM300 2.0 62.5 1.0 NB D:HEM300 2.0 63.1 1.0 NA D:HEM300 2.1 64.4 1.0 NE2 D:HIS77 2.1 60.6 1.0 ND D:HEM300 2.2 61.2 1.0 N C:PRO2 2.3 62.5 1.0 C4B D:HEM300 3.0 62.5 1.0 C1C D:HEM300 3.0 61.5 1.0 C4C D:HEM300 3.0 65.1 1.0 C1B D:HEM300 3.0 60.0 1.0 CD2 D:HIS77 3.1 60.1 1.0 C4A D:HEM300 3.1 65.3 1.0 CE1 D:HIS77 3.1 60.7 1.0 C1A D:HEM300 3.1 66.0 1.0 CA C:PRO2 3.2 62.2 1.0 C1D D:HEM300 3.2 63.3 1.0 C4D D:HEM300 3.2 61.7 1.0 CD C:PRO2 3.3 59.3 1.0 CHC D:HEM300 3.4 59.5 1.0 CHB D:HEM300 3.4 60.6 1.0 CHD D:HEM300 3.5 64.3 1.0 CHA D:HEM300 3.5 61.4 1.0 C C:PRO2 4.0 65.7 1.0 O C:PRO2 4.2 68.0 1.0 ND1 D:HIS77 4.2 62.5 1.0 C3B D:HEM300 4.2 58.2 1.0 CG D:HIS77 4.2 66.7 1.0 C2B D:HEM300 4.2 58.6 1.0 C3C D:HEM300 4.2 67.8 1.0 C2C D:HEM300 4.2 64.2 1.0 C3A D:HEM300 4.3 72.3 1.0 C2A D:HEM300 4.3 72.9 1.0 CB C:PRO2 4.4 63.4 1.0 C2D D:HEM300 4.4 66.3 1.0 C3D D:HEM300 4.4 71.6 1.0 CG C:PRO2 4.5 58.5 1.0 SG D:CYS75 4.9 59.8 1.0 N C:PRO3 4.9 66.2 1.0

M.Kuchinskas, H.Li, M.Conrad, G.Roberts, T.L.Poulos. The Role of the Dna-Binding Domains in Cooa Activation. Biochemistry V. 45 7148 2006.
ISSN: ISSN 0006-2960
PubMed: 16752905
DOI: 10.1021/BI052609O