Iron in PDB 6m0a: The Heme-Bound Structure of the Chloroplast Protein AT3G03890

The structure of The Heme-Bound Structure of the Chloroplast Protein AT3G03890, PDB code: 6m0a was solved by J.Wang, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.84 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.346, 79.936, 80.105, 99.95, 109.41, 104.05
R / Rfree (%)	19.2 / 23.3

The binding sites of Iron atom in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890 (pdb code 6m0a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890, PDB code: 6m0a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Heme-Bound Structure of the Chloroplast Protein AT3G03890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:59.8 occ:0.80 FE A:HEM401 0.0 59.8 0.8 NC A:HEM401 2.0 69.7 0.8 NB A:HEM401 2.1 65.0 0.8 ND A:HEM401 2.1 61.7 0.8 NA A:HEM401 2.1 57.5 0.8 O B:HOH526 2.5 65.0 1.0 C1C A:HEM401 3.0 70.4 0.8 C4B A:HEM401 3.1 67.6 0.8 C4D A:HEM401 3.1 57.2 0.8 C1A A:HEM401 3.1 53.2 0.8 C4C A:HEM401 3.1 69.8 0.8 C1D A:HEM401 3.1 63.5 0.8 C1B A:HEM401 3.1 67.1 0.8 C4A A:HEM401 3.1 55.1 0.8 N1 A:AZI402 3.2 61.3 0.8 CHC A:HEM401 3.4 67.5 0.8 CHA A:HEM401 3.4 52.2 0.8 CHD A:HEM401 3.5 65.8 0.8 CHB A:HEM401 3.5 58.3 0.8 N2 A:AZI402 4.2 68.0 0.8 C2C A:HEM401 4.3 72.2 0.8 C3B A:HEM401 4.3 70.5 0.8 C3C A:HEM401 4.3 72.6 0.8 C3D A:HEM401 4.3 56.8 0.8 C2A A:HEM401 4.3 52.9 0.8 C2B A:HEM401 4.3 62.8 0.8 C2D A:HEM401 4.3 59.9 0.8 C3A A:HEM401 4.3 53.2 0.8 N B:ALA214 4.4 72.5 1.0 CA B:ALA214 4.7 73.2 1.0 O B:THR215 4.9 81.2 1.0

Iron binding site 2 out of 4 in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Heme-Bound Structure of the Chloroplast Protein AT3G03890 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:57.2 occ:0.50 FE B:HEM401 0.0 57.2 0.5 NC B:HEM401 1.9 70.0 0.5 NB B:HEM401 2.0 69.6 0.5 ND B:HEM401 2.1 65.3 0.5 NA B:HEM401 2.1 61.3 0.5 O A:HOH536 2.7 69.3 1.0 N3 B:AZI402 2.7 61.8 0.5 C1C B:HEM401 2.9 70.8 0.5 C4C B:HEM401 3.0 67.8 0.5 C4B B:HEM401 3.0 66.0 0.5 C1B B:HEM401 3.1 67.8 0.5 C1D B:HEM401 3.1 64.0 0.5 C4A B:HEM401 3.1 64.2 0.5 C4D B:HEM401 3.2 61.3 0.5 C1A B:HEM401 3.2 62.0 0.5 CHC B:HEM401 3.3 70.2 0.5 CHD B:HEM401 3.4 69.0 0.5 CHB B:HEM401 3.5 65.0 0.5 N2 B:AZI402 3.6 67.3 0.5 CHA B:HEM401 3.6 57.6 0.5 C2C B:HEM401 4.1 72.4 0.5 C3C B:HEM401 4.2 69.2 0.5 C3B B:HEM401 4.2 70.0 0.5 C2B B:HEM401 4.2 68.0 0.5 C2D B:HEM401 4.4 58.7 0.5 C3A B:HEM401 4.4 64.2 0.5 C3D B:HEM401 4.4 58.1 0.5 C2A B:HEM401 4.4 59.5 0.5 N A:ALA214 4.5 76.8 1.0 N1 B:AZI402 4.5 69.8 0.5

Iron binding site 3 out of 4 in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Heme-Bound Structure of the Chloroplast Protein AT3G03890 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:55.4 occ:0.50 FE C:HEM401 0.0 55.4 0.5 NB C:HEM401 2.0 57.8 0.5 NC C:HEM401 2.0 59.9 0.5 NA C:HEM401 2.1 54.1 0.5 ND C:HEM401 2.1 54.8 0.5 O D:HOH538 2.6 66.1 1.0 N3 C:AZI402 2.9 51.9 0.5 C1B C:HEM401 3.0 60.8 0.5 C4B C:HEM401 3.0 60.7 0.5 C4C C:HEM401 3.0 60.9 0.5 C1C C:HEM401 3.1 57.9 0.5 C4A C:HEM401 3.1 54.8 0.5 C1D C:HEM401 3.1 57.0 0.5 C1A C:HEM401 3.1 52.3 0.5 C4D C:HEM401 3.2 52.7 0.5 CHB C:HEM401 3.4 56.2 0.5 CHD C:HEM401 3.4 57.7 0.5 CHC C:HEM401 3.4 59.2 0.5 CHA C:HEM401 3.5 52.0 0.5 N2 C:AZI402 3.7 52.4 0.5 C2B C:HEM401 4.2 61.5 0.5 C3B C:HEM401 4.2 64.0 0.5 C3C C:HEM401 4.3 61.0 0.5 C2C C:HEM401 4.3 62.5 0.5 C3A C:HEM401 4.3 51.6 0.5 C2D C:HEM401 4.3 53.0 0.5 N D:ALA214 4.3 67.5 1.0 C2A C:HEM401 4.3 53.5 0.5 C3D C:HEM401 4.4 50.5 0.5 CA D:ALA214 4.6 66.0 0.5 N1 C:AZI402 4.7 56.6 0.5

Iron binding site 4 out of 4 in the The Heme-Bound Structure of the Chloroplast Protein AT3G03890


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Heme-Bound Structure of the Chloroplast Protein AT3G03890 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:63.5 occ:0.50 FE D:HEM401 0.0 63.5 0.5 NC D:HEM401 2.0 72.1 0.5 NA D:HEM401 2.0 66.5 0.5 ND D:HEM401 2.1 67.6 0.5 NB D:HEM401 2.1 69.9 0.5 O D:HOH534 2.4 75.5 1.0 N1 D:AZI402 2.7 64.6 0.5 C1C D:HEM401 3.0 72.0 0.5 C4C D:HEM401 3.0 71.5 0.5 C4B D:HEM401 3.1 72.5 0.5 C1A D:HEM401 3.1 62.7 0.5 C1D D:HEM401 3.1 66.5 0.5 C4D D:HEM401 3.1 64.0 0.5 C4A D:HEM401 3.1 67.0 0.5 C1B D:HEM401 3.1 72.1 0.5 N2 D:AZI402 3.3 67.2 0.5 CHC D:HEM401 3.4 73.5 0.5 CHD D:HEM401 3.4 68.9 0.5 CHA D:HEM401 3.4 61.1 0.5 CHB D:HEM401 3.5 67.8 0.5 N3 D:AZI402 4.1 65.2 0.5 C2C D:HEM401 4.2 72.2 0.5 C3C D:HEM401 4.3 72.2 0.5 C2A D:HEM401 4.3 62.9 0.5 C3B D:HEM401 4.3 76.0 0.5 C3A D:HEM401 4.3 62.7 0.5 C2D D:HEM401 4.3 67.3 0.5 C2B D:HEM401 4.3 73.1 0.5 C3D D:HEM401 4.3 64.5 0.5 N C:ALA214 4.4 83.6 1.0 CA C:ALA214 4.6 83.4 1.0 O C:THR215 4.9 87.4 1.0 CD1 C:LEU218 4.9 74.8 1.0

J.Wang, Q.Guo, X.Li, X.Wang, L.Liu. The Arabidopsis Locus AT3G03890 Encodes A Dimeric Beta-Barrel Protein Implicated in Heme Degradation. Biochem.J. 2020.
ISSN: ESSN 1470-8728
PubMed: 33284325
DOI: 10.1042/BCJ20200712