Iron in PDB 5xdh: His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1

The structure of His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1, PDB code: 5xdh was solved by D.Hira, R.Kitamura, T.Nakamura, Y.Yamagata, K.Furukawa, T.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.84 / 1.32
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.794, 47.687, 48.993, 96.46, 99.01, 102.13
R / Rfree (%)	15.5 / 17.5

The binding sites of Iron atom in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1 (pdb code 5xdh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1, PDB code: 5xdh:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:6.8 occ:1.00 FE A:HEC101 0.0 6.8 1.0 OE2 A:DAH60 2.0 7.7 1.0 ND A:HEC101 2.0 6.8 1.0 NA A:HEC101 2.0 7.1 1.0 NE2 A:HIS15 2.0 6.8 1.0 NC A:HEC101 2.0 7.0 1.0 NB A:HEC101 2.1 7.0 1.0 CE1 A:HIS15 3.0 7.0 1.0 C1D A:HEC101 3.0 7.0 1.0 C4D A:HEC101 3.0 7.1 1.0 CE2 A:DAH60 3.0 8.4 1.0 C4A A:HEC101 3.0 7.1 1.0 C1A A:HEC101 3.0 7.2 1.0 C4B A:HEC101 3.0 7.1 1.0 C4C A:HEC101 3.0 7.0 1.0 C1B A:HEC101 3.0 7.0 1.0 C1C A:HEC101 3.1 7.2 1.0 CD2 A:HIS15 3.1 6.8 1.0 CHD A:HEC101 3.4 7.1 1.0 CHB A:HEC101 3.4 7.1 1.0 CHA A:HEC101 3.4 7.2 1.0 CHC A:HEC101 3.4 7.1 1.0 CD2 A:DAH60 3.7 8.1 1.0 CZ A:DAH60 4.0 8.9 1.0 O A:HOH228 4.0 11.4 1.0 OZ A:DAH60 4.0 10.1 1.0 ND1 A:HIS15 4.1 7.1 1.0 CG A:HIS15 4.2 7.1 1.0 C2A A:HEC101 4.2 7.7 1.0 C3A A:HEC101 4.3 7.4 1.0 C2D A:HEC101 4.3 7.2 1.0 C2C A:HEC101 4.3 7.5 1.0 C2B A:HEC101 4.3 7.2 1.0 C3D A:HEC101 4.3 7.2 1.0 C3C A:HEC101 4.3 7.3 1.0 C3B A:HEC101 4.3 7.4 1.0 CG A:DAH60 5.0 8.4 1.0

Iron binding site 2 out of 4 in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:8.1 occ:1.00 FE B:HEC101 0.0 8.1 1.0 OE2 B:DAH60 2.0 8.9 1.0 ND B:HEC101 2.0 8.2 1.0 NA B:HEC101 2.0 8.4 1.0 NE2 B:HIS15 2.0 8.6 1.0 NB B:HEC101 2.0 8.3 1.0 NC B:HEC101 2.1 8.4 1.0 CE2 B:DAH60 3.0 9.5 1.0 CE1 B:HIS15 3.0 8.9 1.0 C4D B:HEC101 3.0 8.6 1.0 C1D B:HEC101 3.0 8.3 1.0 C1A B:HEC101 3.0 8.7 1.0 C4B B:HEC101 3.0 8.5 1.0 C4A B:HEC101 3.0 8.6 1.0 CD2 B:HIS15 3.0 8.7 1.0 C1B B:HEC101 3.0 8.2 1.0 C4C B:HEC101 3.1 8.3 1.0 C1C B:HEC101 3.1 8.5 1.0 CHA B:HEC101 3.4 8.7 1.0 CHD B:HEC101 3.4 8.3 1.0 CHB B:HEC101 3.4 8.4 1.0 CHC B:HEC101 3.4 8.5 1.0 CD2 B:DAH60 3.7 9.8 1.0 CZ B:DAH60 3.9 10.4 1.0 OZ B:DAH60 4.0 10.9 1.0 O B:HOH238 4.1 11.6 1.0 ND1 B:HIS15 4.1 9.1 1.0 CG B:HIS15 4.2 9.1 1.0 C2A B:HEC101 4.2 9.3 1.0 C3A B:HEC101 4.2 9.0 1.0 C2B B:HEC101 4.3 8.5 1.0 C2D B:HEC101 4.3 8.6 1.0 C2C B:HEC101 4.3 8.8 1.0 C3C B:HEC101 4.3 8.7 1.0 C3D B:HEC101 4.3 8.6 1.0 C3B B:HEC101 4.3 8.7 1.0 CG B:DAH60 5.0 10.1 1.0 CD2 B:LEU63 5.0 11.4 1.0

Iron binding site 3 out of 4 in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:8.1 occ:1.00 FE C:HEC101 0.0 8.1 1.0 ND C:HEC101 2.0 8.7 1.0 OE2 C:DAH60 2.0 9.2 1.0 NA C:HEC101 2.0 8.9 1.0 NE2 C:HIS15 2.0 8.5 1.0 NC C:HEC101 2.0 8.2 1.0 NB C:HEC101 2.1 8.2 1.0 CE2 C:DAH60 3.0 9.9 1.0 CE1 C:HIS15 3.0 8.9 1.0 C1D C:HEC101 3.0 8.7 1.0 C4A C:HEC101 3.0 8.9 1.0 C4D C:HEC101 3.0 9.1 1.0 C1A C:HEC101 3.0 9.5 1.0 C1B C:HEC101 3.0 8.3 1.0 C4B C:HEC101 3.0 8.1 1.0 C4C C:HEC101 3.0 8.3 1.0 CD2 C:HIS15 3.1 8.7 1.0 C1C C:HEC101 3.1 8.0 1.0 CHB C:HEC101 3.4 8.8 1.0 CHD C:HEC101 3.4 8.6 1.0 CHA C:HEC101 3.4 9.4 1.0 CHC C:HEC101 3.4 8.0 1.0 CD2 C:DAH60 3.7 9.8 1.0 CZ C:DAH60 3.9 10.6 1.0 OZ C:DAH60 4.0 11.7 1.0 O C:HOH229 4.0 10.9 1.0 ND1 C:HIS15 4.1 9.4 1.0 CG C:HIS15 4.2 8.9 1.0 C2A C:HEC101 4.2 10.5 1.0 C3A C:HEC101 4.2 9.8 1.0 C2D C:HEC101 4.3 9.2 1.0 C2B C:HEC101 4.3 8.3 1.0 C2C C:HEC101 4.3 8.2 1.0 C3D C:HEC101 4.3 9.4 1.0 C3C C:HEC101 4.3 8.4 1.0 C3B C:HEC101 4.3 8.3 1.0 CG C:DAH60 5.0 10.1 1.0

Iron binding site 4 out of 4 in the His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of His/Dopa Ligated Cytochrome C From An Anammox Organism Ksu-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe101 b:7.7 occ:1.00 FE D:HEC101 0.0 7.7 1.0 ND D:HEC101 2.0 8.0 1.0 OE2 D:DAH60 2.0 8.3 1.0 NA D:HEC101 2.0 8.1 1.0 NE2 D:HIS15 2.0 7.7 1.0 NB D:HEC101 2.1 7.7 1.0 NC D:HEC101 2.1 8.0 1.0 CE2 D:DAH60 3.0 9.0 1.0 C4D D:HEC101 3.0 8.4 1.0 CE1 D:HIS15 3.0 8.1 1.0 C1D D:HEC101 3.0 8.2 1.0 C4B D:HEC101 3.0 7.7 1.0 C4A D:HEC101 3.0 7.9 1.0 C4C D:HEC101 3.0 8.2 1.0 C1A D:HEC101 3.0 8.5 1.0 C1B D:HEC101 3.0 7.6 1.0 CD2 D:HIS15 3.1 7.8 1.0 C1C D:HEC101 3.1 7.9 1.0 CHD D:HEC101 3.4 8.2 1.0 CHA D:HEC101 3.4 8.3 1.0 CHB D:HEC101 3.4 7.8 1.0 CHC D:HEC101 3.4 7.8 1.0 CD2 D:DAH60 3.7 9.4 1.0 CZ D:DAH60 3.9 9.4 1.0 OZ D:DAH60 4.0 9.7 1.0 O D:HOH237 4.1 11.3 1.0 ND1 D:HIS15 4.1 8.1 1.0 CG D:HIS15 4.2 8.2 1.0 C2C D:HEC101 4.2 8.3 1.0 C3A D:HEC101 4.2 8.2 1.0 C2A D:HEC101 4.2 8.9 1.0 C3D D:HEC101 4.3 8.7 1.0 C2B D:HEC101 4.3 7.8 1.0 C3C D:HEC101 4.3 8.3 1.0 C2D D:HEC101 4.3 8.6 1.0 C3B D:HEC101 4.3 7.8 1.0 CD2 D:LEU63 4.9 10.4 1.0 CG D:DAH60 5.0 9.9 1.0

D.Hira, R.Kitamura, T.Nakamura, Y.Yamagata, K.Furukawa, T.Fujii. Anammox Organism Ksu-1 Expresses A Novel His/Dopa Ligated Cytochrome C. J. Mol. Biol. V. 430 1189 2018.
ISSN: ESSN 1089-8638
PubMed: 29481839
DOI: 10.1016/J.JMB.2018.02.017