Iron in PDB 3wsf: Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate

The structure of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate, PDB code: 3wsf was solved by T.Fujishiro, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.78 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.190, 137.250, 160.910, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.4

The binding sites of Iron atom in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate (pdb code 3wsf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate, PDB code: 3wsf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:26.0 occ:0.73 O5 A:CIT302 2.0 21.4 0.7 NE2 A:HIS221 2.1 25.4 1.0 NE2 A:HIS71 2.1 38.7 1.0 OE2 A:GLU225 2.2 39.6 1.0 O6 A:CIT302 2.5 22.8 0.7 C6 A:CIT302 2.6 28.6 0.7 CE1 A:HIS221 2.8 24.8 1.0 CD A:GLU225 2.8 33.0 1.0 OE1 A:GLU225 2.8 29.9 1.0 CE1 A:HIS71 3.0 44.5 1.0 CD2 A:HIS71 3.1 38.9 1.0 CD2 A:HIS221 3.2 20.1 1.0 ND1 A:HIS221 3.9 22.7 1.0 C3 A:CIT302 4.1 37.9 0.7 ND1 A:HIS71 4.1 43.4 1.0 CG A:HIS71 4.2 36.2 1.0 CG A:HIS221 4.2 21.5 1.0 CA A:GLY178 4.2 21.6 1.0 O3 A:CIT302 4.2 45.6 0.7 CD2 A:HIS70 4.3 18.3 1.0 CG A:GLU225 4.3 19.0 1.0 O1 A:CIT302 4.4 39.2 0.7 NE2 A:HIS103 4.4 27.3 1.0 NE2 A:HIS70 4.4 22.6 1.0 C5 A:CIT302 4.4 47.1 0.7 CE1 F:HIS204 4.5 40.2 1.0 NE2 F:HIS204 4.5 37.8 1.0 N A:TYR179 4.6 22.1 1.0 O7 A:CIT302 4.7 38.8 0.7 C4 A:CIT302 4.7 42.8 0.7 C A:GLY178 4.9 19.8 1.0 O4 A:CIT302 5.0 53.4 0.7 C2 A:CIT302 5.0 40.8 0.7 CD2 A:HIS103 5.0 22.9 1.0

Iron binding site 2 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:22.4 occ:0.67 O6 B:CIT302 2.0 29.4 0.8 NE2 B:HIS221 2.1 24.6 1.0 NE2 B:HIS71 2.2 40.3 1.0 OE2 B:GLU225 2.3 45.3 1.0 OE1 B:GLU225 2.7 44.3 1.0 C6 B:CIT302 2.7 33.9 0.8 CE1 B:HIS221 2.8 28.0 1.0 CD B:GLU225 2.8 41.1 1.0 O5 B:CIT302 2.8 27.3 0.8 CD2 B:HIS71 3.1 40.4 1.0 CD2 B:HIS221 3.2 19.1 1.0 CE1 B:HIS71 3.2 42.2 1.0 ND1 B:HIS221 3.9 21.6 1.0 CA B:GLY178 4.1 26.7 1.0 CG B:HIS221 4.2 18.1 1.0 O4 B:CIT302 4.2 52.0 0.8 C3 B:CIT302 4.2 37.8 0.8 CD2 B:HIS70 4.2 19.7 1.0 CG B:GLU225 4.2 27.0 1.0 CG B:HIS71 4.3 37.5 1.0 ND1 B:HIS71 4.3 43.9 1.0 NE2 B:HIS70 4.3 24.5 1.0 NE2 B:HIS103 4.4 24.1 1.0 CE1 D:HIS204 4.5 37.1 1.0 NE2 D:HIS204 4.5 41.0 1.0 O2 B:CIT302 4.6 46.4 0.8 N B:TYR179 4.6 22.5 1.0 O7 B:CIT302 4.7 33.8 0.8 C4 B:CIT302 4.8 46.5 0.8 C5 B:CIT302 4.8 49.4 0.8 C B:GLY178 4.9 24.1 1.0 CD2 B:HIS103 5.0 22.2 1.0

Iron binding site 3 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:25.8 occ:0.69 NE2 C:HIS221 2.0 24.8 1.0 OE1 C:GLU225 2.1 41.7 1.0 NE2 C:HIS71 2.1 33.1 1.0 O5 C:CIT302 2.1 25.1 0.8 O6 C:CIT302 2.6 28.9 0.8 CE1 C:HIS221 2.7 30.8 1.0 C6 C:CIT302 2.7 34.3 0.8 CD C:GLU225 2.7 32.5 1.0 OE2 C:GLU225 2.8 32.1 1.0 CE1 C:HIS71 3.0 36.8 1.0 CD2 C:HIS71 3.1 33.3 1.0 CD2 C:HIS221 3.2 24.2 1.0 ND1 C:HIS221 3.8 24.7 1.0 CG C:HIS221 4.1 21.6 1.0 CA C:GLY178 4.1 17.5 1.0 ND1 C:HIS71 4.2 38.9 1.0 CG C:GLU225 4.2 25.3 1.0 CD2 C:HIS70 4.2 17.8 1.0 C3 C:CIT302 4.2 41.7 0.8 NE2 C:HIS70 4.2 22.1 1.0 CG C:HIS71 4.3 37.1 1.0 NE2 C:HIS103 4.4 26.2 1.0 C5 C:CIT302 4.4 49.1 0.8 O3 C:CIT302 4.5 53.0 0.8 O4 C:CIT302 4.5 53.9 0.8 O1 C:CIT302 4.5 46.7 0.8 NE2 E:HIS204 4.6 44.8 1.0 N C:TYR179 4.6 22.3 1.0 CE1 E:HIS204 4.6 43.9 1.0 O7 C:CIT302 4.8 41.9 0.8 C4 C:CIT302 4.8 42.6 0.8 C C:GLY178 4.9 22.8 1.0

Iron binding site 4 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:26.5 occ:0.73 NE2 D:HIS221 2.0 28.6 1.0 OE2 D:GLU225 2.1 35.2 1.0 O6 D:CIT302 2.1 38.6 0.8 NE2 D:HIS71 2.2 38.5 1.0 O5 D:CIT302 2.5 28.5 0.8 OE1 D:GLU225 2.5 38.8 1.0 CD D:GLU225 2.6 35.9 1.0 C6 D:CIT302 2.7 37.4 0.8 CE1 D:HIS221 2.7 31.6 1.0 CE1 D:HIS71 3.2 42.9 1.0 CD2 D:HIS221 3.2 27.6 1.0 CD2 D:HIS71 3.2 36.0 1.0 ND1 D:HIS221 3.9 27.4 1.0 CE1 D:HIS70 4.1 21.1 1.0 CG D:HIS221 4.1 24.8 1.0 CG D:GLU225 4.1 26.0 1.0 CA D:GLY178 4.1 20.5 1.0 C3 D:CIT302 4.2 44.0 0.8 ND1 D:HIS70 4.2 25.5 1.0 ND1 D:HIS71 4.3 48.6 1.0 CG D:HIS71 4.3 39.5 1.0 O1 D:CIT302 4.4 54.6 0.8 NE2 D:HIS103 4.5 27.8 1.0 NE2 B:HIS204 4.6 39.8 1.0 O3 D:CIT302 4.6 55.5 0.8 N D:TYR179 4.6 20.2 1.0 O7 D:CIT302 4.8 43.5 0.8 CE1 B:HIS204 4.8 43.0 1.0 C4 D:CIT302 4.9 47.3 0.8 C D:GLY178 4.9 23.9 1.0 C5 D:CIT302 4.9 51.2 0.8 C2 D:CIT302 5.0 44.8 0.8

Iron binding site 5 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:26.3 occ:0.69 NE2 E:HIS221 2.0 22.6 1.0 O5 E:CIT302 2.0 33.2 0.8 OE2 E:GLU225 2.1 41.7 1.0 NE2 E:HIS71 2.1 31.4 1.0 OE1 E:GLU225 2.7 37.6 1.0 CD E:GLU225 2.7 37.2 1.0 CE1 E:HIS221 2.7 29.3 1.0 C6 E:CIT302 2.7 38.0 0.8 O6 E:CIT302 2.8 28.1 0.8 CE1 E:HIS71 3.0 38.8 1.0 CD2 E:HIS221 3.1 18.2 1.0 CD2 E:HIS71 3.1 36.5 1.0 ND1 E:HIS221 3.9 25.8 1.0 O1 E:CIT302 4.1 41.1 0.8 CG E:HIS221 4.1 23.1 1.0 ND1 E:HIS71 4.1 41.0 1.0 CA E:GLY178 4.1 25.9 1.0 CG E:GLU225 4.2 26.8 1.0 CD2 E:HIS70 4.2 27.2 1.0 O3 E:CIT302 4.2 41.4 0.8 CG E:HIS71 4.2 36.4 1.0 C3 E:CIT302 4.2 49.7 0.8 NE2 E:HIS70 4.3 29.9 1.0 NE2 E:HIS103 4.5 32.5 1.0 CE1 C:HIS204 4.6 40.5 1.0 N E:TYR179 4.6 26.1 1.0 NE2 C:HIS204 4.7 38.6 1.0 C5 E:CIT302 4.8 46.8 0.8 C2 E:CIT302 4.8 50.8 0.8 C1 E:CIT302 4.8 45.1 0.8 C E:GLY178 4.9 21.7 1.0 C4 E:CIT302 4.9 50.3 0.8

Iron binding site 6 out of 6 in the Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxidized Hcgd From Methanocaldococcus Jannaschii with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:26.7 occ:0.80 O5 F:CIT302 2.1 24.7 0.7 NE2 F:HIS221 2.1 27.2 1.0 NE2 F:HIS71 2.1 16.5 0.6 OE2 F:GLU225 2.2 36.0 1.0 O6 F:CIT302 2.6 17.7 0.7 C6 F:CIT302 2.7 29.0 0.7 CE1 F:HIS221 2.8 28.8 1.0 OE1 F:GLU225 2.8 36.9 1.0 CD F:GLU225 2.8 31.6 1.0 CE1 F:HIS71 3.1 34.3 0.6 CD2 F:HIS71 3.1 25.8 0.6 CD2 F:HIS221 3.3 24.4 1.0 ND1 F:HIS221 3.9 28.0 1.0 CD2 F:HIS70 4.1 15.1 1.0 ND1 F:HIS71 4.1 28.1 0.6 O3 F:CIT302 4.2 41.2 0.7 CG F:HIS71 4.2 23.2 0.6 CG F:HIS221 4.2 22.1 1.0 CA F:GLY178 4.2 17.1 1.0 C3 F:CIT302 4.2 37.1 0.7 NE2 F:HIS70 4.2 21.5 1.0 O2 F:CIT302 4.3 47.5 0.7 CG F:GLU225 4.3 22.5 1.0 NE2 F:HIS103 4.4 27.6 1.0 CE1 A:HIS204 4.5 41.6 1.0 NE2 A:HIS204 4.6 41.9 1.0 N F:TYR179 4.6 20.0 1.0 O7 F:CIT302 4.7 38.4 0.7 C4 F:CIT302 4.8 41.1 0.7 C5 F:CIT302 4.9 42.6 0.7 CD2 F:HIS71 4.9 29.0 0.4 C F:GLY178 4.9 16.9 1.0 CD2 F:HIS103 5.0 23.0 1.0

T.Fujishiro, U.Ermler, S.Shima. A Possible Iron Delivery Function of the Dinuclear Iron Center of Hcgd in [Fe]-Hydrogenase Cofactor Biosynthesis Febs Lett. V. 588 2789 2014.
ISSN: ISSN 0014-5793
PubMed: 24931373
DOI: 10.1016/J.FEBSLET.2014.05.059