Iron in PDB 3wsi: Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii

The structure of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii, PDB code: 3wsi 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)	44.93 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.210, 135.830, 161.460, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22

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

Iron binding site 1 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:35.9 occ:1.00 O2 A:PO4302 2.0 49.8 1.0 NE2 A:HIS71 2.2 41.8 1.0 NE2 A:HIS221 2.3 34.2 1.0 OE2 A:GLU225 2.4 36.3 1.0 OE1 A:GLU225 2.8 39.0 1.0 CD A:GLU225 2.9 37.6 1.0 P A:PO4302 3.1 51.4 1.0 CE1 A:HIS71 3.1 40.7 1.0 CD2 A:HIS71 3.2 41.3 1.0 CD2 A:HIS221 3.2 31.6 1.0 CE1 A:HIS221 3.2 36.1 1.0 O1 A:PO4302 3.3 49.3 1.0 O3 A:PO4302 3.5 57.0 1.0 ND1 A:HIS71 4.2 40.3 1.0 CA A:GLY178 4.3 38.6 1.0 CG A:HIS71 4.3 39.3 1.0 ND1 A:HIS221 4.3 37.0 1.0 CG A:GLU225 4.3 36.8 1.0 O4 A:PO4302 4.4 56.8 1.0 CG A:HIS221 4.4 34.1 1.0 CD2 A:HIS70 4.4 33.1 1.0 NE2 F:HIS204 4.4 42.4 1.0 NE2 A:HIS70 4.6 36.8 1.0 NE2 A:HIS103 4.7 48.3 1.0 CE1 F:HIS204 4.7 38.3 1.0 N A:TYR179 4.9 40.0 1.0

Iron binding site 2 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:37.0 occ:1.00 O1 B:PO4302 2.1 54.4 1.0 NE2 B:HIS221 2.3 34.4 1.0 NE2 B:HIS71 2.3 49.1 1.0 OE2 B:GLU225 2.5 44.6 1.0 OE1 B:GLU225 2.6 40.4 1.0 CD B:GLU225 2.8 38.8 1.0 P B:PO4302 3.1 53.0 1.0 CE1 B:HIS221 3.2 36.5 1.0 CD2 B:HIS71 3.3 45.9 1.0 CD2 B:HIS221 3.3 36.0 1.0 O2 B:PO4302 3.3 56.0 1.0 CE1 B:HIS71 3.3 50.0 1.0 O4 B:PO4302 3.3 59.0 1.0 CD2 B:HIS70 4.2 33.9 1.0 NE2 B:HIS70 4.2 37.0 1.0 CA B:GLY178 4.3 33.5 1.0 ND1 B:HIS221 4.3 39.1 1.0 CG B:GLU225 4.3 32.5 1.0 CG B:HIS221 4.4 36.0 1.0 ND1 B:HIS71 4.4 47.1 1.0 O3 B:PO4302 4.4 53.5 1.0 CG B:HIS71 4.4 43.5 1.0 NE2 D:HIS204 4.5 43.7 1.0 NE2 B:HIS103 4.6 43.1 1.0 CE1 D:HIS204 4.6 45.9 1.0 N B:TYR179 4.8 35.8 1.0

Iron binding site 3 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:39.0 occ:1.00 O4 C:PO4302 1.9 53.7 1.0 NE2 C:HIS71 2.3 45.9 1.0 NE2 C:HIS221 2.3 35.0 1.0 OE1 C:GLU225 2.3 42.4 1.0 OE2 C:GLU225 2.6 43.6 1.0 CD C:GLU225 2.8 41.6 1.0 CE1 C:HIS71 3.1 43.0 1.0 CE1 C:HIS221 3.2 36.3 1.0 CD2 C:HIS221 3.3 35.2 1.0 P C:PO4302 3.3 55.4 1.0 CD2 C:HIS71 3.3 46.0 1.0 O3 C:PO4302 3.7 54.3 1.0 O C:HOH415 3.9 38.7 1.0 O1 C:PO4302 4.0 60.2 1.0 CD2 C:HIS70 4.2 39.7 1.0 CA C:GLY178 4.2 36.4 1.0 ND1 C:HIS71 4.3 43.1 1.0 CG C:GLU225 4.3 37.8 1.0 O2 C:PO4302 4.3 60.7 1.0 ND1 C:HIS221 4.3 38.6 1.0 NE2 C:HIS70 4.4 45.7 1.0 CG C:HIS221 4.4 35.9 1.0 CG C:HIS71 4.4 42.5 1.0 NE2 E:HIS204 4.6 51.6 1.0 NE2 C:HIS103 4.7 44.7 1.0 CE1 E:HIS204 4.8 52.1 1.0 N C:TYR179 4.9 37.9 1.0

Iron binding site 4 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:38.8 occ:1.00 O2 D:PO4302 2.0 67.0 1.0 NE2 D:HIS71 2.2 43.1 1.0 NE2 D:HIS221 2.2 39.4 1.0 OE2 D:GLU225 2.4 48.3 1.0 OE1 D:GLU225 2.6 46.8 1.0 CD D:GLU225 2.8 47.6 1.0 CD2 D:HIS221 3.2 39.9 1.0 CE1 D:HIS221 3.2 40.9 1.0 CE1 D:HIS71 3.2 45.0 1.0 P D:PO4302 3.2 64.1 1.0 CD2 D:HIS71 3.2 43.8 1.0 O4 D:PO4302 3.4 63.6 1.0 O D:HOH403 4.0 37.6 1.0 O3 D:PO4302 4.0 68.7 1.0 CA D:GLY178 4.3 40.3 1.0 O1 D:PO4302 4.3 65.7 1.0 ND1 D:HIS221 4.3 43.0 1.0 CG D:HIS221 4.3 40.8 1.0 CD2 D:HIS70 4.3 45.5 1.0 CG D:GLU225 4.3 45.5 1.0 ND1 D:HIS71 4.3 45.1 1.0 CG D:HIS71 4.4 43.1 1.0 NE2 D:HIS70 4.4 47.2 1.0 NE2 B:HIS204 4.5 51.7 1.0 CE1 B:HIS204 4.7 54.1 1.0 NE2 D:HIS103 4.8 46.0 1.0 N D:TYR179 4.9 39.8 1.0

Iron binding site 5 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:41.0 occ:1.00 O3 E:PO4302 2.0 64.1 1.0 NE2 E:HIS221 2.2 36.6 1.0 NE2 E:HIS71 2.3 46.0 1.0 OE1 E:GLU225 2.5 47.7 1.0 OE2 E:GLU225 2.5 52.1 1.0 CD E:GLU225 2.8 48.5 1.0 CE1 E:HIS221 3.1 38.9 1.0 P E:PO4302 3.1 63.8 1.0 CE1 E:HIS71 3.2 44.9 1.0 CD2 E:HIS221 3.2 36.7 1.0 O1 E:PO4302 3.3 63.3 1.0 CD2 E:HIS71 3.3 45.8 1.0 O4 E:PO4302 3.8 66.6 1.0 ND1 E:HIS221 4.2 41.1 1.0 CA E:GLY178 4.2 38.9 1.0 CD2 E:HIS70 4.2 38.6 1.0 CG E:HIS221 4.2 39.6 1.0 CG E:GLU225 4.3 47.2 1.0 ND1 E:HIS71 4.3 43.6 1.0 NE2 E:HIS70 4.3 39.5 1.0 O2 E:PO4302 4.3 66.8 1.0 CG E:HIS71 4.4 42.4 1.0 NE2 C:HIS204 4.6 48.9 1.0 CE1 C:HIS204 4.6 50.0 1.0 NE2 E:HIS103 4.7 48.1 1.0 N E:TYR179 4.9 38.4 1.0

Iron binding site 6 out of 6 in the Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Edta-Treated, Reduced Hcgd From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe301 b:31.8 occ:1.00 O3 F:PO4302 2.0 46.9 1.0 NE2 F:HIS71 2.2 40.0 1.0 NE2 F:HIS221 2.2 35.6 1.0 OE2 F:GLU225 2.3 34.8 1.0 OE1 F:GLU225 2.7 36.7 1.0 CD F:GLU225 2.8 35.0 1.0 CE1 F:HIS221 3.1 34.3 1.0 P F:PO4302 3.2 51.6 1.0 CE1 F:HIS71 3.2 43.3 1.0 CD2 F:HIS71 3.2 39.9 1.0 CD2 F:HIS221 3.3 33.2 1.0 O2 F:PO4302 3.6 51.6 1.0 O1 F:PO4302 3.6 54.2 1.0 ND1 F:HIS221 4.2 35.9 1.0 CD2 F:HIS70 4.2 30.6 1.0 CA F:GLY178 4.3 35.9 1.0 CG F:GLU225 4.3 31.9 1.0 ND1 F:HIS71 4.3 43.0 1.0 CG F:HIS221 4.3 32.2 1.0 NE2 F:HIS70 4.3 34.8 1.0 CG F:HIS71 4.3 39.3 1.0 NE2 A:HIS204 4.4 39.6 1.0 O4 F:PO4302 4.4 55.0 1.0 CE1 A:HIS204 4.6 38.5 1.0 NE2 F:HIS103 4.6 38.9 1.0 N F:TYR179 4.9 28.2 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