Iron in PDB 1hfe: 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans

All present enzymatic activity of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans:
1.18.99.1;

The structure of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans, PDB code: 1hfe was solved by Y.Nicolet, C.Piras, P.Legrand, E.C.Hatchikian, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.970, 123.070, 65.070, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.2

The structure of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans (pdb code 1hfe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans, PDB code: 1hfe:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe426 b:21.9 occ:1.00 C L:CMO430 1.8 23.0 1.0 C L:CYN429 1.8 20.7 1.0 S1 L:PDT425 2.3 26.8 1.0 S2 L:PDT425 2.3 22.8 1.0 SG L:CYS382 2.5 9.5 1.0 FE L:FE2427 2.6 26.1 1.0 O L:HOH433 2.9 20.1 1.0 O L:CMO430 2.9 23.6 1.0 N L:CYN429 2.9 18.5 1.0 C1 L:PDT425 3.3 24.0 1.0 C3 L:PDT425 3.4 23.1 1.0 CB L:CYS382 3.4 9.2 1.0 C2 L:PDT425 3.7 24.9 1.0 C L:CYN428 3.7 25.8 1.0 C L:CMO431 3.8 25.7 1.0 FE2 L:SF4424 4.1 8.6 1.0 S3 L:SF4424 4.3 9.2 1.0 CE L:LYS237 4.6 5.9 1.0 N L:CYN428 4.7 22.1 1.0 CG L:PRO233 4.7 7.2 1.0 O L:CMO431 4.8 24.9 1.0 CB L:ALA107 4.8 10.3 1.0 CA L:CYS382 4.8 8.8 1.0

Iron binding site 2 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe427 b:26.1 occ:1.00 C L:CMO431 1.8 25.7 1.0 C L:CYN428 1.8 25.8 1.0 S2 L:PDT425 2.3 22.8 1.0 S1 L:PDT425 2.3 26.8 1.0 FE L:FE2426 2.6 21.9 1.0 O L:HOH433 2.6 20.1 1.0 O L:CMO431 2.9 24.9 1.0 N L:CYN428 3.0 22.1 1.0 C2 L:PDT425 3.1 24.9 1.0 C1 L:PDT425 3.4 24.0 1.0 C3 L:PDT425 3.4 23.1 1.0 C L:CYN429 3.5 20.7 1.0 C L:CMO430 3.8 23.0 1.0 CG L:PRO203 4.0 11.2 1.0 CD L:PRO203 4.1 10.9 1.0 CD2 L:PHE296 4.4 10.9 1.0 N L:CYN429 4.4 18.5 1.0 NZ L:LYS237 4.4 7.8 1.0 CB L:PRO203 4.5 10.2 1.0 CE L:LYS237 4.7 5.9 1.0 SG L:CYS382 4.7 9.5 1.0 CD L:PRO108 4.7 10.0 1.0 O L:CMO430 4.7 23.6 1.0

Iron binding site 3 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe422 b:11.0 occ:1.00 FE1 L:SF4422 0.0 11.0 1.0 SG L:CYS41 2.3 11.0 1.0 S2 L:SF4422 2.3 12.3 1.0 S3 L:SF4422 2.3 11.5 1.0 S4 L:SF4422 2.3 13.1 1.0 FE3 L:SF4422 2.6 11.5 1.0 FE2 L:SF4422 2.7 12.6 1.0 FE4 L:SF4422 2.7 10.2 1.0 CB L:CYS41 3.3 11.0 1.0 S1 L:SF4422 3.8 13.9 1.0 N L:CYS41 3.9 10.1 1.0 CA L:CYS41 4.2 11.4 1.0 CD1 L:ILE81 4.4 10.3 1.0 CD2 L:HIS58 4.5 10.7 1.0 SG L:CYS35 4.6 13.1 1.0 CG L:HIS58 4.6 10.4 1.0 SG L:CYS38 4.7 12.9 1.0 CB L:HIS58 4.7 11.4 1.0 N L:THR40 4.8 10.3 1.0 SG L:CYS76 4.8 11.3 1.0 N L:ASP39 4.9 12.1 1.0 O L:HOH664 4.9 35.2 1.0

Iron binding site 4 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe422 b:12.6 occ:1.00 FE2 L:SF4422 0.0 12.6 1.0 S3 L:SF4422 2.3 11.5 1.0 S1 L:SF4422 2.3 13.9 1.0 S4 L:SF4422 2.3 13.1 1.0 SG L:CYS38 2.3 12.9 1.0 FE1 L:SF4422 2.7 11.0 1.0 FE4 L:SF4422 2.7 10.2 1.0 FE3 L:SF4422 2.7 11.5 1.0 N L:CYS38 3.4 13.9 1.0 CB L:CYS38 3.6 13.7 1.0 S2 L:SF4422 3.9 12.3 1.0 CA L:CYS38 3.9 13.6 1.0 N L:ASP39 4.0 12.1 1.0 N L:THR40 4.3 10.3 1.0 C L:CYS38 4.3 12.9 1.0 CD L:PRO77 4.4 12.1 1.0 C L:GLY37 4.5 14.0 1.0 N L:GLY37 4.5 14.3 1.0 SG L:CYS41 4.6 11.0 1.0 SG L:CYS76 4.7 11.3 1.0 CB L:THR40 4.7 10.6 1.0 CA L:GLY37 4.7 13.8 1.0 SG L:CYS35 4.7 13.1 1.0 CG L:PRO77 4.8 13.2 1.0 CG1 L:ILE36 4.8 15.6 1.0 N L:CYS41 4.9 10.1 1.0 OG1 L:THR40 4.9 11.6 1.0 CA L:ASP39 4.9 12.0 1.0

Iron binding site 5 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe422 b:11.5 occ:1.00 FE3 L:SF4422 0.0 11.5 1.0 S1 L:SF4422 2.3 13.9 1.0 S2 L:SF4422 2.3 12.3 1.0 S4 L:SF4422 2.3 13.1 1.0 SG L:CYS35 2.3 13.1 1.0 FE1 L:SF4422 2.6 11.0 1.0 FE4 L:SF4422 2.7 10.2 1.0 FE2 L:SF4422 2.7 12.6 1.0 CB L:CYS35 3.3 13.9 1.0 CA L:CYS35 3.7 14.9 1.0 S3 L:SF4422 3.8 11.5 1.0 N L:GLY37 3.9 14.3 1.0 N L:ILE36 4.0 16.2 1.0 C L:CYS35 4.2 15.6 1.0 CA L:GLY37 4.4 13.8 1.0 N L:CYS38 4.6 13.9 1.0 CB L:HIS58 4.6 11.4 1.0 SG L:CYS41 4.6 11.0 1.0 CG L:HIS58 4.6 10.4 1.0 ND1 L:HIS58 4.8 10.7 1.0 SG L:CYS76 4.8 11.3 1.0 CB L:ALA80 4.9 11.3 1.0 C L:ILE36 4.9 15.2 1.0 SG L:CYS38 4.9 12.9 1.0 N L:CYS35 5.0 14.9 1.0

Iron binding site 6 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe422 b:10.2 occ:1.00 FE4 L:SF4422 0.0 10.2 1.0 S3 L:SF4422 2.3 11.5 1.0 S2 L:SF4422 2.3 12.3 1.0 SG L:CYS76 2.3 11.3 1.0 S1 L:SF4422 2.3 13.9 1.0 FE1 L:SF4422 2.7 11.0 1.0 FE3 L:SF4422 2.7 11.5 1.0 FE2 L:SF4422 2.7 12.6 1.0 CB L:CYS76 3.3 9.9 1.0 S4 L:SF4422 3.9 13.1 1.0 CA L:CYS76 3.9 10.3 1.0 CB L:ALA80 4.3 11.3 1.0 CD L:PRO77 4.4 12.1 1.0 CD1 L:ILE81 4.4 10.3 1.0 CG1 L:ILE81 4.5 8.7 1.0 C L:CYS76 4.6 10.5 1.0 SG L:CYS38 4.6 12.9 1.0 N L:PRO77 4.7 11.9 1.0 CB L:GLU78 4.7 14.3 1.0 SG L:CYS41 4.8 11.0 1.0 N L:GLU78 4.8 12.8 1.0 SG L:CYS35 4.9 13.1 1.0 N L:ALA80 4.9 11.1 1.0

Iron binding site 7 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe423 b:8.6 occ:1.00 FE1 L:SF4423 0.0 8.6 1.0 SG L:CYS45 2.3 9.4 1.0 S2 L:SF4423 2.3 10.8 1.0 S4 L:SF4423 2.3 11.3 1.0 S3 L:SF4423 2.3 10.1 1.0 FE2 L:SF4423 2.7 8.4 1.0 FE4 L:SF4423 2.7 9.0 1.0 FE3 L:SF4423 2.8 9.0 1.0 CB L:CYS45 3.2 10.6 1.0 CA L:CYS45 3.8 11.3 1.0 S1 L:SF4423 3.9 9.6 1.0 CD L:PRO46 3.9 10.8 1.0 CB L:ALA49 4.4 10.9 1.0 OG1 L:THR47 4.5 12.6 1.0 CD1 L:ILE50 4.5 8.6 1.0 CG1 L:ILE50 4.5 9.5 1.0 N L:PRO46 4.6 11.7 1.0 C L:CYS45 4.6 11.2 1.0 SG L:CYS69 4.7 8.8 1.0 SG L:CYS72 4.8 9.5 1.0 CG L:PRO46 4.8 10.6 1.0 N L:CYS45 4.9 11.4 1.0 SG L:CYS66 4.9 10.3 1.0 N L:ALA49 5.0 11.3 1.0

Iron binding site 8 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe423 b:8.4 occ:1.00 FE2 L:SF4423 0.0 8.4 1.0 S1 L:SF4423 2.3 9.6 1.0 S3 L:SF4423 2.3 10.1 1.0 SG L:CYS66 2.3 10.3 1.0 S4 L:SF4423 2.3 11.3 1.0 FE1 L:SF4423 2.7 8.6 1.0 FE4 L:SF4423 2.7 9.0 1.0 FE3 L:SF4423 2.7 9.0 1.0 CB L:CYS66 3.4 10.0 1.0 CA L:CYS66 3.8 10.0 1.0 S2 L:SF4423 3.9 10.8 1.0 N L:ILE67 4.0 9.1 1.0 N L:ASN68 4.0 9.4 1.0 CG2 L:VAL28 4.2 12.7 0.5 C L:CYS66 4.3 10.2 1.0 CA L:ASN68 4.6 9.6 1.0 N L:CYS69 4.7 9.0 1.0 SG L:CYS45 4.7 9.4 1.0 SG L:CYS72 4.9 9.5 1.0 CB L:ALA49 4.9 10.9 1.0 CD1 L:ILE60 4.9 11.8 1.0 C L:ILE67 4.9 8.8 1.0 SG L:CYS69 5.0 8.8 1.0

Iron binding site 9 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe423 b:9.0 occ:1.00 FE3 L:SF4423 0.0 9.0 1.0 SG L:CYS69 2.3 8.8 1.0 S4 L:SF4423 2.3 11.3 1.0 S1 L:SF4423 2.3 9.6 1.0 S2 L:SF4423 2.3 10.8 1.0 FE2 L:SF4423 2.7 8.4 1.0 FE4 L:SF4423 2.8 9.0 1.0 FE1 L:SF4423 2.8 8.6 1.0 N L:CYS69 3.6 9.0 1.0 CB L:CYS69 3.6 8.4 1.0 N L:GLY70 3.8 8.0 1.0 S3 L:SF4423 4.0 10.1 1.0 CA L:CYS69 4.0 8.8 1.0 CD L:PRO46 4.2 10.8 1.0 C L:CYS69 4.3 9.1 1.0 N L:GLN71 4.4 8.2 1.0 CG1 L:ILE67 4.5 8.1 1.0 N L:ASN68 4.5 9.4 1.0 C L:ASN68 4.6 9.7 1.0 SG L:CYS72 4.7 9.5 1.0 SG L:CYS66 4.7 10.3 1.0 CG L:PRO46 4.8 10.6 1.0 SG L:CYS45 4.8 9.4 1.0 CA L:GLY70 4.8 7.9 1.0 O L:HOH482 4.8 9.0 1.0 N L:ILE67 4.9 9.1 1.0 CA L:ASN68 4.9 9.6 1.0 N L:CYS72 5.0 8.2 1.0

Iron binding site 10 out of 28 in the 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 1.6 A Resolution Structure of the Fe-Only Hydrogenase From Desulfovibrio Desulfuricans within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe423 b:9.0 occ:1.00 FE4 L:SF4423 0.0 9.0 1.0 S2 L:SF4423 2.3 10.8 1.0 SG L:CYS72 2.3 9.5 1.0 S3 L:SF4423 2.3 10.1 1.0 S1 L:SF4423 2.3 9.6 1.0 FE1 L:SF4423 2.7 8.6 1.0 FE2 L:SF4423 2.7 8.4 1.0 FE3 L:SF4423 2.8 9.0 1.0 CB L:CYS72 3.3 9.2 1.0 S4 L:SF4423 3.9 11.3 1.0 N L:CYS72 4.1 8.2 1.0 CG2 L:VAL28 4.3 12.7 0.5 CA L:CYS72 4.3 9.3 1.0 CD1 L:ILE50 4.3 8.6 1.0 CG1 L:VAL28 4.5 11.8 0.5 SG L:CYS69 4.6 8.8 1.0 N L:GLY70 4.7 8.0 1.0 CD1 L:ILE60 4.7 11.8 1.0 SG L:CYS66 4.7 10.3 1.0 SG L:CYS45 4.8 9.4 1.0 CG1 L:ILE50 4.8 9.5 1.0 N L:GLN71 4.8 8.2 1.0 CA L:GLY70 4.9 7.9 1.0

Y.Nicolet, C.Piras, P.Legrand, C.E.Hatchikian, J.C.Fontecilla-Camps. Desulfovibrio Desulfuricans Iron Hydrogenase: the Structure Shows Unusual Coordination to An Active Site Fe Binuclear Center. Structure Fold.Des. V. 7 13 1999.
ISSN: ISSN 0969-2126
PubMed: 10368269
DOI: 10.1016/S0969-2126(99)80005-7