Iron in PDB 3c8y: 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase

All present enzymatic activity of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase:
1.12.7.2;

The structure of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase, PDB code: 3c8y was solved by A.S.Pandey, B.J.Lemon, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.39
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.750, 110.750, 103.540, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 19.4

Pages:

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

Binding sites:

The binding sites of Iron atom in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase (pdb code 3c8y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase, PDB code: 3c8y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe575 b:9.0 occ:1.00 FE1 A:HCN575 0.0 9.0 1.0 C3 A:HCN575 1.7 7.9 1.0 C4 A:HCN575 1.8 8.9 1.0 C5 A:HCN575 1.9 9.2 1.0 S1 A:HCN575 2.3 10.5 1.0 S2 A:HCN575 2.3 10.0 1.0 SG A:CYS503 2.4 7.4 1.0 FE2 A:HCN575 2.6 11.4 1.0 O3 A:HCN575 3.0 10.8 1.0 O5 A:HCN575 3.0 13.9 1.0 N4 A:HCN575 3.0 5.2 1.0 CB A:CYS503 3.4 6.2 1.0 C10 A:HCN575 3.5 12.6 1.0 C9 A:HCN575 3.5 14.5 1.0 C7 A:HCN575 3.8 13.0 1.0 C6 A:HCN575 3.9 8.3 1.0 O1 A:HCN575 3.9 16.0 1.0 FE3 A:SF4576 4.0 7.0 1.0 S4 A:SF4576 4.4 6.9 1.0 O2 A:HCN575 4.4 24.9 1.0 CG A:PRO354 4.7 7.0 1.0 O7 A:HCN575 4.7 10.2 1.0 CA A:CYS503 4.8 6.4 1.0 N6 A:HCN575 4.8 6.5 1.0 CE A:LYS358 4.9 8.6 1.0 CD A:PRO231 5.0 8.5 1.0 CD A:PRO354 5.0 7.0 1.0

Iron binding site 2 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe575 b:11.4 occ:1.00 FE2 A:HCN575 0.0 11.4 1.0 C7 A:HCN575 1.8 13.0 1.0 C6 A:HCN575 1.9 8.3 1.0 C5 A:HCN575 2.0 9.2 1.0 S2 A:HCN575 2.3 10.0 1.0 S1 A:HCN575 2.3 10.5 1.0 O2 A:HCN575 2.4 24.9 1.0 FE1 A:HCN575 2.6 9.0 1.0 O5 A:HCN575 2.9 13.9 1.0 O7 A:HCN575 2.9 10.2 1.0 N6 A:HCN575 3.1 6.5 1.0 O1 A:HCN575 3.4 16.0 1.0 C9 A:HCN575 3.4 14.5 1.0 C10 A:HCN575 3.4 12.6 1.0 C3 A:HCN575 3.7 7.9 1.0 C4 A:HCN575 3.7 8.9 1.0 CG A:PRO324 4.1 9.8 1.0 CB A:PRO324 4.3 9.2 1.0 CD A:PRO324 4.3 8.4 1.0 CD2 A:PHE417 4.4 10.9 1.0 SG A:CYS503 4.6 7.4 1.0 NZ A:LYS358 4.7 8.6 1.0 N4 A:HCN575 4.7 5.2 1.0 O3 A:HCN575 4.8 10.8 1.0 CE A:LYS358 4.8 8.6 1.0 CD A:PRO231 4.8 8.5 1.0 O A:CYS299 5.0 9.3 1.0

Iron binding site 3 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe576 b:7.3 occ:1.00 FE1 A:SF4576 0.0 7.3 1.0 S4 A:SF4576 2.2 6.9 1.0 SG A:CYS300 2.3 7.5 1.0 S2 A:SF4576 2.3 7.7 1.0 S3 A:SF4576 2.3 8.0 1.0 FE2 A:SF4576 2.7 7.5 1.0 FE4 A:SF4576 2.7 7.4 1.0 FE3 A:SF4576 2.7 7.0 1.0 CB A:CYS300 3.3 8.6 1.0 S1 A:SF4576 3.8 7.5 1.0 CA A:CYS300 3.9 7.5 1.0 N A:ALA498 4.0 8.3 1.0 CB A:ALA498 4.3 6.9 1.0 C A:CYS300 4.4 7.8 1.0 CD A:PRO301 4.5 7.5 1.0 N A:GLY302 4.5 7.4 1.0 N A:PRO301 4.6 6.9 1.0 SG A:CYS499 4.7 7.5 1.0 CA A:ALA498 4.7 8.0 1.0 N A:CYS499 4.7 7.4 1.0 SG A:CYS503 4.8 7.4 1.0 C10 A:HCN575 4.8 12.6 1.0 SD A:MET497 4.8 11.6 1.0 SG A:CYS355 4.8 7.7 1.0 CA A:GLY302 4.9 6.5 1.0

Iron binding site 4 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe576 b:7.5 occ:1.00 FE2 A:SF4576 0.0 7.5 1.0 S4 A:SF4576 2.2 6.9 1.0 S1 A:SF4576 2.3 7.5 1.0 S3 A:SF4576 2.3 8.0 1.0 SG A:CYS355 2.3 7.7 1.0 FE1 A:SF4576 2.7 7.3 1.0 FE4 A:SF4576 2.7 7.4 1.0 FE3 A:SF4576 2.7 7.0 1.0 CB A:CYS355 3.3 6.2 1.0 O A:HOH585 3.8 8.4 1.0 S2 A:SF4576 3.8 7.7 1.0 O3 A:HCN575 4.0 10.8 1.0 CA A:CYS355 4.3 7.0 1.0 CB A:SER357 4.6 11.8 1.0 C3 A:HCN575 4.6 7.9 1.0 CD A:PRO301 4.6 7.5 1.0 SG A:CYS300 4.7 7.5 1.0 SG A:CYS499 4.7 7.5 1.0 SG A:CYS503 4.8 7.4 1.0 CG A:LYS358 4.8 6.5 1.0 CG A:PRO301 4.9 10.3 1.0

Iron binding site 5 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe576 b:7.0 occ:1.00 FE3 A:SF4576 0.0 7.0 1.0 SG A:CYS503 2.3 7.4 1.0 S4 A:SF4576 2.3 6.9 1.0 S1 A:SF4576 2.3 7.5 1.0 S2 A:SF4576 2.4 7.7 1.0 FE2 A:SF4576 2.7 7.5 1.0 FE1 A:SF4576 2.7 7.3 1.0 FE4 A:SF4576 2.8 7.4 1.0 CB A:CYS503 3.2 6.2 1.0 CA A:CYS503 3.4 6.4 1.0 C3 A:HCN575 3.7 7.9 1.0 O3 A:HCN575 3.8 10.8 1.0 N A:CYS503 3.9 7.3 1.0 FE1 A:HCN575 4.0 9.0 1.0 S3 A:SF4576 4.0 8.0 1.0 C10 A:HCN575 4.1 12.6 1.0 S2 A:HCN575 4.1 10.0 1.0 C A:GLY502 4.7 6.9 1.0 SD A:MET497 4.7 11.6 1.0 SG A:CYS355 4.8 7.7 1.0 C A:CYS503 4.8 6.7 1.0 SG A:CYS300 4.8 7.5 1.0 CB A:CYS355 5.0 6.2 1.0 C4 A:HCN575 5.0 8.9 1.0 SG A:CYS499 5.0 7.5 1.0

Iron binding site 6 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe576 b:7.4 occ:1.00 FE4 A:SF4576 0.0 7.4 1.0 S2 A:SF4576 2.3 7.7 1.0 S1 A:SF4576 2.3 7.5 1.0 SG A:CYS499 2.3 7.5 1.0 S3 A:SF4576 2.3 8.0 1.0 FE2 A:SF4576 2.7 7.5 1.0 FE1 A:SF4576 2.7 7.3 1.0 FE3 A:SF4576 2.8 7.0 1.0 CB A:CYS499 3.2 7.7 1.0 N A:CYS499 3.8 7.4 1.0 S4 A:SF4576 3.9 6.9 1.0 O A:HOH585 4.1 8.4 1.0 CA A:CYS499 4.1 7.1 1.0 CA A:GLY506 4.3 6.7 1.0 SG A:CYS355 4.6 7.7 1.0 SG A:CYS300 4.7 7.5 1.0 CB A:ALA498 4.7 6.9 1.0 C A:ALA498 4.7 6.8 1.0 CA A:CYS503 4.7 6.4 1.0 N A:ALA498 4.9 8.3 1.0 SG A:CYS503 5.0 7.4 1.0 CA A:ALA498 5.0 8.0 1.0

Iron binding site 7 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe577 b:7.3 occ:1.00 FE1 A:SF4577 0.0 7.3 1.0 S4 A:SF4577 2.3 7.7 1.0 SG A:CYS193 2.3 7.7 1.0 S3 A:SF4577 2.3 7.3 1.0 S2 A:SF4577 2.4 7.6 1.0 FE3 A:SF4577 2.8 7.3 1.0 FE2 A:SF4577 2.8 7.7 1.0 FE4 A:SF4577 2.8 7.4 1.0 CB A:CYS193 3.6 7.8 1.0 N A:CYS193 3.6 6.8 1.0 N A:GLY194 3.8 6.8 1.0 S1 A:SF4577 4.0 7.7 1.0 CG2 A:THR161 4.0 9.7 1.0 CA A:CYS193 4.0 6.9 1.0 N A:GLN195 4.2 7.2 1.0 C A:CYS193 4.2 6.5 1.0 N A:LEU192 4.4 7.6 1.0 C A:LEU192 4.6 6.6 1.0 CB A:LEU191 4.6 8.2 1.0 N A:LEU191 4.7 7.4 1.0 SG A:CYS190 4.7 7.1 1.0 SG A:CYS196 4.8 7.3 1.0 CA A:GLY194 4.8 7.7 1.0 CB A:GLN195 4.8 8.3 1.0 SG A:CYS157 4.8 7.8 1.0 CA A:LEU192 4.8 7.2 1.0 C A:LEU191 4.9 7.1 1.0 C A:GLY194 4.9 6.1 1.0

Iron binding site 8 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe577 b:7.7 occ:1.00 FE2 A:SF4577 0.0 7.7 1.0 S3 A:SF4577 2.3 7.3 1.0 SG A:CYS196 2.3 7.3 1.0 S1 A:SF4577 2.3 7.7 1.0 S4 A:SF4577 2.3 7.7 1.0 FE4 A:SF4577 2.7 7.4 1.0 FE3 A:SF4577 2.7 7.3 1.0 FE1 A:SF4577 2.8 7.3 1.0 CB A:CYS196 3.3 6.8 1.0 N A:CYS196 3.9 7.8 1.0 S2 A:SF4577 3.9 7.6 1.0 CA A:CYS196 4.2 7.3 1.0 N A:GLY194 4.5 6.8 1.0 N A:GLN195 4.5 7.2 1.0 CD1 A:LEU140 4.5 19.6 1.0 CE A:MET166 4.6 9.9 1.0 SG A:CYS190 4.6 7.1 1.0 CA A:GLY194 4.7 7.7 1.0 SG A:CYS157 4.7 7.8 1.0 SG A:CYS193 4.7 7.7 1.0 C A:GLY194 4.8 6.1 1.0 CB A:CYS157 4.9 7.4 1.0

Iron binding site 9 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe577 b:7.3 occ:1.00 FE3 A:SF4577 0.0 7.3 1.0 SG A:CYS157 2.3 7.8 1.0 S2 A:SF4577 2.3 7.6 1.0 S1 A:SF4577 2.3 7.7 1.0 S4 A:SF4577 2.3 7.7 1.0 FE4 A:SF4577 2.7 7.4 1.0 FE2 A:SF4577 2.7 7.7 1.0 FE1 A:SF4577 2.8 7.3 1.0 CB A:CYS157 3.2 7.4 1.0 S3 A:SF4577 3.9 7.3 1.0 CA A:CYS157 4.0 7.6 1.0 OG1 A:THR163 4.1 8.8 1.0 CB A:ALA165 4.1 10.1 1.0 OG1 A:THR161 4.2 7.4 1.0 N A:MET166 4.4 7.2 1.0 CG2 A:THR161 4.4 9.7 1.0 N A:ALA165 4.6 7.8 1.0 CB A:MET166 4.7 7.5 1.0 CA A:ALA165 4.8 8.4 1.0 SG A:CYS193 4.8 7.7 1.0 C A:ALA165 4.8 8.1 1.0 C A:CYS157 4.9 8.0 1.0 SG A:CYS196 4.9 7.3 1.0 SG A:CYS190 4.9 7.1 1.0 O A:CYS157 4.9 10.6 1.0 CB A:THR161 5.0 7.6 1.0

Iron binding site 10 out of 20 in the 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 1.39 Angstrom Crystal Structure of Fe-Only Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe577 b:7.4 occ:1.00 FE4 A:SF4577 0.0 7.4 1.0 S1 A:SF4577 2.2 7.7 1.0 S2 A:SF4577 2.3 7.6 1.0 SG A:CYS190 2.3 7.1 1.0 S3 A:SF4577 2.3 7.3 1.0 FE3 A:SF4577 2.7 7.3 1.0 FE2 A:SF4577 2.7 7.7 1.0 FE1 A:SF4577 2.8 7.3 1.0 CB A:CYS190 3.4 7.0 1.0 CA A:CYS190 3.8 8.8 1.0 N A:LEU191 3.9 7.4 1.0 S4 A:SF4577 3.9 7.7 1.0 N A:LEU192 4.0 7.6 1.0 CB A:ALA165 4.1 10.1 1.0 C A:CYS190 4.3 9.0 1.0 CA A:LEU192 4.5 7.2 1.0 CD1 A:LEU140 4.6 19.6 1.0 CD2 A:PHE185 4.6 9.2 1.0 SG A:CYS157 4.7 7.8 1.0 SG A:CYS196 4.8 7.3 1.0 CA A:LEU191 4.8 7.0 1.0 N A:CYS193 4.8 6.8 1.0 C A:LEU191 4.9 7.1 1.0 CE2 A:PHE185 5.0 8.4 1.0

A.S.Pandey, T.V.Harris, L.J.Giles, J.W.Peters, R.K.Szilagyi. Dithiomethylether As A Ligand in the Hydrogenase H-Cluster. J.Am.Chem.Soc. V. 130 4533 2008.
ISSN: ISSN 0002-7863
PubMed: 18324814
DOI: 10.1021/JA711187E