Iron in PDB 6nac: Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data

All present enzymatic activity of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data:
1.12.7.2;

The structure of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data, PDB code: 6nac was solved by A.E.Cohen, C.M.Davidson, O.A.Zadvornyy, S.M.Keable, A.Y.Lyubimov, J.Song, S.E.Mcphillips, S.M.Soltis, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.10 / 1.55
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.165, 111.165, 104.007, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.5

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data (pdb code 6nac). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data, PDB code: 6nac:
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 Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:9.8 occ:1.00 FE1 A:402601 0.0 9.8 1.0 C3 A:402601 1.7 11.0 0.8 C4 A:402601 1.8 10.0 0.7 C5 A:402601 1.9 10.1 1.0 S1 A:402601 2.3 9.7 1.0 S2 A:402601 2.3 10.5 1.0 FE2 A:402601 2.5 9.9 0.9 SG A:CYS503 2.6 8.3 1.0 O3 A:402601 2.9 11.2 1.0 O5 A:402601 3.0 10.0 1.0 N4 A:402601 3.0 9.6 1.0 CB A:CYS503 3.4 8.1 1.0 C2 A:402601 3.5 10.5 0.8 C1 A:402601 3.5 10.3 1.0 C7 A:402601 3.8 10.4 1.0 C6 A:402601 3.8 9.8 1.0 N1 A:402601 3.9 10.5 1.0 FE3 A:SF4602 4.1 8.5 1.0 S4 A:SF4602 4.2 8.3 1.0 O A:HOH769 4.7 30.8 1.0 N6 A:402601 4.7 9.7 1.0 O7 A:402601 4.8 10.8 1.0 CE A:LYS358 4.8 6.8 1.0 CG A:PRO354 4.8 7.1 1.0 CA A:CYS503 4.9 7.9 1.0 CD A:PRO354 4.9 7.2 1.0 CD A:PRO231 5.0 8.8 1.0

Iron binding site 2 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:9.9 occ:0.90 FE2 A:402601 0.0 9.9 0.9 C7 A:402601 1.8 10.4 1.0 C6 A:402601 1.9 9.8 1.0 C5 A:402601 2.0 10.1 1.0 S1 A:402601 2.3 9.7 1.0 S2 A:402601 2.3 10.5 1.0 FE1 A:402601 2.5 9.8 1.0 O A:HOH769 2.6 30.8 1.0 O5 A:402601 2.9 10.0 1.0 N6 A:402601 3.0 9.7 1.0 O7 A:402601 3.0 10.8 1.0 C2 A:402601 3.4 10.5 0.8 N1 A:402601 3.4 10.5 1.0 C1 A:402601 3.4 10.3 1.0 C4 A:402601 3.6 10.0 0.7 C3 A:402601 3.6 11.0 0.8 CG A:PRO324 4.0 8.5 0.9 CB A:PRO324 4.3 8.4 1.0 CD2 A:PHE417 4.3 8.7 1.0 CD A:PRO324 4.4 8.3 1.0 N4 A:402601 4.6 9.6 1.0 O3 A:402601 4.7 11.2 1.0 CE A:LYS358 4.7 6.8 1.0 SG A:CYS503 4.7 8.3 1.0 NZ A:LYS358 4.7 7.2 1.0 CD A:PRO231 4.8 8.8 1.0 O A:CYS299 4.9 8.8 1.0 CB A:PHE417 5.0 8.8 0.8

Iron binding site 3 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:8.1 occ:1.00 FE1 A:SF4602 0.0 8.1 1.0 S4 A:SF4602 2.3 8.3 1.0 S3 A:SF4602 2.3 8.2 0.9 S2 A:SF4602 2.3 7.8 1.0 SG A:CYS355 2.5 7.3 0.8 FE2 A:SF4602 2.6 8.1 1.0 FE4 A:SF4602 2.7 8.9 1.0 FE3 A:SF4602 2.7 8.5 1.0 CB A:CYS355 3.2 7.3 1.0 OG A:SER357 3.6 6.2 0.1 S1 A:SF4602 3.8 8.5 1.0 O A:HOH779 3.9 7.9 0.9 O3 A:402601 4.0 11.2 1.0 CA A:CYS355 4.3 7.3 1.0 CB A:SER357 4.6 7.5 0.8 C3 A:402601 4.6 11.0 0.8 CD A:PRO301 4.7 7.5 1.0 CG A:PRO301 4.8 7.7 0.9 CB A:SER357 4.8 6.3 0.2 SG A:CYS499 4.9 8.8 1.0 SG A:CYS300 4.9 9.2 1.0 CG A:LYS358 4.9 6.5 1.0 SG A:CYS503 4.9 8.3 1.0

Iron binding site 4 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:8.1 occ:1.00 FE2 A:SF4602 0.0 8.1 1.0 S4 A:SF4602 2.3 8.3 1.0 S3 A:SF4602 2.3 8.2 0.9 S1 A:SF4602 2.3 8.5 1.0 SG A:CYS300 2.5 9.2 1.0 FE1 A:SF4602 2.6 8.1 1.0 FE3 A:SF4602 2.7 8.5 1.0 FE4 A:SF4602 2.7 8.9 1.0 CB A:CYS300 3.4 8.7 1.0 S2 A:SF4602 3.9 7.8 1.0 CA A:CYS300 4.0 8.4 1.0 N A:ALA498 4.3 9.0 0.7 C A:CYS300 4.4 7.7 1.0 N A:GLY302 4.5 7.3 1.0 CD A:PRO301 4.5 7.5 1.0 N A:PRO301 4.6 7.5 1.0 CB A:ALA498 4.7 9.3 1.0 OG A:SER357 4.7 6.2 0.1 SD A:MET497 4.8 8.9 0.9 SG A:CYS503 4.8 8.3 1.0 C1 A:402601 4.8 10.3 1.0 SG A:CYS499 4.9 8.8 1.0 N A:CYS499 4.9 9.2 1.0 CA A:GLY302 5.0 7.3 0.8 CA A:ALA498 5.0 9.1 0.8

Iron binding site 5 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:8.5 occ:1.00 FE3 A:SF4602 0.0 8.5 1.0 S2 A:SF4602 2.3 7.8 1.0 S1 A:SF4602 2.3 8.5 1.0 S4 A:SF4602 2.3 8.3 1.0 SG A:CYS503 2.5 8.3 1.0 FE1 A:SF4602 2.7 8.1 1.0 FE2 A:SF4602 2.7 8.1 1.0 FE4 A:SF4602 2.7 8.9 1.0 CB A:CYS503 3.3 8.1 1.0 CA A:CYS503 3.5 7.9 1.0 C3 A:402601 3.8 11.0 0.8 O3 A:402601 3.8 11.2 1.0 S3 A:SF4602 3.9 8.2 0.9 N A:CYS503 4.0 8.0 1.0 FE1 A:402601 4.1 9.8 1.0 S1 A:402601 4.3 9.7 1.0 C1 A:402601 4.3 10.3 1.0 C A:GLY502 4.7 8.1 1.0 SD A:MET497 4.7 8.9 0.9 C A:CYS503 4.8 7.9 1.0 CB A:CYS355 4.8 7.3 1.0 SG A:CYS355 4.9 7.3 0.8 O A:GLY502 4.9 8.2 1.0 SG A:CYS300 5.0 9.2 1.0 O A:CYS503 5.0 7.7 1.0

Iron binding site 6 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:8.9 occ:1.00 FE4 A:SF4602 0.0 8.9 1.0 S2 A:SF4602 2.3 7.8 1.0 S1 A:SF4602 2.3 8.5 1.0 S3 A:SF4602 2.3 8.2 0.9 SG A:CYS499 2.5 8.8 1.0 FE1 A:SF4602 2.7 8.1 1.0 FE2 A:SF4602 2.7 8.1 1.0 FE3 A:SF4602 2.7 8.5 1.0 CB A:CYS499 3.2 9.1 1.0 S4 A:SF4602 3.9 8.3 1.0 N A:CYS499 4.0 9.2 1.0 CA A:CYS499 4.2 9.4 1.0 O A:HOH779 4.2 7.9 0.9 CA A:GLY506 4.3 10.3 0.8 CA A:CYS503 4.8 7.9 1.0 SG A:CYS355 4.8 7.3 0.8 C A:ALA498 4.8 9.0 1.0 SG A:CYS300 4.9 9.2 1.0 O A:GLY502 4.9 8.2 1.0 N A:ALA498 5.0 9.0 0.7

Iron binding site 7 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:8.8 occ:1.00 FE1 A:SF4603 0.0 8.8 1.0 S4 A:SF4603 2.3 8.3 1.0 S3 A:SF4603 2.3 8.3 1.0 S2 A:SF4603 2.3 8.7 1.0 SG A:CYS193 2.6 8.2 0.9 FE4 A:SF4603 2.7 8.6 1.0 FE3 A:SF4603 2.7 8.7 1.0 FE2 A:SF4603 2.7 7.3 0.9 N A:CYS193 3.6 8.4 1.0 CB A:CYS193 3.8 7.8 1.0 N A:GLY194 3.8 8.1 1.0 S1 A:SF4603 3.9 8.2 1.0 CA A:CYS193 4.1 8.0 0.8 C A:CYS193 4.2 8.0 1.0 N A:GLN195 4.2 8.4 1.0 CG2 A:THR161 4.3 10.5 1.0 N A:LEU192 4.4 7.7 1.0 C A:LEU192 4.6 8.7 1.0 N A:LEU191 4.7 7.1 1.0 CB A:LEU191 4.7 6.6 1.0 CA A:GLY194 4.8 8.2 1.0 SG A:CYS190 4.8 7.3 1.0 CB A:GLN195 4.8 9.0 1.0 SG A:CYS196 4.9 9.0 1.0 CA A:LEU192 4.9 8.3 1.0 SG A:CYS157 4.9 8.4 0.9 C A:LEU191 4.9 7.2 0.9 N A:CYS196 5.0 8.6 1.0 C A:GLY194 5.0 8.2 0.8

Iron binding site 8 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:7.3 occ:0.89 FE2 A:SF4603 0.0 7.3 0.9 S4 A:SF4603 2.3 8.3 1.0 S3 A:SF4603 2.3 8.3 1.0 S1 A:SF4603 2.3 8.2 1.0 SG A:CYS196 2.5 9.0 1.0 FE3 A:SF4603 2.7 8.7 1.0 FE4 A:SF4603 2.7 8.6 1.0 FE1 A:SF4603 2.7 8.8 1.0 CB A:CYS196 3.4 8.8 1.0 N A:CYS196 3.9 8.6 1.0 S2 A:SF4603 3.9 8.7 1.0 CA A:CYS196 4.3 8.5 1.0 N A:GLY194 4.5 8.1 1.0 CE A:MET166 4.5 9.8 1.0 N A:GLN195 4.5 8.4 1.0 CD1 A:LEU140 4.6 15.6 1.0 CA A:GLY194 4.7 8.2 1.0 SG A:CYS190 4.8 7.3 1.0 SG A:CYS157 4.9 8.4 0.9 C A:GLY194 4.9 8.2 0.8 CB A:CYS157 4.9 8.8 0.8 SG A:CYS193 4.9 8.2 0.9 C A:GLN195 5.0 8.7 0.9 CB A:MET166 5.0 9.8 1.0

Iron binding site 9 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:8.7 occ:1.00 FE3 A:SF4603 0.0 8.7 1.0 S1 A:SF4603 2.3 8.2 1.0 S2 A:SF4603 2.3 8.7 1.0 S4 A:SF4603 2.3 8.3 1.0 SG A:CYS190 2.5 7.3 1.0 FE4 A:SF4603 2.7 8.6 1.0 FE2 A:SF4603 2.7 7.3 0.9 FE1 A:SF4603 2.7 8.8 1.0 CB A:CYS190 3.4 7.8 0.7 N A:LEU191 3.8 7.1 1.0 S3 A:SF4603 3.9 8.3 1.0 CA A:CYS190 3.9 8.0 0.8 N A:LEU192 3.9 7.7 1.0 CB A:ALA165 4.1 9.0 1.0 C A:CYS190 4.2 7.4 0.5 CA A:LEU192 4.5 8.3 1.0 CD1 A:LEU140 4.6 15.6 1.0 CD2 A:PHE185 4.7 8.9 1.0 N A:CYS193 4.7 8.4 1.0 CA A:LEU191 4.8 6.9 1.0 C A:LEU191 4.8 7.2 0.9 SG A:CYS157 4.9 8.4 0.9 SG A:CYS196 5.0 9.0 1.0

Iron binding site 10 out of 20 in the Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of [Fefe]-Hydrogenase I (Cpi) Solved with Single Pulse Free Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:8.6 occ:1.00 FE4 A:SF4603 0.0 8.6 1.0 S2 A:SF4603 2.3 8.7 1.0 S1 A:SF4603 2.3 8.2 1.0 S3 A:SF4603 2.3 8.3 1.0 SG A:CYS157 2.5 8.4 0.9 FE3 A:SF4603 2.7 8.7 1.0 FE1 A:SF4603 2.7 8.8 1.0 FE2 A:SF4603 2.7 7.3 0.9 CB A:CYS157 3.3 8.8 0.8 S4 A:SF4603 3.9 8.3 1.0 CA A:CYS157 4.1 8.9 0.9 CB A:ALA165 4.1 9.0 1.0 OG1 A:THR163 4.2 11.1 1.0 OG1 A:THR161 4.4 9.9 0.9 N A:MET166 4.4 10.3 0.9 CG2 A:THR161 4.5 10.5 1.0 N A:ALA165 4.7 9.8 1.0 CB A:MET166 4.7 9.8 1.0 CA A:ALA165 4.8 9.5 1.0 C A:ALA165 4.8 9.9 1.0 C A:CYS157 4.9 8.9 0.7 O A:CYS157 5.0 8.9 1.0 SG A:CYS193 5.0 8.2 0.9

J.H.Artz, O.A.Zadvornyy, D.W.Mulder, S.M.Keable, A.E.Cohen, M.W.Ratzloff, S.G.Williams, B.Ginovska, N.Kumar, J.Song, S.E.Mcphillips, C.Davidson, A.Y.Lyubimov, N.Pence, G.J.Schut, A.K.Jones, S.M.Soltis, M.Adams, S.Raugei, P.W.King, J.W.Peters. Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases. J.Am.Chem.Soc. 2019.
ISSN: ESSN 1520-5126
PubMed: 31816235
DOI: 10.1021/JACS.9B08756