Iron in PDB 6g7m: Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2

All present enzymatic activity of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2:
1.12.99.6;

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m was solved by S.B.Carr, F.A.Armstrong, L.Zhang, S.E.Beaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.75 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.237, 100.986, 169.425, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19

The structure of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 (pdb code 6g7m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2, PDB code: 6g7m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:15.0 occ:1.00 FE1 S:SF4401 0.0 15.0 1.0 S2 S:SF4401 2.3 15.9 1.0 SG S:CYS220 2.3 15.7 1.0 S4 S:SF4401 2.3 15.1 1.0 S3 S:SF4401 2.3 15.4 1.0 FE3 S:SF4401 2.7 16.3 1.0 FE4 S:SF4401 2.7 14.6 1.0 FE2 S:SF4401 2.8 15.0 1.0 CB S:CYS220 3.4 14.9 1.0 N S:LEU221 3.9 13.6 1.0 S1 S:SF4401 3.9 15.4 1.0 CA S:CYS220 4.0 14.6 1.0 N S:CYS222 4.1 16.4 1.0 C S:CYS220 4.4 15.0 1.0 ND1 S:HIS192 4.5 16.9 1.0 CB S:PHE201 4.5 17.1 1.0 CB S:ARG197 4.5 15.8 1.0 CD2 S:PHE201 4.5 18.2 1.0 CB S:CYS222 4.6 20.6 1.0 O S:ARG197 4.6 15.7 1.0 CA S:CYS222 4.7 17.3 1.0 CE1 S:HIS192 4.8 16.3 1.0 C S:LEU221 4.8 15.5 1.0 SG S:CYS195 4.8 14.1 1.0 CA S:LEU221 4.8 14.5 1.0 C S:ARG197 4.9 15.5 1.0 SG S:CYS226 4.9 13.7 1.0 CG S:PHE201 5.0 17.8 1.0

Iron binding site 2 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:15.0 occ:1.00 FE2 S:SF4401 0.0 15.0 1.0 S1 S:SF4401 2.3 15.4 1.0 S3 S:SF4401 2.3 15.4 1.0 SG S:CYS226 2.3 13.7 1.0 S4 S:SF4401 2.3 15.1 1.0 FE4 S:SF4401 2.7 14.6 1.0 FE3 S:SF4401 2.8 16.3 1.0 FE1 S:SF4401 2.8 15.0 1.0 CB S:CYS226 3.3 14.1 1.0 S2 S:SF4401 3.9 15.9 1.0 CA S:GLY228 4.6 15.2 1.0 CD S:PRO229 4.6 16.0 1.0 N S:GLY228 4.6 14.1 1.0 CA S:CYS226 4.6 14.2 1.0 SG S:CYS195 4.7 14.1 1.0 ND1 S:HIS192 4.7 16.9 1.0 N S:CYS222 4.7 16.4 1.0 SG S:CYS220 4.8 15.7 1.0 CG2 S:VAL249 4.8 14.1 1.0 N S:LEU221 4.9 13.6 1.0 C S:CYS226 4.9 15.4 1.0

Iron binding site 3 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:16.3 occ:1.00 FE3 S:SF4401 0.0 16.3 1.0 ND1 S:HIS192 2.1 16.9 1.0 S4 S:SF4401 2.3 15.1 1.0 S2 S:SF4401 2.3 15.9 1.0 S1 S:SF4401 2.3 15.4 1.0 FE1 S:SF4401 2.7 15.0 1.0 FE4 S:SF4401 2.7 14.6 1.0 FE2 S:SF4401 2.8 15.0 1.0 CE1 S:HIS192 2.9 16.3 1.0 CG S:HIS192 3.2 16.7 1.0 CB S:HIS192 3.6 15.2 1.0 S3 S:SF4401 3.9 15.4 1.0 CA S:HIS192 4.0 14.1 1.0 NE2 S:HIS192 4.1 16.3 1.0 CD2 S:HIS192 4.3 17.0 1.0 CD S:PRO229 4.3 16.0 1.0 CG S:PRO229 4.4 16.9 1.0 CB S:CYS195 4.6 14.2 1.0 SG S:CYS195 4.6 14.1 1.0 SG S:CYS220 4.7 15.7 1.0 O S:HIS192 4.8 13.6 1.0 CD2 S:PHE201 4.8 18.2 1.0 SG S:CYS226 4.8 13.7 1.0 N S:PRO229 4.9 15.1 1.0 C S:HIS192 5.0 14.1 1.0

Iron binding site 4 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:14.6 occ:1.00 FE4 S:SF4401 0.0 14.6 1.0 SG S:CYS195 2.2 14.1 1.0 S3 S:SF4401 2.3 15.4 1.0 S2 S:SF4401 2.3 15.9 1.0 S1 S:SF4401 2.3 15.4 1.0 FE2 S:SF4401 2.7 15.0 1.0 FE3 S:SF4401 2.7 16.3 1.0 FE1 S:SF4401 2.7 15.0 1.0 CB S:CYS195 3.1 14.2 1.0 S4 S:SF4401 3.9 15.1 1.0 CB S:ARG197 4.0 15.8 1.0 ND1 S:HIS192 4.5 16.9 1.0 CA S:CYS195 4.6 14.1 1.0 CA S:ARG197 4.6 15.6 1.0 C S:ARG197 4.6 15.5 1.0 N S:ARG197 4.6 14.8 1.0 N S:ARG198 4.7 14.6 1.0 SG S:CYS226 4.8 13.7 1.0 CG1 S:VAL249 4.9 13.7 1.0 CG S:ARG197 4.9 15.6 1.0 C S:CYS195 4.9 14.2 1.0 SG S:CYS220 5.0 15.7 1.0

Iron binding site 5 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:12.3 occ:1.00 FE1 S:F3S402 0.0 12.3 1.0 S1 S:F3S402 2.2 12.8 1.0 S2 S:F3S402 2.3 12.4 1.0 S3 S:F3S402 2.3 13.5 1.0 SG S:CYS258 2.3 12.4 1.0 FE3 S:F3S402 2.7 12.6 1.0 FE4 S:F3S402 2.7 12.5 1.0 CB S:CYS258 3.5 12.5 1.0 O L:HOH818 3.7 13.3 1.0 N S:CYS258 3.7 12.6 1.0 S4 S:F3S402 3.8 12.4 1.0 CA S:CYS258 4.0 12.2 1.0 N S:ASN259 4.2 11.7 1.0 OD1 S:ASN259 4.2 12.4 1.0 O S:HOH571 4.3 13.4 1.0 C S:CYS258 4.4 12.4 1.0 SG S:CYS235 4.7 13.9 1.0 C S:GLY257 4.8 12.3 1.0 CG S:ASN259 4.9 12.4 1.0 O S:HOH505 4.9 16.1 1.0 SG S:CYS255 4.9 13.7 1.0 OE1 L:GLN216 5.0 13.8 1.0 CE L:LYS211 5.0 13.9 1.0 N S:GLY257 5.0 11.8 1.0

Iron binding site 6 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:12.6 occ:1.00 FE3 S:F3S402 0.0 12.6 1.0 S4 S:F3S402 2.2 12.4 1.0 S1 S:F3S402 2.2 12.8 1.0 SG S:CYS235 2.3 13.9 1.0 S3 S:F3S402 2.3 13.5 1.0 FE4 S:F3S402 2.7 12.5 1.0 FE1 S:F3S402 2.7 12.3 1.0 CB S:CYS235 3.3 13.3 1.0 S2 S:F3S402 4.0 12.4 1.0 O S:HOH571 4.1 13.4 1.0 CD1 S:ILE191 4.2 13.8 1.0 CE1 S:PHE240 4.5 11.1 1.0 CZ S:PHE240 4.5 11.6 1.0 CA S:CYS235 4.7 13.0 1.0 SG S:CYS255 4.7 13.7 1.0 OD1 S:ASN259 4.7 12.4 1.0 SG S:CYS258 4.8 12.4 1.0 O S:HOH589 5.0 13.7 1.0 ND2 S:ASN259 5.0 11.7 1.0

Iron binding site 7 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:12.5 occ:1.00 FE4 S:F3S402 0.0 12.5 1.0 S4 S:F3S402 2.2 12.4 1.0 S3 S:F3S402 2.3 13.5 1.0 S2 S:F3S402 2.3 12.4 1.0 SG S:CYS255 2.4 13.7 1.0 FE3 S:F3S402 2.7 12.6 1.0 FE1 S:F3S402 2.7 12.3 1.0 CB S:CYS255 3.3 13.7 1.0 CA S:CYS255 3.7 13.0 1.0 S1 S:F3S402 3.9 12.8 1.0 N S:TYR256 3.9 11.1 1.0 N S:GLY257 4.0 11.8 1.0 C S:CYS255 4.2 13.1 1.0 CD1 S:ILE191 4.3 13.8 1.0 N S:CYS258 4.4 12.6 1.0 CA S:GLY257 4.5 12.6 1.0 NE2 L:GLN216 4.7 12.6 1.0 SG S:CYS235 4.7 13.9 1.0 CG2 S:THR231 4.8 15.0 1.0 SG S:CYS258 4.9 12.4 1.0 C S:TYR256 4.9 12.1 1.0 C S:GLY257 4.9 12.3 1.0 CA S:TYR256 4.9 12.1 1.0

Iron binding site 8 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:14.6 occ:1.00 FE1 S:SF4403 0.0 14.6 1.0 SG S:CYS22 2.3 13.1 1.0 S4 S:SF4403 2.3 15.6 1.0 S2 S:SF4403 2.3 13.9 1.0 S3 S:SF4403 2.5 24.1 1.0 FE3 S:SF4403 2.7 12.9 1.0 FE4 S:SF4403 2.8 26.2 1.0 FE2 S:SF4403 3.0 16.7 1.0 CB S:CYS22 3.4 12.2 1.0 N S:CYS22 3.7 12.6 1.0 S1 S:SF4403 3.9 15.6 1.0 CA S:CYS22 4.0 12.2 1.0 N S:GLY24 4.0 13.3 1.0 O S:HOH501 4.3 30.0 1.0 NE2 L:HIS214 4.3 11.7 1.0 CA S:GLY24 4.4 12.3 1.0 N S:THR23 4.4 12.2 1.0 C S:CYS22 4.4 12.7 1.0 SG S:CYS154 4.7 13.0 1.0 SG S:CYS25 4.7 18.4 1.0 O S:HOH593 4.8 14.5 1.0 N S:CYS25 4.8 12.8 1.0 CD2 L:HIS214 4.9 12.7 1.0 C S:GLU21 4.9 15.7 1.0

Iron binding site 9 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:16.7 occ:1.00 FE2 S:SF4403 0.0 16.7 1.0 S1 S:SF4403 2.3 15.6 1.0 S4 S:SF4403 2.3 15.6 1.0 SG S:CYS120 2.4 15.2 1.0 S3 S:SF4403 2.5 24.1 1.0 FE3 S:SF4403 2.6 12.9 1.0 FE4 S:SF4403 2.9 26.2 1.0 FE1 S:SF4403 3.0 14.6 1.0 CB S:CYS120 3.3 13.6 1.0 O S:HOH527 3.9 12.4 1.0 O S:HOH607 3.9 17.1 1.0 N S:CYS120 4.0 12.7 1.0 O S:HOH593 4.0 14.5 1.0 S2 S:SF4403 4.1 13.9 1.0 CA S:CYS120 4.2 13.6 1.0 SG S:CYS154 4.5 13.0 1.0 SG S:CYS25 4.8 18.4 1.0

Iron binding site 10 out of 24 in the Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Four-Site Variant (Y222C, C197S, C432S, C433S) of E. Coli Hydrogenase- 2 within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:12.9 occ:1.00 FE3 S:SF4403 0.0 12.9 1.0 S1 S:SF4403 2.2 15.6 1.0 SG S:CYS154 2.3 13.0 1.0 S4 S:SF4403 2.3 15.6 1.0 S2 S:SF4403 2.3 13.9 1.0 FE2 S:SF4403 2.6 16.7 1.0 FE1 S:SF4403 2.7 14.6 1.0 FE4 S:SF4403 2.8 26.2 1.0 CB S:CYS154 3.4 11.7 1.0 CA S:CYS154 3.5 11.8 1.0 O S:HOH607 3.8 17.1 1.0 C S:CYS154 3.9 12.5 1.0 S3 S:SF4403 3.9 24.1 1.0 O S:CYS154 4.4 11.6 1.0 CG L:ARG59 4.4 12.4 1.0 N S:PRO155 4.4 12.5 1.0 SG S:CYS120 4.5 15.2 1.0 CD2 L:HIS214 4.6 12.7 1.0 SG S:CYS22 4.6 13.1 1.0 O S:GLY153 4.6 11.1 1.0 NE2 L:HIS214 4.7 11.7 1.0 N S:CYS154 4.8 10.9 1.0 CA S:PRO155 4.8 12.1 1.0 SG S:CYS25 4.9 18.4 1.0 NE L:ARG59 4.9 12.1 1.0

L.Zhang, S.E.Beaton, S.B.Carr, F.A.Armstrong. Direct Visible Light Activation of A Surface Cysteine-Engineered [Nife]-Hydrogenase By Silver Nanoclusters Energy Environ Sci 2019.
ISSN: ISSN 1754-5706
DOI: 10.1039/C8EE02361A