Iron in PDB 6g94: Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B

All present enzymatic activity of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B:
1.12.99.6;

The structure of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B, PDB code: 6g94 was solved by A.Volbeda, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.410, 165.030, 206.220, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.3

The structure of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50;

Binding sites:

The binding sites of Iron atom in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B (pdb code 6g94). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 50 binding sites of Iron where determined in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B, PDB code: 6g94:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:41.2 occ:1.00 FE1 S:SF4401 0.0 41.2 1.0 SG S:CYS215 2.2 38.0 1.0 S4 S:SF4401 2.3 40.5 1.0 S3 S:SF4401 2.3 39.7 1.0 S2 S:SF4401 2.3 40.7 1.0 FE2 S:SF4401 2.7 40.9 1.0 FE4 S:SF4401 2.7 41.0 1.0 FE3 S:SF4401 2.7 40.5 1.0 CB S:CYS215 3.5 36.7 1.0 S1 S:SF4401 3.9 40.3 1.0 N S:LEU216 3.9 41.1 1.0 CA S:CYS215 4.0 39.0 1.0 CB S:PHE196 4.2 38.9 1.0 N S:TYR217 4.3 41.3 1.0 CD1 S:PHE196 4.3 44.1 1.0 C S:CYS215 4.4 40.6 1.0 ND1 S:HIS187 4.5 38.0 1.0 CE1 S:HIS187 4.5 38.4 1.0 CB S:TYR217 4.6 42.0 1.0 CG S:PHE196 4.6 41.5 1.0 O S:ARG192 4.7 39.5 1.0 CA S:TYR217 4.8 42.5 1.0 SG S:CYS190 4.8 36.5 1.0 C S:LEU216 4.8 40.8 1.0 CA S:LEU216 4.9 40.4 1.0 SG S:CYS221 4.9 53.0 1.0 CB S:ARG192 4.9 43.5 1.0

Iron binding site 2 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:40.9 occ:1.00 FE2 S:SF4401 0.0 40.9 1.0 S3 S:SF4401 2.3 39.7 1.0 S1 S:SF4401 2.3 40.3 1.0 S4 S:SF4401 2.3 40.5 1.0 SG S:CYS190 2.3 36.5 1.0 FE4 S:SF4401 2.6 41.0 1.0 FE1 S:SF4401 2.7 41.2 1.0 FE3 S:SF4401 2.7 40.5 1.0 CB S:CYS190 3.1 34.1 1.0 S2 S:SF4401 3.8 40.7 1.0 CD1 S:ILE243 4.2 31.1 1.0 CB S:ARG192 4.3 43.5 1.0 CG2 S:ILE243 4.4 34.8 1.0 ND1 S:HIS187 4.5 38.0 1.0 CA S:CYS190 4.6 35.5 1.0 SG S:CYS221 4.7 53.0 1.0 C S:ARG192 4.7 38.2 1.0 CG1 S:ILE243 4.7 32.0 1.0 SG S:CYS215 4.8 38.0 1.0 N S:ARG193 4.8 38.1 1.0 CA S:ARG192 4.9 40.6 1.0 N S:ARG192 4.9 39.3 1.0

Iron binding site 3 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:40.5 occ:1.00 FE3 S:SF4401 0.0 40.5 1.0 ND1 S:HIS187 2.0 38.0 1.0 S2 S:SF4401 2.3 40.7 1.0 S4 S:SF4401 2.3 40.5 1.0 S1 S:SF4401 2.3 40.3 1.0 CE1 S:HIS187 2.6 38.4 1.0 FE1 S:SF4401 2.7 41.2 1.0 FE2 S:SF4401 2.7 40.9 1.0 FE4 S:SF4401 2.7 41.0 1.0 CG S:HIS187 3.2 38.2 1.0 CB S:HIS187 3.8 38.2 1.0 NE2 S:HIS187 3.9 38.8 1.0 S3 S:SF4401 3.9 39.7 1.0 CA S:HIS187 4.0 38.0 1.0 CD S:PRO224 4.1 39.3 1.0 CD2 S:HIS187 4.1 37.8 1.0 CG S:PRO224 4.2 37.1 1.0 CB S:CYS190 4.5 34.1 1.0 O S:HIS187 4.6 39.2 1.0 SG S:CYS215 4.6 38.0 1.0 SG S:CYS190 4.7 36.5 1.0 CD1 S:PHE196 4.7 44.1 1.0 CD S:ARG193 4.7 42.8 1.0 SG S:CYS221 4.8 53.0 1.0 N S:PRO224 4.8 39.7 1.0 C S:HIS187 4.8 40.1 1.0 CG S:PHE196 4.9 41.5 1.0 N S:HIS187 5.0 38.2 1.0

Iron binding site 4 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:41.0 occ:1.00 FE4 S:SF4401 0.0 41.0 1.0 S1 S:SF4401 2.3 40.3 1.0 S3 S:SF4401 2.3 39.7 1.0 S2 S:SF4401 2.3 40.7 1.0 SG S:CYS221 2.4 53.0 1.0 FE2 S:SF4401 2.6 40.9 1.0 FE1 S:SF4401 2.7 41.2 1.0 FE3 S:SF4401 2.7 40.5 1.0 CB S:CYS221 3.3 44.6 1.0 S4 S:SF4401 3.9 40.5 1.0 CD1 S:ILE243 4.0 31.1 1.0 CG1 S:ILE243 4.4 32.0 1.0 CD S:PRO224 4.4 39.3 1.0 CA S:GLY223 4.5 41.3 1.0 ND1 S:HIS187 4.5 38.0 1.0 SG S:CYS215 4.6 38.0 1.0 N S:GLY223 4.6 42.6 1.0 CA S:CYS221 4.7 42.3 1.0 SG S:CYS190 4.8 36.5 1.0 N S:LEU216 4.8 41.1 1.0 N S:TYR217 4.9 41.3 1.0 C S:CYS221 4.9 42.5 1.0 C S:LEU216 4.9 40.8 1.0

Iron binding site 5 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:40.7 occ:1.00 FE1 S:F3S402 0.0 40.7 1.0 S3 S:F3S402 2.2 38.6 1.0 S2 S:F3S402 2.2 39.5 1.0 S1 S:F3S402 2.2 40.1 1.0 SG S:CYS252 2.3 39.5 1.0 FE4 S:F3S402 2.7 40.2 1.0 FE3 S:F3S402 2.7 40.2 1.0 CB S:CYS252 3.3 36.7 1.0 O L:HOH802 3.4 35.8 1.0 O S:HOH545 3.5 41.1 1.0 N S:CYS252 3.8 34.6 1.0 S4 S:F3S402 3.8 45.0 1.0 CA S:CYS252 4.0 35.0 1.0 N S:ALA253 4.3 32.4 1.0 C S:CYS252 4.4 33.5 1.0 ND2 S:ASN228 4.4 38.3 1.0 SG S:CYS230 4.6 36.7 1.0 SG S:CYS249 4.6 38.9 1.0 O L:HOH749 4.7 39.2 1.0 C S:GLY251 4.9 34.6 1.0 N S:GLY251 5.0 34.0 1.0

Iron binding site 6 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:40.2 occ:1.00 FE3 S:F3S402 0.0 40.2 1.0 S3 S:F3S402 2.2 38.6 1.0 S1 S:F3S402 2.2 40.1 1.0 S4 S:F3S402 2.2 45.0 1.0 SG S:CYS230 2.3 36.7 1.0 FE4 S:F3S402 2.6 40.2 1.0 FE1 S:F3S402 2.7 40.7 1.0 CB S:CYS230 3.2 33.7 1.0 ND2 S:ASN228 3.8 38.3 1.0 S2 S:F3S402 3.8 39.5 1.0 O S:HOH545 3.8 41.1 1.0 CD1 S:ILE186 4.0 33.3 1.0 NE1 S:TRP235 4.4 36.9 1.0 CG S:PRO242 4.5 36.5 1.0 CG S:ASN228 4.5 38.6 1.0 CD S:PRO242 4.5 37.1 1.0 CB S:ASN228 4.7 36.8 1.0 CA S:CYS230 4.7 34.0 1.0 SG S:CYS252 4.7 39.5 1.0 SG S:CYS249 4.7 38.9 1.0 CG1 S:ILE186 4.9 33.0 1.0

Iron binding site 7 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:40.2 occ:1.00 FE4 S:F3S402 0.0 40.2 1.0 S4 S:F3S402 2.2 45.0 1.0 S3 S:F3S402 2.2 38.6 1.0 S2 S:F3S402 2.2 39.5 1.0 SG S:CYS249 2.3 38.9 1.0 FE3 S:F3S402 2.6 40.2 1.0 FE1 S:F3S402 2.7 40.7 1.0 CB S:CYS249 3.3 34.6 1.0 S1 S:F3S402 3.7 40.1 1.0 CA S:CYS249 3.8 35.2 1.0 N S:GLY251 4.1 34.0 1.0 N S:LEU250 4.2 35.0 1.0 C S:CYS249 4.4 36.0 1.0 N S:CYS252 4.5 34.6 1.0 CD1 S:ILE186 4.5 33.3 1.0 CG2 S:THR226 4.6 36.0 1.0 CA S:GLY251 4.6 34.4 1.0 CG S:PRO242 4.7 36.5 1.0 CG1 S:ILE186 4.8 33.0 1.0 SG S:CYS230 4.8 36.7 1.0 SG S:CYS252 4.8 39.5 1.0

Iron binding site 8 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:45.4 occ:1.00 FE3 S:ER2403 0.0 45.4 1.0 S3 S:ER2403 2.3 41.6 1.0 S2 S:ER2403 2.3 39.9 1.0 SG S:CYS149 2.3 42.2 1.0 SG S:CYS120 2.3 36.7 1.0 FE2 S:ER2403 2.7 42.4 1.0 CB S:CYS149 3.4 34.0 1.0 CB S:CYS120 3.6 34.7 1.0 FE1 S:ER2403 3.7 39.8 1.0 FE4 S:ER2403 3.7 40.2 1.0 S4 S:ER2403 3.8 39.5 1.0 SG S:CYS115 3.9 46.1 1.0 CA S:CYS149 4.0 34.3 1.0 N S:CYS115 4.3 43.1 1.0 CB S:THR114 4.4 43.7 1.0 CG L:ARG74 4.4 35.1 1.0 S1 S:ER2403 4.6 40.1 1.0 O S:GLY148 4.7 32.8 1.0 N S:THR114 4.8 41.1 1.0 CB S:CYS115 4.9 40.8 1.0 C S:CYS149 4.9 35.1 1.0 CA S:CYS120 4.9 37.1 1.0 CA S:THR114 5.0 41.1 1.0

Iron binding site 9 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:40.2 occ:1.00 FE4 S:ER2403 0.0 40.2 1.0 S1 S:ER2403 2.3 40.1 1.0 S4 S:ER2403 2.3 39.5 1.0 S3 S:ER2403 2.3 41.6 1.0 SG S:CYS20 2.3 43.1 1.0 FE1 S:ER2403 2.7 39.8 1.0 FE2 S:ER2403 2.7 42.4 1.0 N S:CYS20 3.6 34.5 1.0 CB S:CYS20 3.7 36.0 1.0 FE3 S:ER2403 3.7 45.4 1.0 O S:HOH528 3.8 39.4 1.0 S2 S:ER2403 3.9 39.9 1.0 CA S:CYS20 4.1 35.7 1.0 CB S:PRO150 4.3 32.5 1.0 C S:GLY19 4.3 34.6 1.0 CA S:PRO150 4.3 33.6 1.0 CA S:GLY19 4.5 34.7 1.0 N S:GLY19 4.6 34.8 1.0 SG S:CYS17 4.6 38.2 1.0 CA S:GLY113 4.8 41.0 1.0 O S:GLY148 4.8 32.8 1.0 SG S:CYS115 4.8 46.1 1.0 N S:PRO150 4.8 34.8 1.0 CA S:CYS149 4.8 34.3 1.0 SG S:CYS149 4.8 42.2 1.0

Iron binding site 10 out of 50 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:39.8 occ:1.00 FE1 S:ER2403 0.0 39.8 1.0 SG S:CYS17 2.2 38.2 1.0 S4 S:ER2403 2.3 39.5 1.0 S2 S:ER2403 2.3 39.9 1.0 S1 S:ER2403 2.3 40.1 1.0 FE2 S:ER2403 2.6 42.4 1.0 FE4 S:ER2403 2.7 40.2 1.0 CB S:CYS17 3.3 36.4 1.0 FE3 S:ER2403 3.7 45.4 1.0 N S:CYS17 3.7 36.9 1.0 N S:GLY19 3.8 34.8 1.0 S3 S:ER2403 3.8 41.6 1.0 CA S:CYS17 3.9 38.2 1.0 NE2 L:HIS229 4.1 35.5 1.0 CA S:GLY19 4.1 34.7 1.0 C S:CYS17 4.3 39.5 1.0 N S:THR18 4.3 39.0 1.0 SG S:CYS149 4.6 42.2 1.0 N S:CYS20 4.6 34.5 1.0 SG S:CYS115 4.6 46.1 1.0 O S:HOH515 4.7 35.2 1.0 CD2 L:HIS229 4.8 36.0 1.0 C S:GLY19 4.8 34.6 1.0 C S:GLU16 4.9 39.2 1.0 SG S:CYS20 4.9 43.1 1.0 C S:THR18 4.9 39.1 1.0

A.Volbeda, J.M.Mouesca, C.Darnault, M.M.Roessler, A.Parkin, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Structural, Functional and Computational Studies of the O2-Sensitive E. Coli Hydrogenase-1 C19G Variant Reveal An Unusual [4FE-4S] Cluster. Chem. Commun. (Camb.) V. 54 7175 2018.
ISSN: ESSN 1364-548X
PubMed: 29888350
DOI: 10.1039/C8CC02896F