Iron in PDB 4gd3: Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B

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

The structure of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3 was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.000, 165.300, 212.800, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.6

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

Nickel	(Ni)	4 atoms
Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	10 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; Page 6, Binding sites: 51 - 54;

Binding sites:

The binding sites of Iron atom in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B (pdb code 4gd3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 54 binding sites of Iron where determined in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:64.9 occ:1.00 FE1 S:SF4401 0.0 64.9 1.0 S2 S:SF4401 2.3 63.4 1.0 S4 S:SF4401 2.3 64.0 1.0 S3 S:SF4401 2.3 67.9 1.0 SG S:CYS221 2.4 72.8 1.0 FE4 S:SF4401 2.7 65.5 1.0 FE3 S:SF4401 2.7 64.5 1.0 FE2 S:SF4401 2.8 63.0 1.0 CB S:CYS221 3.4 74.8 1.0 CD S:PRO224 3.8 74.0 1.0 S1 S:SF4401 3.9 70.5 1.0 CD1 S:ILE243 3.9 67.9 1.0 ND1 S:HIS187 4.3 70.5 1.0 N S:GLY223 4.6 74.4 1.0 SG S:CYS215 4.6 71.7 1.0 N S:TYR217 4.6 73.0 1.0 CG S:PRO224 4.6 75.7 1.0 CA S:GLY223 4.6 74.0 1.0 CA S:CYS221 4.7 75.4 1.0 SG S:CYS190 4.8 71.9 1.0 C S:CYS221 4.9 76.1 1.0 CA S:TYR217 4.9 74.0 1.0 CG1 S:ILE243 4.9 67.5 1.0 N S:PRO224 4.9 73.7 1.0

Iron binding site 2 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:63.0 occ:1.00 FE2 S:SF4401 0.0 63.0 1.0 SG S:CYS215 2.2 71.7 1.0 S3 S:SF4401 2.3 67.9 1.0 S1 S:SF4401 2.3 70.5 1.0 S4 S:SF4401 2.3 64.0 1.0 FE4 S:SF4401 2.7 65.5 1.0 FE1 S:SF4401 2.8 64.9 1.0 FE3 S:SF4401 2.8 64.5 1.0 CB S:CYS215 3.4 72.7 1.0 N S:LEU216 3.8 72.8 1.0 CA S:CYS215 3.9 72.3 1.0 N S:TYR217 4.0 73.0 1.0 S2 S:SF4401 4.0 63.4 1.0 CB S:PHE196 4.0 76.7 1.0 CD2 S:PHE196 4.3 76.4 1.0 C S:CYS215 4.3 73.8 1.0 CB S:TYR217 4.3 73.7 1.0 CG S:PHE196 4.5 75.7 1.0 CA S:TYR217 4.5 74.0 1.0 ND1 S:HIS187 4.6 70.5 1.0 O S:ARG192 4.6 75.3 1.0 CE1 S:HIS187 4.7 72.7 1.0 SG S:CYS190 4.7 71.9 1.0 C S:LEU216 4.8 72.2 1.0 CA S:LEU216 4.8 72.2 1.0 CB S:ARG192 4.9 73.3 1.0 SG S:CYS221 4.9 72.8 1.0

Iron binding site 3 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:64.5 occ:1.00 FE3 S:SF4401 0.0 64.5 1.0 ND1 S:HIS187 2.0 70.5 1.0 S4 S:SF4401 2.3 64.0 1.0 S2 S:SF4401 2.3 63.4 1.0 S1 S:SF4401 2.3 70.5 1.0 CE1 S:HIS187 2.7 72.7 1.0 FE1 S:SF4401 2.7 64.9 1.0 FE4 S:SF4401 2.7 65.5 1.0 FE2 S:SF4401 2.8 63.0 1.0 CG S:HIS187 3.2 71.6 1.0 CB S:HIS187 3.8 70.9 1.0 CA S:HIS187 3.8 70.2 1.0 S3 S:SF4401 3.9 67.9 1.0 NE2 S:HIS187 3.9 73.6 1.0 CD S:PRO224 4.0 74.0 1.0 CD2 S:HIS187 4.2 73.1 1.0 CG S:PRO224 4.2 75.7 1.0 CB S:CYS190 4.2 72.3 1.0 CD S:ARG193 4.3 71.8 1.0 O S:HIS187 4.4 72.9 1.0 SG S:CYS190 4.4 71.9 1.0 C S:HIS187 4.6 70.7 1.0 SG S:CYS215 4.7 71.7 1.0 CG S:PHE196 4.7 75.7 1.0 CD2 S:PHE196 4.7 76.4 1.0 CB S:PHE196 4.7 76.7 1.0 CG S:ARG193 4.8 71.2 1.0 N S:HIS187 4.9 68.6 1.0 N S:PRO224 4.9 73.7 1.0 SG S:CYS221 4.9 72.8 1.0

Iron binding site 4 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe401 b:65.5 occ:1.00 FE4 S:SF4401 0.0 65.5 1.0 SG S:CYS190 2.3 71.9 1.0 S3 S:SF4401 2.3 67.9 1.0 S1 S:SF4401 2.3 70.5 1.0 S2 S:SF4401 2.3 63.4 1.0 FE1 S:SF4401 2.7 64.9 1.0 FE2 S:SF4401 2.7 63.0 1.0 FE3 S:SF4401 2.7 64.5 1.0 CB S:CYS190 3.2 72.3 1.0 CD1 S:ILE243 3.8 67.9 1.0 S4 S:SF4401 3.8 64.0 1.0 CG2 S:ILE243 4.1 69.9 1.0 CB S:ARG192 4.4 73.3 1.0 CA S:CYS190 4.6 72.0 1.0 ND1 S:HIS187 4.6 70.5 1.0 SG S:CYS221 4.7 72.8 1.0 C S:ARG192 4.8 73.5 1.0 SG S:CYS215 4.8 71.7 1.0 CG1 S:ILE243 4.8 67.5 1.0 N S:ARG193 4.9 71.2 1.0 CA S:ARG192 4.9 73.5 1.0 N S:ARG192 4.9 73.1 1.0 CB S:ILE243 5.0 72.4 1.0

Iron binding site 5 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:72.2 occ:1.00 FE1 S:SF4402 0.0 72.2 1.0 SG S:CYS252 2.3 73.6 1.0 S4 S:SF4402 2.3 71.8 1.0 S3 S:SF4402 2.3 73.6 1.0 S2 S:SF4402 2.3 70.8 1.0 FE3 S:SF4402 2.7 73.4 1.0 FE2 S:SF4402 2.7 72.1 1.0 FE4 S:SF4402 2.8 72.0 1.0 N S:CYS252 3.4 75.8 1.0 CB S:CYS252 3.5 76.3 1.0 CA S:CYS252 3.8 75.7 1.0 S1 S:SF4402 3.9 71.7 1.0 N S:ALA253 4.2 74.3 1.0 C S:CYS252 4.2 74.7 1.0 ND2 S:ASN228 4.3 72.8 1.0 NZ L:LYS226 4.3 85.1 1.0 C S:GLY251 4.5 75.6 1.0 N S:GLY251 4.6 74.3 1.0 SG S:CYS249 4.7 75.8 1.0 SG S:CYS230 4.7 72.1 1.0 SG S:CYS242 4.8 82.3 1.0 CA S:GLY251 4.9 74.7 1.0

Iron binding site 6 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:72.1 occ:1.00 FE2 S:SF4402 0.0 72.1 1.0 SG S:CYS249 2.2 75.8 1.0 S1 S:SF4402 2.3 71.7 1.0 S4 S:SF4402 2.3 71.8 1.0 S3 S:SF4402 2.3 73.6 1.0 FE3 S:SF4402 2.7 73.4 1.0 FE1 S:SF4402 2.7 72.2 1.0 FE4 S:SF4402 2.8 72.0 1.0 CB S:CYS249 3.2 76.7 1.0 CA S:CYS249 3.5 76.8 1.0 N S:LEU250 3.8 76.1 1.0 N S:GLY251 3.8 74.3 1.0 S2 S:SF4402 3.9 70.8 1.0 C S:CYS249 4.0 77.4 1.0 SG S:CYS242 4.3 82.3 1.0 N S:CYS252 4.4 75.8 1.0 CA S:GLY251 4.4 74.7 1.0 CB S:CYS242 4.7 76.8 1.0 CG2 S:THR226 4.7 73.3 1.0 SG S:CYS252 4.8 73.6 1.0 N S:CYS249 4.8 77.8 1.0 CG1 S:ILE186 4.8 64.3 1.0 C S:LEU250 4.8 75.0 1.0 CA S:LEU250 4.9 75.1 1.0 C S:GLY251 4.9 75.6 1.0 SG S:CYS230 5.0 72.1 1.0

Iron binding site 7 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:73.4 occ:1.00 FE3 S:SF4402 0.0 73.4 1.0 S4 S:SF4402 2.3 71.8 1.0 S2 S:SF4402 2.3 70.8 1.0 S1 S:SF4402 2.3 71.7 1.0 SG S:CYS230 2.4 72.1 1.0 FE2 S:SF4402 2.7 72.1 1.0 FE4 S:SF4402 2.7 72.0 1.0 FE1 S:SF4402 2.7 72.2 1.0 CB S:CYS230 3.3 73.2 1.0 ND2 S:ASN228 3.8 72.8 1.0 S3 S:SF4402 3.8 73.6 1.0 CD1 S:ILE186 3.9 62.6 1.0 CB S:ASN228 4.3 69.9 1.0 CG S:ASN228 4.4 72.2 1.0 SG S:CYS249 4.5 75.8 1.0 CG1 S:ILE186 4.6 64.3 1.0 NE1 S:TRP235 4.6 75.2 1.0 CA S:CYS230 4.7 72.4 1.0 SG S:CYS242 4.8 82.3 1.0 SG S:CYS252 4.9 73.6 1.0 N S:CYS230 4.9 71.5 1.0

Iron binding site 8 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe402 b:72.0 occ:1.00 FE4 S:SF4402 0.0 72.0 1.0 SG S:CYS242 2.2 82.3 1.0 S1 S:SF4402 2.3 71.7 1.0 S2 S:SF4402 2.3 70.8 1.0 S3 S:SF4402 2.3 73.6 1.0 FE3 S:SF4402 2.7 73.4 1.0 FE2 S:SF4402 2.8 72.1 1.0 FE1 S:SF4402 2.8 72.2 1.0 CB S:CYS242 3.3 76.8 1.0 NZ L:LYS226 3.8 85.1 1.0 S4 S:SF4402 4.0 71.8 1.0 CD L:LYS226 4.1 79.7 1.0 SG S:CYS252 4.3 73.6 1.0 SG S:CYS230 4.5 72.1 1.0 CE L:LYS226 4.5 81.7 1.0 N S:CYS242 4.5 75.2 1.0 CA S:CYS242 4.5 76.1 1.0 NE1 S:TRP235 4.7 75.2 1.0 SG S:CYS249 4.9 75.8 1.0 CB S:CYS230 4.9 73.2 1.0

Iron binding site 9 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:79.0 occ:1.00 FE1 S:F4S403 0.0 79.0 1.0 S2 S:F4S403 2.2 78.3 1.0 SG S:CYS19 2.2 80.9 1.0 S1 S:F4S403 2.3 84.2 1.0 SG S:CYS17 2.3 81.3 1.0 FE2 S:F4S403 2.6 80.2 1.0 FE4 S:F4S403 2.7 86.9 1.0 CB S:CYS19 3.0 80.9 1.0 FE3 S:F4S403 3.3 76.8 1.0 S3 S:F4S403 3.5 77.7 1.0 CB S:CYS17 3.5 84.7 1.0 NE2 L:HIS229 3.7 81.2 1.0 N S:CYS19 3.7 83.1 1.0 CA S:CYS19 3.9 81.3 1.0 SG S:CYS149 3.9 74.5 1.0 N S:CYS17 4.1 85.4 1.0 CD2 L:HIS229 4.2 80.3 1.0 CA S:CYS17 4.2 86.0 1.0 C S:CYS17 4.5 86.9 1.0 N S:THR18 4.5 85.9 1.0 C S:CYS19 4.6 79.4 1.0 N S:CYS20 4.6 78.0 1.0 SG S:CYS115 4.8 87.0 1.0 CG L:ARG74 4.8 74.5 1.0 CE1 L:HIS229 4.8 82.1 1.0 C S:THR18 4.9 83.9 1.0 SG S:CYS20 5.0 78.2 1.0

Iron binding site 10 out of 54 in the Structure of E. Coli Hydrogenase-1 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 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe403 b:80.2 occ:1.00 FE2 S:F4S403 0.0 80.2 1.0 S3 S:F4S403 2.2 77.7 1.0 SG S:CYS115 2.2 87.0 1.0 S1 S:F4S403 2.2 84.2 1.0 S2 S:F4S403 2.3 78.3 1.0 FE1 S:F4S403 2.6 79.0 1.0 FE3 S:F4S403 2.6 76.8 1.0 FE4 S:F4S403 2.8 86.9 1.0 CB S:CYS115 3.4 83.9 1.0 SG S:CYS19 4.1 80.9 1.0 N S:CYS17 4.2 85.4 1.0 SG S:CYS120 4.3 74.3 1.0 N S:CYS115 4.3 79.8 1.0 CA S:CYS115 4.4 82.2 1.0 SG S:CYS17 4.4 81.3 1.0 CB S:CYS120 4.5 79.1 1.0 SG S:CYS149 4.6 74.5 1.0 SG S:CYS20 4.7 78.2 1.0 CA S:GLU16 4.8 85.0 1.0 CB S:CYS17 4.9 84.7 1.0 NE2 S:GLN122 5.0 95.9 1.0

A.Volbeda, C.Darnault, A.Parkin, F.Sargent, F.A.Armstrong, J.C.Fontecilla-Camps. Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 From Escherichia Coli in Complex with Its Cognate Cytochrome B. Structure V. 21 184 2013.
ISSN: ISSN 0969-2126
PubMed: 23260654
DOI: 10.1016/J.STR.2012.11.010