Iron in PDB 7o1o: Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)

The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant), PDB code: 7o1o was solved by R.Rohac, L.Martin, L.Liu, D.Basu, L.Tao, R.D.Britt, T.Rauchfuss, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.35 / 1.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.42, 81.76, 70.42, 90, 90, 90
R / Rfree (%)	12.8 / 15.2

The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) (pdb code 7o1o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant), PDB code: 7o1o:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:14.8 occ:1.00 C A:CYN405 1.7 16.1 1.0 C A:CMO404 1.8 14.1 1.0 C A:CMO403 1.8 15.5 0.9 N A:CYS401 2.0 15.5 1.0 OXT A:CYS401 2.1 18.8 1.0 SG A:CYS401 2.3 14.5 1.0 CA A:CYS401 2.8 14.5 1.0 C A:CYS401 2.9 19.5 1.0 N A:CYN405 2.9 14.9 1.0 O A:CMO404 3.0 15.7 1.0 O A:CMO403 3.0 17.1 0.9 CB A:CYS401 3.1 15.7 1.0 HB3 A:CYS401 3.6 18.9 1.0 HA A:CYS401 3.7 17.4 1.0 HB2 A:CYS401 3.9 18.9 1.0 HD13 A:ILE56 3.9 18.4 0.8 HB A:THR268 3.9 16.5 1.0 HH21 A:ARG159 4.0 19.8 1.0 HE22 A:GLN107 4.0 16.8 1.0 HG21 A:THR268 4.1 17.2 1.0 H A:THR269 4.1 16.5 1.0 O A:CYS401 4.1 21.3 1.0 HD21 A:LEU157 4.2 23.4 1.0 OG1 A:THR269 4.3 16.6 1.0 HG1 A:THR269 4.4 19.9 1.0 HD2 A:ARG159 4.4 19.1 1.0 SD A:MET291 4.4 16.6 0.8 HG22 A:THR268 4.5 17.2 1.0 O A:HOH580 4.5 18.0 1.0 HD11 A:ILE56 4.5 18.4 0.8 NH2 A:ARG159 4.5 16.5 1.0 CG2 A:THR268 4.6 14.3 1.0 HH22 A:ARG159 4.6 19.8 1.0 HA A:THR268 4.6 15.5 1.0 CD1 A:ILE56 4.6 15.3 0.8 HE3 A:MET291 4.6 32.2 0.2 HD22 A:LEU157 4.6 23.4 1.0 CB A:THR268 4.7 13.7 1.0 HE1 A:MET291 4.7 32.2 0.2 HB2 A:MET291 4.7 16.5 0.8 SD A:MET291 4.8 16.4 0.2 NE2 A:GLN107 4.8 14.0 1.0 HB2 A:MET291 4.8 18.9 0.2 CD2 A:LEU157 4.8 19.5 1.0 N A:THR269 4.9 13.8 1.0 HB A:THR269 4.9 19.5 1.0 CE A:MET291 4.9 26.8 0.2

Iron binding site 2 out of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe415 b:14.5 occ:1.00 FE1 A:SF4415 0.0 14.5 1.0 S3 A:SF4415 2.2 14.7 1.0 SG A:CYS70 2.3 14.4 1.0 S2 A:SF4415 2.3 14.9 1.0 S4 A:SF4415 2.3 14.9 1.0 FE2 A:SF4415 2.7 14.5 1.0 FE3 A:SF4415 2.7 14.7 1.0 FE4 A:SF4415 2.9 16.4 1.0 HB3 A:CYS70 3.0 17.2 1.0 CB A:CYS70 3.1 14.3 1.0 HB2 A:CYS70 3.1 17.2 1.0 HB2 A:LEU72 3.3 16.2 1.0 S1 A:SF4415 3.9 15.4 1.0 H8 A:SAH408 4.0 18.4 1.0 HB2 A:CYS67 4.0 16.5 1.0 H A:LEU72 4.2 16.7 1.0 HD22 A:LEU305 4.2 20.4 1.0 CB A:LEU72 4.2 13.5 1.0 HD12 A:LEU72 4.3 19.1 1.0 SD A:SAH408 4.4 19.1 1.0 HG A:LEU72 4.5 21.3 1.0 CA A:CYS70 4.5 14.0 1.0 HE1 A:TYR69 4.5 16.1 1.0 HD23 A:LEU305 4.6 20.4 1.0 H A:ARG73 4.7 16.6 1.0 SG A:CYS67 4.7 15.2 1.0 HG1 A:SAH408 4.8 22.0 1.0 N A:SAH408 4.8 15.5 1.0 N A:ARG73 4.8 13.9 1.0 HB3 A:LEU72 4.8 16.2 1.0 CD2 A:LEU305 4.8 17.0 1.0 CB A:CYS67 4.8 13.8 1.0 N A:LEU72 4.8 13.9 1.0 CG A:LEU72 4.8 17.8 1.0 SG A:CYS63 4.8 14.5 1.0 OXT A:SAH408 4.8 16.9 1.0 C A:LEU72 4.9 14.6 1.0 CA A:LEU72 4.9 14.3 1.0 HA A:ARG73 4.9 17.4 1.0 HA A:CYS70 4.9 16.8 1.0 HN2 A:SAH408 4.9 18.6 1.0 HB2 A:CYS63 4.9 18.0 1.0 HD21 A:LEU305 5.0 20.4 1.0

Iron binding site 3 out of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe415 b:14.5 occ:1.00 FE2 A:SF4415 0.0 14.5 1.0 S4 A:SF4415 2.3 14.9 1.0 SG A:CYS63 2.3 14.5 1.0 S3 A:SF4415 2.3 14.7 1.0 S1 A:SF4415 2.3 15.4 1.0 FE1 A:SF4415 2.7 14.5 1.0 FE3 A:SF4415 2.7 14.7 1.0 FE4 A:SF4415 2.9 16.4 1.0 HB2 A:CYS63 3.3 18.0 1.0 CB A:CYS63 3.3 15.0 1.0 HB2 A:LYS65 3.3 18.4 1.0 HB3 A:CYS63 3.4 18.0 1.0 H A:GLU110 3.7 16.5 1.0 HN2 A:SAH408 3.8 18.6 1.0 S2 A:SF4415 3.9 14.9 1.0 HA2 A:GLY109 3.9 15.7 1.0 N A:SAH408 4.1 15.5 1.0 HB2 A:LEU72 4.1 16.2 1.0 H A:LYS65 4.1 17.4 1.0 HN1 A:SAH408 4.2 18.6 1.0 CB A:LYS65 4.2 15.3 1.0 HG3 A:GLU110 4.2 17.9 1.0 HB3 A:LYS65 4.3 18.4 1.0 N A:GLU110 4.5 13.8 1.0 HA A:ARG73 4.6 17.4 1.0 HB2 A:GLU110 4.6 17.1 1.0 HA3 A:GLY109 4.6 15.7 1.0 CA A:GLY109 4.7 13.1 1.0 CA A:CYS63 4.7 15.2 1.0 SG A:CYS67 4.8 15.2 1.0 H A:CYS67 4.8 17.2 1.0 SG A:CYS70 4.8 14.4 1.0 HD2 A:LYS65 4.8 19.8 1.0 N A:LYS65 4.8 14.5 1.0 O A:LYS65 4.8 15.7 1.0 C A:LYS65 4.8 14.3 1.0 CA A:LYS65 4.8 15.9 1.0 OXT A:SAH408 4.9 16.9 1.0 HA A:CYS63 4.9 18.2 1.0 CB A:LEU72 4.9 13.5 1.0 HB3 A:LEU72 5.0 16.2 1.0 HB3 A:CYS70 5.0 17.2 1.0 HD12 A:LEU72 5.0 19.1 1.0

Iron binding site 4 out of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe415 b:14.7 occ:1.00 FE3 A:SF4415 0.0 14.7 1.0 S1 A:SF4415 2.2 15.4 1.0 S2 A:SF4415 2.3 14.9 1.0 SG A:CYS67 2.3 15.2 1.0 S4 A:SF4415 2.3 14.9 1.0 FE2 A:SF4415 2.7 14.5 1.0 FE1 A:SF4415 2.7 14.5 1.0 FE4 A:SF4415 2.9 16.4 1.0 HB2 A:CYS67 3.0 16.5 1.0 CB A:CYS67 3.3 13.8 1.0 H A:CYS67 3.5 17.2 1.0 HH21 A:ARG172 3.5 19.2 1.0 HB2 A:LYS65 3.8 18.4 1.0 HB3 A:CYS67 3.9 16.5 1.0 S3 A:SF4415 3.9 14.7 1.0 O A:HOH563 3.9 21.0 1.0 HB3 A:LYS65 3.9 18.4 1.0 HB3 A:CYS70 4.1 17.2 1.0 HH A:TYR69 4.1 20.0 1.0 HB2 A:CYS70 4.2 17.2 1.0 HE A:ARG172 4.2 18.3 1.0 OXT A:SAH408 4.2 16.9 1.0 N A:CYS67 4.2 14.3 1.0 CB A:LYS65 4.4 15.3 1.0 CA A:CYS67 4.4 13.9 1.0 HE1 A:TYR69 4.4 16.1 1.0 HD3 A:LYS65 4.4 19.8 1.0 NH2 A:ARG172 4.4 16.0 1.0 CB A:CYS70 4.5 14.3 1.0 OH A:TYR69 4.6 16.6 1.0 SG A:CYS70 4.6 14.4 1.0 HN2 A:SAH408 4.7 18.6 1.0 HD2 A:LYS65 4.7 19.8 1.0 SG A:CYS63 4.7 14.5 1.0 CE1 A:TYR69 4.8 13.4 1.0 HH22 A:ARG172 4.9 19.2 1.0 HA A:CYS67 4.9 16.7 1.0 O A:HOH593 4.9 18.3 1.0 N A:SAH408 4.9 15.5 1.0 CD A:LYS65 4.9 16.5 1.0 NE A:ARG172 5.0 15.2 1.0 CZ A:TYR69 5.0 14.6 1.0

Iron binding site 5 out of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde Fromt. Maritima (Auxiliary Cluster Deleted Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe415 b:16.4 occ:1.00 FE4 A:SF4415 0.0 16.4 1.0 OXT A:SAH408 2.2 16.9 1.0 N A:SAH408 2.2 15.5 1.0 HN2 A:SAH408 2.3 18.6 1.0 S2 A:SF4415 2.3 14.9 1.0 S3 A:SF4415 2.4 14.7 1.0 S1 A:SF4415 2.4 15.4 1.0 FE2 A:SF4415 2.9 14.5 1.0 HN1 A:SAH408 2.9 18.6 1.0 FE1 A:SF4415 2.9 14.5 1.0 FE3 A:SF4415 2.9 14.7 1.0 C A:SAH408 3.1 15.6 1.0 CA A:SAH408 3.1 14.0 1.0 SD A:SAH408 3.3 19.1 1.0 HG1 A:SAH408 3.4 22.0 1.0 CG A:SAH408 3.7 18.3 1.0 CB A:SAH408 3.9 16.8 1.0 HA A:SAH408 4.0 16.8 1.0 H3' A:SAH408 4.0 17.5 1.0 O A:HOH563 4.1 21.0 1.0 O A:HOH593 4.1 18.3 1.0 S4 A:SF4415 4.1 14.9 1.0 O A:SAH408 4.2 15.4 1.0 HA2 A:GLY109 4.2 15.7 1.0 HG3 A:GLU110 4.4 17.9 1.0 HB2 A:SAH408 4.5 20.1 1.0 HH21 A:ARG172 4.7 19.2 1.0 SG A:CYS63 4.7 14.5 1.0 HG2 A:SAH408 4.7 22.0 1.0 HB1 A:SAH408 4.7 20.1 1.0 H A:GLU110 4.8 16.5 1.0 SG A:CYS70 4.9 14.4 1.0 C5' A:SAH408 4.9 19.7 1.0

Y.Nicolet, J.K.Rubach, M.C.Posewitz, P.Amara, C.Mathevon, M.Atta, M.Fontecave, J.C.Fontecilla-Camps. X-Ray Structure of the [Fefe]-Hydrogenase Maturase Hyde From Thermotoga Maritima* Journal of Biological V. 283 18861 2008CHEMISTRY.
DOI: 10.1074/JBC.M801161200