Iron in PDB 2wpn: Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough

All present enzymatic activity of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough:
1.18.99.1;

The structure of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough, PDB code: 2wpn was solved by M.C.Marques, R.Coelho, A.L.De Lacey, I.A.C.Pereira, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.36 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.596, 91.223, 66.751, 90.00, 101.73, 90.00
R / Rfree (%)	14.4 / 20.1

The structure of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Chlorine	(Cl)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough (pdb code 2wpn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough, PDB code: 2wpn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1284 b:23.3 occ:1.00 FE1 A:SF41284 0.0 23.3 1.0 S2 A:SF41284 2.3 20.1 1.0 S3 A:SF41284 2.3 18.8 1.0 SG A:CYS238 2.3 20.0 1.0 S4 A:SF41284 2.3 20.8 1.0 FE3 A:SF41284 2.7 24.6 1.0 FE4 A:SF41284 2.7 23.1 1.0 FE2 A:SF41284 2.7 24.0 1.0 CB A:CYS238 3.1 18.5 1.0 S1 A:SF41284 3.9 16.8 1.0 CA A:GLY240 4.4 17.1 1.0 CD A:PRO241 4.4 17.7 1.0 N A:GLY240 4.5 17.6 1.0 CA A:CYS238 4.5 18.8 1.0 CG1 A:VAL260 4.5 16.7 1.0 ND1 A:HIS208 4.6 21.4 1.0 CB A:ARG233 4.6 16.9 1.0 SG A:CYS211 4.7 20.0 1.0 SG A:CYS232 4.7 20.1 1.0 N A:TYR234 4.7 17.7 1.0 C A:CYS238 4.8 18.4 1.0 CG2 A:VAL260 4.8 18.2 1.0 N A:ARG233 4.8 17.1 1.0 O A:CYS238 4.9 17.8 1.0 C A:ARG233 4.9 17.5 1.0

Iron binding site 2 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1284 b:24.0 occ:1.00 FE2 A:SF41284 0.0 24.0 1.0 S4 A:SF41284 2.3 20.8 1.0 SG A:CYS232 2.3 20.1 1.0 S1 A:SF41284 2.3 16.8 1.0 S3 A:SF41284 2.3 18.8 1.0 FE3 A:SF41284 2.7 24.6 1.0 FE4 A:SF41284 2.7 23.1 1.0 FE1 A:SF41284 2.7 23.3 1.0 CB A:CYS232 3.5 18.2 1.0 N A:ARG233 3.7 17.1 1.0 S2 A:SF41284 3.9 20.1 1.0 CA A:CYS232 4.0 17.7 1.0 N A:TYR234 4.0 17.7 1.0 CB A:TYR217 4.3 22.7 1.0 C A:CYS232 4.3 17.2 1.0 CD1 A:TYR217 4.4 22.4 1.0 ND1 A:HIS208 4.4 21.4 1.0 CB A:TYR234 4.5 18.6 1.0 CA A:ARG233 4.6 17.0 1.0 CB A:TYR213 4.6 20.8 1.0 CA A:TYR234 4.7 19.0 1.0 CE1 A:HIS208 4.7 19.4 1.0 C A:ARG233 4.7 17.5 1.0 O A:TYR213 4.7 21.0 1.0 CG A:TYR217 4.7 22.6 1.0 SG A:CYS238 4.8 20.0 1.0 SG A:CYS211 4.9 20.0 1.0 CB A:CYS238 4.9 18.5 1.0 CB A:ARG233 5.0 16.9 1.0

Iron binding site 3 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1284 b:24.6 occ:1.00 FE3 A:SF41284 0.0 24.6 1.0 S1 A:SF41284 2.3 16.8 1.0 SG A:CYS211 2.3 20.0 1.0 S2 A:SF41284 2.3 20.1 1.0 S4 A:SF41284 2.3 20.8 1.0 FE4 A:SF41284 2.6 23.1 1.0 FE1 A:SF41284 2.7 23.3 1.0 FE2 A:SF41284 2.7 24.0 1.0 CB A:CYS211 3.1 21.1 1.0 S3 A:SF41284 3.8 18.8 1.0 CB A:TYR213 4.2 20.8 1.0 CG1 A:VAL260 4.3 16.7 1.0 ND1 A:HIS208 4.3 21.4 1.0 CD2 A:TYR213 4.5 22.4 1.0 CA A:CYS211 4.5 21.4 1.0 C A:TYR213 4.6 20.9 1.0 N A:TYR213 4.7 20.3 1.0 CA A:TYR213 4.7 20.7 1.0 N A:LEU214 4.8 21.8 1.0 SG A:CYS238 4.8 20.0 1.0 CA A:HIS208 4.9 18.7 1.0 CG A:TYR213 4.9 22.4 1.0 SG A:CYS232 4.9 20.1 1.0 O A:TYR213 5.0 21.0 1.0

Iron binding site 4 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1284 b:23.1 occ:1.00 FE4 A:SF41284 0.0 23.1 1.0 ND1 A:HIS208 2.0 21.4 1.0 S2 A:SF41284 2.3 20.1 1.0 S3 A:SF41284 2.3 18.8 1.0 S1 A:SF41284 2.3 16.8 1.0 FE3 A:SF41284 2.6 24.6 1.0 FE2 A:SF41284 2.7 24.0 1.0 FE1 A:SF41284 2.7 23.3 1.0 CE1 A:HIS208 2.9 19.4 1.0 CG A:HIS208 3.1 20.1 1.0 CB A:HIS208 3.6 18.9 1.0 S4 A:SF41284 3.9 20.8 1.0 CA A:HIS208 3.9 18.7 1.0 NE2 A:HIS208 4.0 19.5 1.0 CD A:PRO241 4.1 17.7 1.0 CD2 A:HIS208 4.2 19.0 1.0 CG A:PRO241 4.3 19.0 1.0 CB A:CYS211 4.5 21.1 1.0 O A:HIS208 4.6 18.5 1.0 N A:PRO241 4.6 17.6 1.0 SG A:CYS211 4.6 20.0 1.0 CD1 A:TYR217 4.7 22.4 1.0 SG A:CYS232 4.7 20.1 1.0 C A:HIS208 4.7 19.6 1.0 SG A:CYS238 4.8 20.0 1.0 CG A:TYR217 4.9 22.6 1.0 CB A:TYR217 4.9 22.7 1.0 CA A:GLY240 4.9 17.1 1.0 C A:GLY240 4.9 16.9 1.0

Iron binding site 5 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1285 b:24.0 occ:1.00 FE1 A:SF41285 0.0 24.0 1.0 S4 A:SF41285 2.3 17.3 1.0 S3 A:SF41285 2.3 18.1 1.0 SG A:CYS268 2.3 18.7 1.0 S2 A:SF41285 2.3 17.7 1.0 FE2 A:SF41285 2.8 23.0 1.0 FE3 A:SF41285 2.8 22.2 1.0 FE4 A:SF41285 2.9 22.2 1.0 CB A:CYS268 3.4 17.9 1.0 N A:CYS268 3.6 17.7 1.0 NH2 B:ARG182 3.8 19.9 1.0 CA A:CYS268 4.0 17.3 1.0 S1 A:SF41285 4.0 17.6 1.0 NH1 B:ARG182 4.1 20.3 1.0 CZ B:ARG182 4.2 19.1 1.0 N A:VAL269 4.5 17.9 1.0 C A:CYS268 4.6 17.7 1.0 CG1 A:VAL269 4.6 15.4 1.0 C A:GLY267 4.7 17.2 1.0 SG A:CYS247 4.8 19.8 1.0 SG A:CYS259 4.9 19.9 1.0 SG A:CYS265 4.9 19.0 1.0 N A:GLY267 4.9 17.9 1.0

Iron binding site 6 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1285 b:23.0 occ:1.00 FE2 A:SF41285 0.0 23.0 1.0 S4 A:SF41285 2.3 17.3 1.0 SG A:CYS259 2.3 19.9 1.0 S3 A:SF41285 2.3 18.1 1.0 S1 A:SF41285 2.3 17.6 1.0 FE3 A:SF41285 2.7 22.2 1.0 FE1 A:SF41285 2.8 24.0 1.0 FE4 A:SF41285 2.8 22.2 1.0 CB A:CYS259 3.1 17.1 1.0 S2 A:SF41285 3.9 17.7 1.0 NE2 B:GLN187 4.1 21.5 1.0 CZ B:ARG182 4.1 19.1 1.0 NH2 B:ARG182 4.1 19.9 1.0 NE B:ARG182 4.3 21.8 1.0 CA A:CYS259 4.4 18.3 1.0 N A:CYS259 4.5 17.9 1.0 NE1 A:TRP252 4.5 17.1 1.0 NH1 B:ARG182 4.6 20.3 1.0 SG A:CYS247 4.6 19.8 1.0 SG A:CYS268 4.7 18.7 1.0 SG A:CYS265 4.8 19.0 1.0 CA A:CYS265 4.9 18.9 1.0 CD B:ARG182 4.9 23.4 1.0

Iron binding site 7 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1285 b:22.2 occ:1.00 FE3 A:SF41285 0.0 22.2 1.0 S1 A:SF41285 2.3 17.6 1.0 SG A:CYS247 2.3 19.8 1.0 S2 A:SF41285 2.3 17.7 1.0 S4 A:SF41285 2.3 17.3 1.0 FE2 A:SF41285 2.7 23.0 1.0 FE4 A:SF41285 2.7 22.2 1.0 FE1 A:SF41285 2.8 24.0 1.0 CB A:CYS247 3.3 16.9 1.0 S3 A:SF41285 3.8 18.1 1.0 CD1 A:ILE207 4.0 16.7 1.0 NE1 A:TRP252 4.2 17.1 1.0 CB A:ALA245 4.5 14.3 1.0 CH2 A:TRP165 4.5 15.2 1.0 SG A:CYS259 4.7 19.9 1.0 CA A:CYS247 4.7 17.6 1.0 SG A:CYS268 4.8 18.7 1.0 SG A:CYS265 4.8 19.0 1.0 CZ2 A:TRP165 5.0 15.7 1.0

Iron binding site 8 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1285 b:22.2 occ:1.00 FE4 A:SF41285 0.0 22.2 1.0 S3 A:SF41285 2.3 18.1 1.0 SG A:CYS265 2.3 19.0 1.0 S2 A:SF41285 2.3 17.7 1.0 S1 A:SF41285 2.3 17.6 1.0 FE3 A:SF41285 2.7 22.2 1.0 FE2 A:SF41285 2.8 23.0 1.0 FE1 A:SF41285 2.9 24.0 1.0 CB A:CYS265 3.4 19.0 1.0 CD1 A:ILE207 3.8 16.7 1.0 CA A:CYS265 3.8 18.9 1.0 S4 A:SF41285 3.9 17.3 1.0 N A:GLY267 4.1 17.9 1.0 N A:ILE266 4.1 18.4 1.0 C A:CYS265 4.4 18.4 1.0 CG2 A:THR243 4.4 17.8 1.0 N A:CYS268 4.5 17.7 1.0 CA A:GLY267 4.6 17.0 1.0 CB A:CYS259 4.7 17.1 1.0 SG A:CYS259 4.8 19.9 1.0 SG A:CYS247 4.8 19.8 1.0 SG A:CYS268 5.0 18.7 1.0

Iron binding site 9 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1286 b:21.3 occ:0.60 FE1 A:SF41286 0.0 21.3 0.6 FE4 A:FSX1287 0.6 23.8 0.4 O24 A:FSX1287 1.5 21.1 0.4 S3 A:FSX1287 2.0 19.5 0.4 S4 A:SF41286 2.3 18.6 0.6 S2 A:SF41286 2.3 17.2 0.6 S3 A:SF41286 2.3 18.4 0.6 SG A:CYS18 2.3 19.8 1.0 S4 A:FSX1287 2.4 14.4 0.4 FE2 A:SF41286 2.7 24.5 0.6 FE3 A:SF41286 2.7 22.5 0.6 FE4 A:SF41286 2.7 21.7 0.6 FE3 A:FSX1287 2.7 25.4 0.4 FE2 A:FSX1287 2.9 25.7 0.4 O1 A:FSX1287 3.0 24.8 0.4 O12 A:FSX1287 3.2 19.1 0.4 CB A:CYS18 3.2 18.7 1.0 FE1 A:FSX1287 3.2 24.9 0.4 N A:CYS18 3.6 20.1 1.0 S2 A:FSX1287 3.8 20.1 0.4 S1 A:SF41286 3.9 20.5 0.6 CA A:CYS18 3.9 18.8 1.0 N A:GLY20 4.1 18.8 1.0 CE1 B:HIS185 4.3 18.4 1.0 CA A:GLY20 4.3 19.5 1.0 C A:CYS18 4.4 19.1 1.0 O B:HOH2029 4.5 17.9 1.0 N A:THR19 4.6 18.6 1.0 C A:GLY17 4.6 20.6 1.0 N A:CYS21 4.7 19.1 1.0 SG A:CYS159 4.8 19.4 1.0 SG A:CYS21 4.8 21.5 1.0 CA A:GLY17 4.8 20.2 1.0 SG A:CYS121 4.9 20.1 1.0 CG B:ARG73 4.9 16.6 1.0 C A:GLY20 4.9 18.8 1.0

Iron binding site 10 out of 18 in the Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Oxidised, As-Isolated Nifese Hydrogenase From D. Vulgaris Hildenborough within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1286 b:24.5 occ:0.60 FE2 A:SF41286 0.0 24.5 0.6 O1 A:FSX1287 0.5 24.8 0.4 FE2 A:FSX1287 1.9 25.7 0.4 S2 A:FSX1287 2.3 20.1 0.4 S4 A:SF41286 2.3 18.6 0.6 S4 A:FSX1287 2.3 14.4 0.4 S1 A:SF41286 2.3 20.5 0.6 S3 A:SF41286 2.3 18.4 0.6 SG A:CYS21 2.3 21.5 1.0 O12 A:FSX1287 2.6 19.1 0.4 FE1 A:SF41286 2.7 21.3 0.6 O24 A:FSX1287 2.7 21.1 0.4 FE4 A:SF41286 2.8 21.7 0.6 FE3 A:SF41286 2.8 22.5 0.6 FE3 A:FSX1287 2.9 25.4 0.4 FE4 A:FSX1287 3.0 23.8 0.4 FE1 A:FSX1287 3.2 24.9 0.4 S3 A:FSX1287 3.6 19.5 0.4 N A:CYS21 3.8 19.1 1.0 CB A:CYS21 3.8 20.2 1.0 S2 A:SF41286 4.0 17.2 0.6 O A:HOH2031 4.2 21.9 1.0 CA A:GLY119 4.3 16.0 1.0 CA A:CYS21 4.3 19.6 1.0 CA A:PRO160 4.4 17.8 1.0 C A:GLY20 4.5 18.8 1.0 OE2 A:GLU77 4.5 27.9 1.0 O A:GLY158 4.6 16.7 1.0 CD A:PRO161 4.6 16.4 1.0 CB A:PRO160 4.7 17.7 1.0 SG A:CYS18 4.7 19.8 1.0 CA A:GLY20 4.7 19.5 1.0 CA A:CYS159 4.8 18.2 1.0 N A:GLY20 4.8 18.8 1.0 CG A:GLU77 4.9 23.3 1.0 SG A:CYS159 5.0 19.4 1.0

M.C.Marques, R.Coelho, A.L.De Lacey, I.A.Pereira, P.M.Matias. The Three-Dimensional Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough: A Hydrogenase Without A Bridging Ligand in the Active Site in Its Oxidised, "As-Isolated" State. J.Mol.Biol. V. 396 893 2010.
ISSN: ESSN 1089-8638
PubMed: 20026074
DOI: 10.1016/J.JMB.2009.12.013