Nickel in PDB 1e3d: [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774

The structure of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774, PDB code: 1e3d was solved by P.M.Matias, C.M.Soares, L.M.Saraiva, R.Coelho, J.Morais, J.Le Gall, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.090, 169.980, 72.620, 90.00, 92.80, 90.00
R / Rfree (%)	16.7 / 22.3

The structure of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	24 atoms

The binding sites of Nickel atom in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 (pdb code 1e3d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774, PDB code: 1e3d:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni543 b:22.2 occ:1.00 NI B:FNE543 0.0 22.2 1.0 S4 B:FNE543 1.9 18.3 0.5 SG B:CYS71 2.2 20.3 1.0 SG B:CYS536 2.2 17.3 0.7 SG B:CYS539 2.5 16.9 1.0 SG B:CYS74 2.6 16.2 1.0 SG B:CYS536 2.6 17.3 0.1 HB3 B:CYS536 2.7 17.5 0.2 HB2 B:CYS536 2.8 17.5 0.1 FE B:FNE543 2.9 14.6 1.0 CB B:CYS71 3.0 20.8 1.0 HB3 B:CYS71 3.0 24.9 1.0 HB2 B:CYS71 3.0 24.9 1.0 SG B:CYS536 3.0 17.3 0.2 HB2 B:CYS536 3.1 17.5 0.2 CB B:CYS536 3.1 14.6 0.2 CB B:CYS536 3.1 14.6 0.1 H B:CYS74 3.1 18.2 1.0 HB3 B:CYS536 3.1 17.5 0.7 CB B:CYS536 3.1 14.6 0.7 HB2 B:CYS539 3.2 13.1 1.0 HB3 B:CYS536 3.2 17.5 0.1 HB2 B:CYS536 3.3 17.5 0.7 CB B:CYS539 3.5 10.9 1.0 HB3 B:CYS74 3.5 20.0 1.0 CB B:CYS74 3.6 16.7 1.0 HB B:VAL73 3.7 16.6 1.0 C3 B:FNE543 3.9 16.1 1.0 N B:CYS74 3.9 15.2 1.0 H B:CYS539 4.0 15.2 1.0 C1 B:FNE543 4.1 17.2 1.0 HB3 B:CYS539 4.2 13.1 1.0 HD2 B:ARG469 4.3 15.9 1.0 HG3 B:GLU24 4.3 17.4 1.0 CA B:CYS74 4.3 10.0 1.0 HH11 B:ARG469 4.4 16.7 1.0 CA B:CYS71 4.4 18.5 1.0 HB2 B:CYS74 4.4 20.0 1.0 C2 B:FNE543 4.4 17.2 1.0 H B:VAL73 4.5 16.4 1.0 CA B:CYS539 4.5 12.4 1.0 N B:CYS539 4.5 12.7 1.0 CA B:CYS536 4.6 13.0 1.0 NH1 B:ARG469 4.6 13.9 1.0 HB3 B:GLU24 4.6 13.5 1.0 HA B:CYS539 4.6 14.9 1.0 CB B:VAL73 4.6 13.8 1.0 HA B:CYS71 4.7 22.2 1.0 O3 B:FNE543 4.7 21.0 1.0 HB2 B:ALA538 4.8 20.9 1.0 HH12 B:ARG469 4.8 16.7 1.0 CZ B:ARG469 4.8 15.8 1.0 HA B:CYS536 4.9 15.6 1.0 HG11 B:VAL73 4.9 19.1 1.0 C B:CYS71 4.9 17.2 1.0 CD B:ARG469 4.9 13.3 1.0 C B:VAL73 5.0 13.5 1.0 NE B:ARG469 5.0 14.8 1.0

Nickel binding site 2 out of 2 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni543 b:23.5 occ:1.00 NI D:FNE543 0.0 23.5 1.0 S4 D:FNE543 2.0 19.9 0.5 SG D:CYS536 2.2 15.9 0.6 SG D:CYS71 2.2 19.2 1.0 SG D:CYS539 2.5 14.9 1.0 SG D:CYS74 2.6 16.7 1.0 HB2 D:CYS536 2.7 19.3 0.2 HB3 D:CYS536 2.8 19.3 0.3 FE D:FNE543 3.0 15.2 1.0 HB2 D:CYS536 3.0 19.3 0.3 SG D:CYS536 3.0 15.9 0.3 CB D:CYS71 3.1 14.0 1.0 HB3 D:CYS71 3.1 16.8 1.0 SG D:CYS536 3.1 15.9 0.2 CB D:CYS536 3.1 16.1 0.3 H D:CYS74 3.1 23.2 1.0 CB D:CYS536 3.1 16.1 0.2 HB2 D:CYS71 3.1 16.8 1.0 HB3 D:CYS536 3.1 19.3 0.2 HB3 D:CYS536 3.2 19.3 0.6 CB D:CYS536 3.2 16.1 0.6 HB2 D:CYS539 3.3 16.9 1.0 HB2 D:CYS536 3.3 19.3 0.6 HB3 D:CYS74 3.4 22.1 1.0 CB D:CYS539 3.5 14.1 1.0 CB D:CYS74 3.6 18.4 1.0 HB D:VAL73 3.7 15.2 1.0 N D:CYS74 3.9 19.3 1.0 H D:CYS539 3.9 19.4 1.0 C3 D:FNE543 4.1 16.4 1.0 C1 D:FNE543 4.2 18.5 1.0 HB3 D:CYS539 4.2 16.9 1.0 HG3 D:GLU24 4.3 15.5 1.0 CA D:CYS74 4.3 16.6 1.0 HD2 D:ARG469 4.4 17.4 1.0 H D:VAL73 4.4 14.9 1.0 HB2 D:CYS74 4.4 22.1 1.0 HH11 D:ARG469 4.4 19.3 1.0 N D:CYS539 4.5 16.2 1.0 CA D:CYS539 4.5 18.4 1.0 C2 D:FNE543 4.5 18.9 1.0 CA D:CYS71 4.5 12.5 1.0 HB3 D:GLU24 4.6 16.4 1.0 CA D:CYS536 4.6 13.8 1.0 CB D:VAL73 4.6 12.6 1.0 NH1 D:ARG469 4.6 16.1 1.0 HA D:CYS539 4.7 22.1 1.0 O3 D:FNE543 4.8 15.9 1.0 HA D:CYS71 4.8 15.0 1.0 HH12 D:ARG469 4.9 19.3 1.0 HB1 D:ALA538 4.9 22.1 1.0 HA D:CYS536 4.9 16.6 1.0 OE1 D:GLU24 5.0 21.5 1.0 C D:CYS71 5.0 13.8 1.0 N D:VAL73 5.0 12.4 1.0 C D:VAL73 5.0 15.5 1.0 CZ D:ARG469 5.0 16.8 1.0 CG D:GLU24 5.0 12.9 1.0

P.M.Matias, C.M.Soares, L.M.Saraiva, R.Coelho, J.Morais, J.Le Gall, M.A.Carrondo. [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of Its Interaction with the Tetrahaem Cytochrome C3. J.Biol.Inorg.Chem. V. 6 63 2001.
ISSN: ISSN 0949-8257
PubMed: 11191224
DOI: 10.1007/S007750000167