Magnesium 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:

Nickel	(Ni)	2 atoms
Iron	(Fe)	24 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg binding site number 1 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:15.8 occ:1.00 O B:HOH2358 2.1 12.1 1.0 O B:LEU488 2.1 16.4 1.0 O B:HOH2355 2.1 12.7 1.0 OE2 B:GLU52 2.2 14.3 1.0 NE2 B:HIS542 2.2 14.6 1.0 O B:HOH2070 2.2 16.4 1.0 CE1 B:HIS542 3.1 15.8 1.0 CD B:GLU52 3.1 15.8 1.0 HE1 B:HIS542 3.2 19.0 1.0 CD2 B:HIS542 3.3 10.8 1.0 H B:LEU488 3.3 16.5 1.0 C B:LEU488 3.3 14.6 1.0 HZ3 B:LYS365 3.4 22.8 1.0 HD2 B:HIS542 3.5 12.9 1.0 OE1 B:GLU52 3.5 18.3 1.0 HB2 B:LEU488 3.7 18.4 1.0 N B:LEU488 3.8 13.8 1.0 HD2 B:LYS365 3.8 23.7 1.0 CA B:LEU488 4.0 11.4 1.0 OE1 B:GLN487 4.1 20.1 1.0 OE2 B:GLU329 4.1 20.1 1.0 HA B:VAL489 4.1 18.6 1.0 OE1 B:GLU329 4.2 16.1 1.0 NZ B:LYS365 4.2 15.2 1.0 ND1 B:HIS542 4.3 11.7 1.0 HB3 B:GLN487 4.3 22.1 1.0 HG23 B:VAL489 4.3 25.1 1.0 CG B:HIS542 4.4 10.1 1.0 CB B:LEU488 4.4 15.3 1.0 O B:HOH2510 4.4 17.3 1.0 N B:VAL489 4.4 14.7 1.0 O B:HOH2509 4.4 12.2 1.0 CG B:GLU52 4.5 14.0 1.0 HA B:GLN487 4.5 19.2 1.0 HG1 B:THR348 4.5 23.9 1.0 CD B:GLU329 4.6 17.9 1.0 HZ1 B:LYS365 4.6 22.8 1.0 HG3 B:GLU52 4.6 16.8 1.0 HG2 B:GLU52 4.7 16.8 1.0 CD B:LYS365 4.7 19.7 1.0 HZ2 B:LYS365 4.7 22.8 1.0 CA B:VAL489 4.7 15.5 1.0 HE3 B:LYS365 4.7 23.4 1.0 C B:GLN487 4.8 16.6 1.0 CE B:LYS365 4.8 19.5 1.0 HB3 B:LEU488 4.8 18.4 1.0 HG21 B:VAL490 4.9 23.4 1.0 HA B:LEU488 4.9 13.7 1.0 HD12 B:LEU488 5.0 25.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg binding site number 2 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:17.3 occ:1.00 O D:LEU488 2.0 17.5 1.0 O D:HOH2043 2.1 16.4 1.0 O D:HOH2300 2.1 17.4 1.0 O D:HOH2299 2.1 19.5 1.0 OE2 D:GLU52 2.2 17.8 1.0 NE2 D:HIS542 2.2 13.4 1.0 CE1 D:HIS542 3.0 17.1 1.0 HZ3 D:LYS365 3.1 34.5 1.0 HE1 D:HIS542 3.1 20.6 1.0 CD D:GLU52 3.1 17.4 1.0 C D:LEU488 3.2 14.7 1.0 CD2 D:HIS542 3.3 12.9 1.0 H D:LEU488 3.4 26.2 1.0 OE1 D:GLU52 3.5 22.2 1.0 HD2 D:HIS542 3.5 15.5 1.0 HB2 D:LEU488 3.7 21.4 1.0 N D:LEU488 3.8 21.8 1.0 HD2 D:LYS365 3.9 20.4 1.0 NZ D:LYS365 3.9 23.0 1.0 CA D:LEU488 4.0 19.1 1.0 HA D:VAL489 4.0 23.4 1.0 OE1 D:GLN487 4.1 31.3 1.0 OE2 D:GLU329 4.1 22.5 1.0 HE3 D:LYS365 4.1 24.1 1.0 OE1 D:GLU329 4.2 22.1 1.0 ND1 D:HIS542 4.2 15.9 1.0 HG23 D:VAL489 4.2 38.7 1.0 HZ2 D:LYS365 4.2 34.5 1.0 N D:VAL489 4.3 17.3 1.0 O D:HOH2412 4.3 18.4 1.0 CB D:LEU488 4.3 17.9 1.0 O D:HOH2413 4.3 14.5 1.0 CG D:HIS542 4.4 14.1 1.0 CE D:LYS365 4.4 20.1 1.0 HB3 D:GLN487 4.4 27.7 1.0 CG D:GLU52 4.5 15.2 1.0 HZ1 D:LYS365 4.5 34.5 1.0 HG1 D:THR348 4.5 41.3 1.0 CD D:GLU329 4.6 22.7 1.0 HA D:GLN487 4.6 28.4 1.0 CD D:LYS365 4.6 17.0 1.0 HG3 D:GLU52 4.6 18.2 1.0 HG2 D:GLU52 4.7 18.2 1.0 CA D:VAL489 4.7 19.5 1.0 C D:GLN487 4.7 23.6 1.0 HB3 D:LEU488 4.7 21.4 1.0 HG21 D:VAL490 4.8 29.6 1.0 HA D:LEU488 4.9 23.0 1.0 HG21 D:VAL489 4.9 38.7 1.0 CG2 D:VAL489 5.0 25.8 1.0 HD1 D:HIS542 5.0 19.1 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