Magnesium in PDB 4ucq: Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

The structure of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucq was solved by A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.Delacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.800, 99.900, 183.300, 90.00, 91.90, 90.00
R / Rfree (%)	19.777 / 24.133

The structure of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Nickel	(Ni)	3 atoms
Iron	(Fe)	36 atoms

The binding sites of Magnesium atom in the Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase (pdb code 4ucq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase, PDB code: 4ucq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg1553 b:39.4 occ:1.00 O Q:HOH2014 2.0 41.1 1.0 O Q:HOH2065 2.0 38.9 1.0 O Q:HOH2013 2.1 38.3 1.0 O Q:LEU495 2.1 38.8 1.0 OE2 Q:GLU53 2.1 39.7 1.0 NE2 Q:HIS549 2.2 37.7 1.0 CD Q:GLU53 3.0 39.7 1.0 CE1 Q:HIS549 3.1 37.8 1.0 C Q:LEU495 3.2 39.6 1.0 CD2 Q:HIS549 3.2 36.8 1.0 OE1 Q:GLU53 3.4 39.2 1.0 N Q:LEU495 3.7 40.0 1.0 CA Q:LEU495 3.9 39.4 1.0 OE1 Q:GLN494 3.9 44.2 1.0 OE2 Q:GLU334 4.1 39.4 1.0 CB Q:LEU495 4.2 37.7 1.0 NZ Q:LYS372 4.2 40.0 1.0 OE1 Q:GLU334 4.2 40.1 1.0 ND1 Q:HIS549 4.3 36.5 1.0 N Q:VAL496 4.3 40.0 1.0 CG Q:HIS549 4.3 35.3 1.0 O Q:HOH2079 4.4 35.5 1.0 CG Q:GLU53 4.4 39.1 1.0 CD Q:LYS372 4.5 39.3 1.0 O Q:HOH2069 4.5 36.6 1.0 CD Q:GLU334 4.6 39.7 1.0 C Q:GLN494 4.6 41.3 1.0 CA Q:VAL496 4.7 39.4 1.0 CE Q:LYS372 4.7 39.2 1.0 CA Q:GLN494 4.9 42.1 1.0 CG2 Q:VAL496 5.0 41.0 1.0 CB Q:GLN494 5.0 43.6 1.0

Magnesium binding site 2 out of 3 in the Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1553 b:38.2 occ:1.00 O R:HOH2014 2.0 41.8 1.0 O R:HOH2061 2.1 38.9 1.0 O R:LEU495 2.1 37.2 1.0 OE2 R:GLU53 2.1 40.0 1.0 O R:HOH2013 2.1 41.4 1.0 NE2 R:HIS549 2.2 35.4 1.0 CE1 R:HIS549 3.1 34.0 1.0 CD R:GLU53 3.1 42.0 1.0 C R:LEU495 3.2 37.0 1.0 CD2 R:HIS549 3.3 35.0 1.0 OE1 R:GLU53 3.4 43.4 1.0 N R:LEU495 3.7 39.9 1.0 CA R:LEU495 3.9 36.8 1.0 OE1 R:GLN494 3.9 53.1 1.0 OE2 R:GLU334 4.0 45.2 1.0 O R:HOH2073 4.1 39.1 1.0 O R:HOH2065 4.2 38.5 1.0 CB R:LEU495 4.2 34.1 1.0 OE1 R:GLU334 4.2 47.3 1.0 ND1 R:HIS549 4.2 32.8 1.0 NZ R:LYS372 4.3 51.7 1.0 N R:VAL496 4.3 36.2 1.0 CG R:HIS549 4.4 33.3 1.0 CG R:GLU53 4.4 40.2 1.0 CD R:GLU334 4.6 47.2 1.0 CD R:LYS372 4.6 50.3 1.0 C R:GLN494 4.7 42.8 1.0 CE R:LYS372 4.7 51.3 1.0 CA R:VAL496 4.7 36.3 1.0 CA R:GLN494 5.0 45.3 1.0

Magnesium binding site 3 out of 3 in the Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the T18D Small Subunit Mutant of D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg1553 b:47.3 occ:1.00 O S:HOH2012 2.0 47.4 1.0 O S:HOH2013 2.0 48.9 1.0 O S:HOH2054 2.1 45.6 1.0 O S:LEU495 2.1 43.4 1.0 OE2 S:GLU53 2.1 49.4 1.0 NE2 S:HIS549 2.2 45.7 1.0 CE1 S:HIS549 3.1 44.8 1.0 CD S:GLU53 3.1 49.8 1.0 C S:LEU495 3.2 43.4 1.0 CD2 S:HIS549 3.3 44.9 1.0 OE1 S:GLU53 3.4 50.0 1.0 N S:LEU495 3.7 46.0 1.0 CA S:LEU495 3.9 43.8 1.0 OE2 S:GLU334 4.1 50.8 1.0 OE1 S:GLN494 4.1 52.2 1.0 O S:HOH2057 4.2 52.9 1.0 O S:HOH2060 4.2 47.6 1.0 ND1 S:HIS549 4.2 43.4 1.0 CB S:LEU495 4.2 42.9 1.0 OE1 S:GLU334 4.2 50.4 1.0 NZ S:LYS372 4.3 49.5 1.0 N S:VAL496 4.3 43.6 1.0 CG S:HIS549 4.4 43.6 1.0 CG S:GLU53 4.5 49.3 1.0 CD S:LYS372 4.5 48.6 1.0 CE S:LYS372 4.5 49.1 1.0 CD S:GLU334 4.6 50.3 1.0 CA S:VAL496 4.6 43.7 1.0 C S:GLN494 4.7 47.6 1.0 CG2 S:VAL496 4.9 47.0 1.0 CA S:GLN494 5.0 50.5 1.0

A.Abou-Hamdan, P.Ceccaldi, H.Lebrette, O.Guttierez-Sanz, P.Richaud, L.Cournac, B.Guigliarelli, A.L.De Lacey, C.Leger, A.Volbeda, B.Burlat, S.Dementin. A Threonine Stabilizes the Nic and Nir Catalytic Intermediates of [Nife]-Hydrogenase During Catalysis in Nife-Hydrogenase J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.630491