Magnesium in PDB 6fpw: Structure of Fully Reduced Hydrogenase (Hyd-1)

All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1):
1.12.99.6;

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1), PDB code: 6fpw was solved by S.B.Carr, F.A.Armstrong, R.M.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.46 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.835, 97.729, 182.911, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 14.4

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Iron	(Fe)	24 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Magnesium atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) (pdb code 6fpw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Fully Reduced Hydrogenase (Hyd-1), PDB code: 6fpw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg602 b:9.8 occ:1.00 HE2 L:HIS582 1.3 9.7 0.0 O L:HOH720 2.1 10.5 1.0 O L:HOH710 2.1 12.1 1.0 O L:CYS528 2.1 10.7 1.0 O L:HOH722 2.1 10.4 1.0 OE1 L:GLU57 2.1 10.0 1.0 NE2 L:HIS582 2.2 9.7 1.0 H L:CYS528 3.0 9.9 1.0 CD L:GLU57 3.1 10.6 1.0 CE1 L:HIS582 3.2 9.8 1.0 CD2 L:HIS582 3.2 10.3 1.0 C L:CYS528 3.3 10.4 1.0 HE1 L:HIS582 3.3 9.7 1.0 HZ1 L:LYS399 3.4 13.4 1.0 HD2 L:HIS582 3.4 9.7 1.0 OE2 L:GLU57 3.4 10.8 1.0 HB2 L:CYS528 3.7 11.5 1.0 HD2 L:LYS399 3.8 12.6 1.0 N L:CYS528 3.8 9.7 1.0 HA L:VAL529 4.0 9.9 1.0 CA L:CYS528 4.0 10.8 1.0 OE2 L:GLU347 4.1 13.7 1.0 HG21 L:VAL529 4.1 12.1 1.0 OE1 L:GLU347 4.2 14.8 1.0 OE1 L:GLN527 4.2 15.3 1.0 O L:HOH955 4.3 10.6 1.0 ND1 L:HIS582 4.3 10.1 1.0 NZ L:LYS399 4.3 13.4 1.0 O L:HOH794 4.3 10.7 1.0 CG L:HIS582 4.3 9.8 1.0 CB L:CYS528 4.3 11.4 1.0 N L:VAL529 4.4 10.3 1.0 CG L:GLU57 4.4 11.0 1.0 HE3 L:LYS399 4.4 12.9 1.0 CD L:GLU347 4.5 12.8 1.0 HG2 L:GLU57 4.6 11.3 1.0 CD L:LYS399 4.6 12.5 1.0 HG3 L:GLU57 4.6 10.9 1.0 HG1 L:THR370 4.6 13.2 0.0 CA L:VAL529 4.7 9.7 1.0 HA L:GLN527 4.7 10.3 1.0 CE L:LYS399 4.7 13.0 1.0 HZ2 L:LYS399 4.7 13.2 1.0 HB3 L:GLN527 4.8 11.3 1.0 HZ3 L:LYS399 4.8 12.7 1.0 HG23 L:VAL530 4.9 11.1 1.0 HB3 L:CYS528 4.9 11.7 1.0 C L:GLN527 4.9 10.5 1.0 HG22 L:THR533 4.9 10.9 1.0 HA L:CYS528 4.9 10.5 1.0 HG3 L:LYS399 4.9 11.1 1.0 HG1 L:THR533 4.9 10.7 0.0 CG2 L:VAL529 5.0 12.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Fully Reduced Hydrogenase (Hyd-1) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg602 b:9.6 occ:1.00 HE2 M:HIS582 1.3 10.3 0.0 O M:HOH733 2.1 11.4 1.0 O M:HOH735 2.1 10.8 1.0 O M:CYS528 2.1 11.0 1.0 OE1 M:GLU57 2.1 10.0 1.0 O M:HOH715 2.1 11.3 1.0 NE2 M:HIS582 2.2 10.2 1.0 H M:CYS528 3.0 9.9 1.0 CD M:GLU57 3.1 11.0 1.0 CE1 M:HIS582 3.1 10.5 1.0 CD2 M:HIS582 3.2 10.6 1.0 HE1 M:HIS582 3.3 10.0 1.0 C M:CYS528 3.3 10.0 1.0 HZ1 M:LYS399 3.3 13.0 1.0 OE2 M:GLU57 3.4 11.2 1.0 HD2 M:HIS582 3.4 10.5 1.0 HB2 M:CYS528 3.7 11.7 1.0 HD2 M:LYS399 3.7 11.6 1.0 N M:CYS528 3.8 9.9 1.0 CA M:CYS528 4.0 10.9 1.0 HA M:VAL529 4.0 9.9 1.0 OE2 M:GLU347 4.1 14.7 1.0 HG21 M:VAL529 4.1 11.6 1.0 OE1 M:GLU347 4.2 14.2 1.0 OE1 M:GLN527 4.2 15.5 1.0 NZ M:LYS399 4.3 13.3 1.0 O M:HOH959 4.3 10.5 1.0 ND1 M:HIS582 4.3 10.1 1.0 O M:HOH780 4.3 10.5 1.0 CB M:CYS528 4.3 11.7 1.0 CG M:HIS582 4.4 11.5 1.0 N M:VAL529 4.4 10.1 1.0 HE3 M:LYS399 4.4 12.1 1.0 CG M:GLU57 4.5 11.3 1.0 CD M:GLU347 4.5 13.1 1.0 CD M:LYS399 4.6 11.6 1.0 HG2 M:GLU57 4.6 11.3 1.0 HG1 M:THR370 4.6 12.4 0.0 CE M:LYS399 4.6 12.1 1.0 HA M:GLN527 4.6 10.3 1.0 HG3 M:GLU57 4.7 11.6 1.0 CA M:VAL529 4.7 9.9 1.0 HZ2 M:LYS399 4.7 13.1 1.0 HB3 M:GLN527 4.7 10.7 1.0 HZ3 M:LYS399 4.8 13.3 1.0 HG23 M:VAL530 4.8 11.7 1.0 C M:GLN527 4.9 10.9 1.0 HG3 M:LYS399 4.9 10.9 1.0 HB3 M:CYS528 4.9 11.9 1.0 HG22 M:THR533 4.9 11.2 1.0 HA M:CYS528 4.9 10.7 1.0 HG1 M:THR533 5.0 10.2 0.0

R.M.Evans, P.A.Ash, S.E.Beaton, E.J.Brooke, K.A.Vincent, S.B.Carr, F.A.Armstrong. Mechanistic Exploitation of A Self-Repairing, Blocked Proton Transfer Pathway in An O2-Tolerant [Nife]-Hydrogenase. J. Am. Chem. Soc. V. 140 10208 2018.
ISSN: ESSN 1520-5126
PubMed: 30070475
DOI: 10.1021/JACS.8B04798