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Magnesium in PDB 6fpi: Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q

Enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q

All present enzymatic activity of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q:
1.12.99.6;

Protein crystallography data

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q, PDB code: 6fpi 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) 83.51 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.820, 97.730, 183.200, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.7

Other elements in 6fpi:

The structure of Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q (pdb code 6fpi). 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) Variant E28Q, PDB code: 6fpi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6fpi

Go back to Magnesium Binding Sites List in 6fpi
Magnesium binding site 1 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q


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) Variant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg602

b:12.2
occ:1.00
HE2 L:HIS582 1.4 13.6 0.0
O L:HOH721 2.1 16.1 1.0
O L:CYS528 2.1 15.8 1.0
O L:HOH731 2.1 14.5 1.0
OE1 L:GLU57 2.1 14.9 1.0
O L:HOH711 2.1 16.6 1.0
NE2 L:HIS582 2.2 13.8 1.0
H L:CYS528 3.0 15.3 1.0
CD L:GLU57 3.1 15.1 1.0
CE1 L:HIS582 3.2 15.1 1.0
CD2 L:HIS582 3.2 14.9 1.0
C L:CYS528 3.3 14.9 1.0
HE1 L:HIS582 3.3 14.8 1.0
OE2 L:GLU57 3.4 15.9 1.0
HZ1 L:LYS399 3.4 17.2 1.0
HD2 L:HIS582 3.4 14.6 1.0
HB2 L:CYS528 3.6 16.9 1.0
HD2 L:LYS399 3.7 16.1 1.0
N L:CYS528 3.8 14.6 1.0
HA L:VAL529 4.0 15.5 1.0
CA L:CYS528 4.0 16.7 1.0
OE2 L:GLU347 4.0 19.2 1.0
OE1 L:GLU347 4.1 20.2 1.0
HG21 L:VAL529 4.2 16.7 1.0
OE1 L:GLN527 4.2 19.7 1.0
O L:HOH944 4.3 15.0 1.0
ND1 L:HIS582 4.3 15.3 1.0
CB L:CYS528 4.3 16.0 1.0
O L:HOH825 4.3 15.2 1.0
NZ L:LYS399 4.3 17.4 1.0
N L:VAL529 4.4 15.1 1.0
CG L:HIS582 4.4 14.4 1.0
CG L:GLU57 4.4 15.4 1.0
CD L:GLU347 4.5 18.2 1.0
HE3 L:LYS399 4.6 16.8 1.0
HG2 L:GLU57 4.6 15.5 1.0
CD L:LYS399 4.6 16.3 1.0
HG3 L:GLU57 4.6 15.5 1.0
CA L:VAL529 4.6 15.4 1.0
HG1 L:THR370 4.6 17.6 0.0
HA L:GLN527 4.6 15.2 1.0
HB3 L:GLN527 4.7 16.1 1.0
CE L:LYS399 4.7 16.8 1.0
HZ2 L:LYS399 4.8 17.2 1.0
HB3 L:CYS528 4.8 16.9 1.0
HZ3 L:LYS399 4.8 17.2 1.0
HG22 L:THR533 4.9 15.6 1.0
C L:GLN527 4.9 15.8 1.0
HA L:CYS528 4.9 15.8 1.0
HG23 L:VAL530 5.0 17.0 1.0
HG1 L:THR533 5.0 14.5 0.0
HG3 L:LYS399 5.0 15.7 1.0

Magnesium binding site 2 out of 2 in 6fpi

Go back to Magnesium Binding Sites List in 6fpi
Magnesium binding site 2 out of 2 in the Structure of Fully Reduced Hydrogenase (Hyd-1) Variant E28Q


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) Variant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg602

b:11.5
occ:1.00
HE2 M:HIS582 1.4 15.1 0.0
O M:HOH723 2.1 15.0 1.0
O M:CYS528 2.1 15.6 1.0
O M:HOH736 2.1 15.3 1.0
O M:HOH722 2.2 16.2 1.0
OE1 M:GLU57 2.2 14.6 1.0
NE2 M:HIS582 2.2 15.2 1.0
H M:CYS528 3.1 15.8 1.0
CD M:GLU57 3.1 15.6 1.0
CE1 M:HIS582 3.2 15.5 1.0
CD2 M:HIS582 3.2 16.3 1.0
C M:CYS528 3.3 15.4 1.0
HE1 M:HIS582 3.3 15.3 1.0
HZ1 M:LYS399 3.3 17.5 1.0
OE2 M:GLU57 3.4 16.2 1.0
HD2 M:HIS582 3.4 16.0 1.0
HB2 M:CYS528 3.6 17.1 1.0
HD2 M:LYS399 3.8 15.7 1.0
N M:CYS528 3.8 15.1 1.0
CA M:CYS528 4.0 16.9 1.0
HA M:VAL529 4.0 16.0 1.0
OE2 M:GLU347 4.1 18.8 1.0
HG21 M:VAL529 4.1 16.9 1.0
OE1 M:GLU347 4.2 19.6 1.0
OE1 M:GLN527 4.2 20.0 1.0
NZ M:LYS399 4.2 17.9 1.0
O M:HOH966 4.3 14.8 1.0
CB M:CYS528 4.3 16.8 1.0
ND1 M:HIS582 4.3 14.8 1.0
O M:HOH804 4.3 15.4 1.0
HE3 M:LYS399 4.3 16.6 1.0
N M:VAL529 4.3 15.5 1.0
CG M:HIS582 4.4 16.4 1.0
CG M:GLU57 4.5 15.4 1.0
CD M:GLU347 4.6 17.0 1.0
HA M:GLN527 4.6 15.6 1.0
CD M:LYS399 4.6 15.5 1.0
HG1 M:THR370 4.6 17.1 0.0
CE M:LYS399 4.6 16.6 1.0
HB3 M:GLN527 4.6 15.8 1.0
CA M:VAL529 4.6 15.8 1.0
HZ2 M:LYS399 4.6 17.5 1.0
HG2 M:GLU57 4.7 15.4 1.0
HG3 M:GLU57 4.7 15.4 1.0
HB3 M:CYS528 4.8 17.1 1.0
HZ3 M:LYS399 4.8 17.5 1.0
C M:GLN527 4.9 16.1 1.0
HG22 M:THR533 4.9 14.6 1.0
HG3 M:LYS399 4.9 15.5 1.0
HG23 M:VAL530 4.9 18.6 1.0
HA M:CYS528 4.9 16.2 1.0
HG1 M:THR533 5.0 14.3 0.0

Reference:

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
Page generated: Tue Oct 1 00:35:23 2024

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