Atomistry » Magnesium » PDB 6g6z-6gfu » 6g7r
Atomistry »
  Magnesium »
    PDB 6g6z-6gfu »
      6g7r »

Magnesium in PDB 6g7r: Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8

Enzymatic activity of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8

All present enzymatic activity of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8:
1.12.99.6;

Protein crystallography data

The structure of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8, PDB code: 6g7r 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) 67.89 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.068, 97.814, 183.210, 90.00, 90.00, 90.00
R / Rfree (%) 11.1 / 13.3

Other elements in 6g7r:

The structure of Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 24 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8 (pdb code 6g7r). 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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8, PDB code: 6g7r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6g7r

Go back to Magnesium Binding Sites List in 6g7r
Magnesium binding site 1 out of 2 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8


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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:6.4
occ:1.00
HE2 L:HIS582 1.3 8.0 0.0
O L:HOH737 2.1 9.4 1.0
O L:HOH734 2.1 9.3 1.0
O L:CYS528 2.1 8.4 1.0
O L:HOH733 2.1 8.8 1.0
OE1 L:GLU57 2.1 8.4 1.0
NE2 L:HIS582 2.2 8.1 1.0
H L:CYS528 3.1 7.9 1.0
CD L:GLU57 3.1 8.5 1.0
CE1 L:HIS582 3.1 7.8 1.0
CD2 L:HIS582 3.2 8.1 1.0
HE1 L:HIS582 3.3 8.0 1.0
C L:CYS528 3.3 8.0 1.0
HZ1 L:LYS399 3.4 9.7 1.0
HD2 L:HIS582 3.4 8.0 1.0
OE2 L:GLU57 3.4 8.8 1.0
HB2 L:CYS528 3.7 9.3 1.0
HD2 L:LYS399 3.7 10.1 1.0
N L:CYS528 3.8 7.7 1.0
HA L:VAL529 4.0 8.2 1.0
CA L:CYS528 4.0 8.2 1.0
OE2 L:GLU347 4.1 11.0 1.0
OE1 L:GLN527 4.2 12.5 1.0
OE1 L:GLU347 4.2 11.1 1.0
NZ L:LYS399 4.2 9.7 1.0
O L:HOH1013 4.3 8.8 1.0
ND1 L:HIS582 4.3 9.1 1.0
HG21 L:VAL529 4.3 9.5 1.0
O L:HOH828 4.3 8.6 1.0
CB L:CYS528 4.3 9.2 1.0
CG L:HIS582 4.3 7.7 1.0
N L:VAL529 4.4 8.0 1.0
CG L:GLU57 4.4 9.4 1.0
HE3 L:LYS399 4.6 10.1 1.0
CD L:LYS399 4.6 9.8 1.0
CD L:GLU347 4.6 10.1 1.0
HG2 L:GLU57 4.6 9.3 1.0
HG1 L:THR370 4.6 10.1 0.0
HA L:GLN527 4.7 8.2 1.0
CA L:VAL529 4.7 8.0 1.0
HG3 L:GLU57 4.7 9.4 1.0
HZ3 L:LYS399 4.7 9.8 1.0
CE L:LYS399 4.7 9.9 1.0
HZ2 L:LYS399 4.7 9.9 1.0
HB3 L:GLN527 4.7 8.7 1.0
HG22 L:THR533 4.9 8.9 1.0
C L:GLN527 4.9 8.5 1.0
HB3 L:CYS528 4.9 9.3 1.0
HG1 L:THR533 4.9 8.4 0.0
HA L:CYS528 4.9 8.2 1.0
HG3 L:LYS399 4.9 9.6 1.0
HG23 L:VAL530 5.0 10.5 1.0

Magnesium binding site 2 out of 2 in 6g7r

Go back to Magnesium Binding Sites List in 6g7r
Magnesium binding site 2 out of 2 in the Structure of Fully Reduced Variant E28Q of E. Coli Hydrogenase-1 at pH 8


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 Variant E28Q of E. Coli Hydrogenase-1 at pH 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg602

b:6.5
occ:1.00
HE2 M:HIS582 1.3 8.3 0.0
O M:HOH745 2.0 10.0 1.0
O M:HOH737 2.1 9.3 1.0
O M:CYS528 2.1 8.8 1.0
O M:HOH736 2.1 8.7 1.0
OE1 M:GLU57 2.2 8.4 1.0
NE2 M:HIS582 2.2 8.3 1.0
H M:CYS528 3.1 8.4 1.0
CE1 M:HIS582 3.1 7.7 1.0
CD M:GLU57 3.1 8.5 1.0
CD2 M:HIS582 3.2 8.8 1.0
HE1 M:HIS582 3.2 7.8 1.0
C M:CYS528 3.3 7.8 1.0
HZ1 M:LYS399 3.4 9.5 1.0
HD2 M:HIS582 3.4 8.6 1.0
OE2 M:GLU57 3.4 9.0 1.0
HB2 M:CYS528 3.6 9.1 1.0
HD2 M:LYS399 3.7 9.3 1.0
N M:CYS528 3.8 8.7 1.0
HA M:VAL529 4.0 8.3 1.0
CA M:CYS528 4.0 8.3 1.0
OE2 M:GLU347 4.1 10.5 1.0
OE1 M:GLU347 4.2 10.6 1.0
OE1 M:GLN527 4.2 11.9 1.0
HG21 M:VAL529 4.2 9.3 1.0
O M:HOH1034 4.3 8.5 1.0
NZ M:LYS399 4.3 9.6 1.0
O M:HOH812 4.3 8.6 1.0
ND1 M:HIS582 4.3 8.5 1.0
CB M:CYS528 4.3 9.0 1.0
CG M:HIS582 4.4 8.0 1.0
N M:VAL529 4.4 8.1 1.0
CG M:GLU57 4.5 8.9 1.0
HE3 M:LYS399 4.5 9.1 1.0
CD M:GLU347 4.6 10.3 1.0
CD M:LYS399 4.6 9.2 1.0
HG1 M:THR370 4.6 10.0 0.0
HG2 M:GLU57 4.6 9.0 1.0
CA M:VAL529 4.7 8.2 1.0
HA M:GLN527 4.7 8.4 1.0
CE M:LYS399 4.7 8.8 1.0
HG3 M:GLU57 4.7 9.2 1.0
HZ2 M:LYS399 4.7 9.5 1.0
HB3 M:GLN527 4.7 9.1 1.0
HZ3 M:LYS399 4.7 9.6 1.0
HB3 M:CYS528 4.8 8.8 1.0
C M:GLN527 4.9 8.6 1.0
HG22 M:THR533 4.9 8.2 1.0
HG23 M:VAL530 4.9 9.6 1.0
HA M:CYS528 4.9 8.5 1.0
HG1 M:THR533 4.9 8.3 0.0
HG3 M:LYS399 5.0 9.3 1.0

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 01:01:50 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy