Atomistry » Magnesium » PDB 5a9f-5avr » 5adu
Atomistry »
  Magnesium »
    PDB 5a9f-5avr »
      5adu »

Magnesium in PDB 5adu: The Mechanism of Hydrogen Activation By Nife-Hydrogenases

Enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases

All present enzymatic activity of The Mechanism of Hydrogen Activation By Nife-Hydrogenases:
1.12.99.6;

Protein crystallography data

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5adu was solved by R.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.V.Phillips, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.78 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.855, 98.979, 185.207, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.2

Other elements in 5adu:

The structure of The Mechanism of Hydrogen Activation By Nife-Hydrogenases also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Iron (Fe) 26 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases (pdb code 5adu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases, PDB code: 5adu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5adu

Go back to Magnesium Binding Sites List in 5adu
Magnesium binding site 1 out of 2 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg603

b:4.5
occ:1.00
O L:HOH2051 2.1 6.5 1.0
O L:HOH2292 2.1 6.1 1.0
O L:HOH2050 2.1 6.2 1.0
O L:CYS528 2.2 5.7 1.0
OE2 L:GLU57 2.2 5.7 1.0
NE2 L:HIS582 2.2 5.3 1.0
CD L:GLU57 3.2 5.8 1.0
CE1 L:HIS582 3.2 5.3 1.0
CD2 L:HIS582 3.3 5.4 1.0
C L:CYS528 3.3 5.3 1.0
OE1 L:GLU57 3.5 5.9 1.0
N L:CYS528 3.8 5.2 1.0
CA L:CYS528 4.1 5.5 1.0
OE2 L:GLU347 4.1 7.7 1.0
OE1 L:GLN527 4.2 8.8 1.0
OE1 L:GLU347 4.2 7.7 1.0
NZ L:LYS399 4.3 6.4 1.0
O L:HOH2331 4.3 5.9 1.0
ND1 L:HIS582 4.3 5.7 1.0
O L:HOH2299 4.3 6.4 1.0
CB L:CYS528 4.4 6.1 1.0
CG L:HIS582 4.4 5.6 1.0
N L:VAL529 4.4 5.4 1.0
CG L:GLU57 4.5 6.0 1.0
CD L:LYS399 4.6 6.7 1.0
CD L:GLU347 4.6 6.8 1.0
CA L:VAL529 4.7 5.4 1.0
CE L:LYS399 4.7 7.1 1.0
C L:GLN527 5.0 5.5 1.0

Magnesium binding site 2 out of 2 in 5adu

Go back to Magnesium Binding Sites List in 5adu
Magnesium binding site 2 out of 2 in the The Mechanism of Hydrogen Activation By Nife-Hydrogenases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Mechanism of Hydrogen Activation By Nife-Hydrogenases within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg603

b:4.4
occ:1.00
O M:HOH2053 2.1 6.5 1.0
O M:HOH2288 2.1 6.1 1.0
O M:HOH2052 2.1 6.0 1.0
O M:CYS528 2.2 5.7 1.0
OE2 M:GLU57 2.2 5.7 1.0
NE2 M:HIS582 2.2 5.6 1.0
CD M:GLU57 3.2 5.6 1.0
CE1 M:HIS582 3.2 5.6 1.0
CD2 M:HIS582 3.3 5.7 1.0
C M:CYS528 3.3 5.7 1.0
OE1 M:GLU57 3.5 6.5 1.0
N M:CYS528 3.8 5.8 1.0
CA M:CYS528 4.0 5.7 1.0
OE2 M:GLU347 4.1 7.1 1.0
OE1 M:GLU347 4.2 7.2 1.0
OE1 M:GLN527 4.3 8.4 1.0
NZ M:LYS399 4.3 6.4 1.0
ND1 M:HIS582 4.3 5.8 1.0
O M:HOH2333 4.3 5.8 1.0
O M:HOH2295 4.3 6.0 1.0
CB M:CYS528 4.4 6.1 1.0
CG M:HIS582 4.4 5.8 1.0
N M:VAL529 4.4 5.7 1.0
CG M:GLU57 4.5 6.2 1.0
CD M:LYS399 4.6 6.5 1.0
CD M:GLU347 4.6 7.0 1.0
CE M:LYS399 4.7 6.4 1.0
CA M:VAL529 4.7 5.7 1.0
C M:GLN527 4.9 5.5 1.0

Reference:

R.M.Evans, E.J.Brooke, S.A.Wehlin, E.Nomerotskaia, F.Sargent, S.B.Carr, S.E.Phillips, F.A.Armstrong. Mechanism of Hydrogen Activation By [Nife] Hydrogenases. Nat. Chem. Biol. V. 12 46 2016.
ISSN: ESSN 1552-4469
PubMed: 26619250
DOI: 10.1038/NCHEMBIO.1976
Page generated: Mon Dec 14 20:00:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy