Atomistry » Magnesium » PDB 4u9h-4ukd » 4ue6
Atomistry »
  Magnesium »
    PDB 4u9h-4ukd »
      4ue6 »

Magnesium in PDB 4ue6: Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue6 was solved by A.Volbeda, L.Martin, P.-P.Liebgott, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.90 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.280, 99.550, 184.020, 90.00, 91.16, 90.00
R / Rfree (%) 15.066 / 18.141

Other elements in 4ue6:

The structure of Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4ue6). 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 Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ue6

Go back to Magnesium Binding Sites List in 4ue6
Magnesium binding site 1 out of 3 in the Structure of Methylene Blue-Treated Anaerobically Purified 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 Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1553

b:24.8
occ:1.00
O Q:HOH2168 2.0 22.8 1.0
O Q:LEU495 2.0 23.2 1.0
O Q:HOH2030 2.1 23.4 1.0
O Q:HOH2029 2.1 22.8 1.0
OE2 Q:GLU53 2.2 25.6 1.0
NE2 Q:HIS549 2.2 20.0 1.0
CE1 Q:HIS549 3.1 18.9 1.0
CD Q:GLU53 3.1 25.2 1.0
C Q:LEU495 3.2 22.9 1.0
CD2 Q:HIS549 3.2 19.7 1.0
OE1 Q:GLU53 3.4 24.0 1.0
N Q:LEU495 3.6 22.1 1.0
CA Q:LEU495 3.9 23.5 1.0
OE2 Q:GLU334 4.0 29.5 1.0
OE1 Q:GLU334 4.0 28.4 1.0
OE1 Q:GLN494 4.1 25.9 1.0
CB Q:LEU495 4.2 22.1 1.0
ND1 Q:HIS549 4.3 18.9 1.0
O Q:HOH2192 4.3 18.0 1.0
N Q:VAL496 4.3 21.6 1.0
O Q:HOH2174 4.3 18.2 1.0
NZ Q:LYS372 4.3 22.6 1.0
CG Q:HIS549 4.4 20.2 1.0
CD Q:GLU334 4.5 28.6 1.0
CG Q:GLU53 4.5 24.0 1.0
CD Q:LYS372 4.5 20.9 1.0
CE Q:LYS372 4.6 22.2 1.0
CA Q:VAL496 4.7 21.2 1.0
C Q:GLN494 4.7 22.4 1.0
CA Q:GLN494 5.0 22.7 1.0

Magnesium binding site 2 out of 3 in 4ue6

Go back to Magnesium Binding Sites List in 4ue6
Magnesium binding site 2 out of 3 in the Structure of Methylene Blue-Treated Anaerobically Purified 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 Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1553

b:31.0
occ:1.00
O R:HOH2035 2.0 29.1 1.0
O R:HOH2034 2.0 27.9 1.0
O R:HOH2144 2.0 26.4 1.0
O R:LEU495 2.1 21.5 1.0
OE2 R:GLU53 2.1 24.2 1.0
NE2 R:HIS549 2.3 21.4 1.0
CD R:GLU53 3.1 25.3 1.0
CE1 R:HIS549 3.2 20.9 1.0
C R:LEU495 3.3 21.1 1.0
CD2 R:HIS549 3.3 21.5 1.0
OE1 R:GLU53 3.4 24.5 1.0
N R:LEU495 3.7 22.4 1.0
CA R:LEU495 3.9 21.8 1.0
OE2 R:GLU334 4.0 25.7 1.0
OE1 R:GLN494 4.1 26.5 1.0
OE1 R:GLU334 4.1 25.5 1.0
CB R:LEU495 4.3 21.4 1.0
O R:HOH2151 4.3 19.1 1.0
ND1 R:HIS549 4.3 21.2 1.0
NZ R:LYS372 4.3 23.3 1.0
N R:VAL496 4.3 20.8 1.0
O R:HOH2171 4.4 16.0 1.0
CG R:HIS549 4.4 21.7 1.0
CG R:GLU53 4.5 25.0 1.0
CD R:LYS372 4.5 22.3 1.0
CD R:GLU334 4.5 25.4 1.0
CE R:LYS372 4.7 23.4 1.0
CA R:VAL496 4.7 21.1 1.0
C R:GLN494 4.7 24.0 1.0
CA R:GLN494 5.0 23.9 1.0

Magnesium binding site 3 out of 3 in 4ue6

Go back to Magnesium Binding Sites List in 4ue6
Magnesium binding site 3 out of 3 in the Structure of Methylene Blue-Treated Anaerobically Purified 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 Methylene Blue-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1553

b:30.8
occ:1.00
O S:HOH2019 2.0 32.5 1.0
O S:HOH2020 2.0 33.4 1.0
O S:HOH2101 2.0 33.6 1.0
OE2 S:GLU53 2.1 26.4 1.0
O S:LEU495 2.1 28.2 1.0
NE2 S:HIS549 2.2 28.2 1.0
CD S:GLU53 3.0 27.0 1.0
CE1 S:HIS549 3.1 28.1 1.0
CD2 S:HIS549 3.2 27.9 1.0
C S:LEU495 3.3 27.6 1.0
OE1 S:GLU53 3.3 26.4 1.0
N S:LEU495 3.7 27.2 1.0
CA S:LEU495 4.0 27.5 1.0
OE2 S:GLU334 4.0 37.1 1.0
OE1 S:GLN494 4.1 29.0 1.0
O S:HOH2106 4.1 28.7 1.0
OE1 S:GLU334 4.1 37.0 1.0
CB S:LEU495 4.2 27.3 1.0
ND1 S:HIS549 4.3 26.5 1.0
O S:HOH2121 4.3 25.1 1.0
NZ S:LYS372 4.3 26.3 1.0
CG S:HIS549 4.3 27.4 1.0
N S:VAL496 4.4 27.9 1.0
CG S:GLU53 4.4 27.9 1.0
CD S:LYS372 4.5 27.3 1.0
CD S:GLU334 4.5 37.1 1.0
CE S:LYS372 4.6 27.0 1.0
C S:GLN494 4.7 26.7 1.0
CA S:VAL496 4.8 27.4 1.0

Reference:

A.Volbeda, L.Martin, P.-P.Liebgott, A.L.De Lacey, J.C.Fontecilla-Camps. [Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H
Page generated: Mon Dec 14 19:37:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy