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Magnesium in PDB 4uew: Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

Enzymatic activity of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

Protein crystallography data

The structure of Structure of H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4uew 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) 21.98 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.770, 100.400, 183.430, 90.00, 91.55, 90.00
R / Rfree (%) 19.475 / 23.499

Other elements in 4uew:

The structure of Structure of H2-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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4uew). 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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4uew:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4uew

Go back to Magnesium Binding Sites List in 4uew
Magnesium binding site 1 out of 3 in the Structure of H2-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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1553

b:9.6
occ:1.00
O Q:HOH2047 2.0 10.1 1.0
O Q:HOH2283 2.0 9.7 1.0
O Q:HOH2046 2.1 9.8 1.0
OE2 Q:GLU53 2.1 9.8 1.0
O Q:LEU495 2.2 9.9 1.0
NE2 Q:HIS549 2.2 9.2 1.0
CD Q:GLU53 3.0 10.2 1.0
CE1 Q:HIS549 3.1 9.0 1.0
CD2 Q:HIS549 3.3 9.0 1.0
C Q:LEU495 3.3 10.0 1.0
OE1 Q:GLU53 3.4 10.5 1.0
N Q:LEU495 3.8 10.1 1.0
CA Q:LEU495 4.0 9.9 1.0
OE2 Q:GLU334 4.1 12.2 1.0
OE1 Q:GLN494 4.1 11.1 1.0
OE1 Q:GLU334 4.2 12.5 1.0
O Q:HOH2317 4.2 10.1 1.0
NZ Q:LYS372 4.2 11.6 1.0
ND1 Q:HIS549 4.3 8.9 1.0
CB Q:LEU495 4.3 9.5 1.0
CG Q:GLU53 4.4 10.2 1.0
CG Q:HIS549 4.4 8.9 1.0
N Q:VAL496 4.4 10.1 1.0
O Q:HOH2288 4.5 15.2 1.0
CD Q:LYS372 4.5 11.2 1.0
CD Q:GLU334 4.6 12.6 1.0
CE Q:LYS372 4.7 11.5 1.0
C Q:GLN494 4.8 10.4 1.0
CA Q:VAL496 4.8 10.3 1.0
CA Q:GLN494 5.0 10.8 1.0

Magnesium binding site 2 out of 3 in 4uew

Go back to Magnesium Binding Sites List in 4uew
Magnesium binding site 2 out of 3 in the Structure of H2-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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1553

b:24.1
occ:1.00
O R:HOH2049 2.0 23.9 1.0
O R:HOH2050 2.0 25.2 1.0
O R:HOH2240 2.0 23.2 1.0
OE2 R:GLU53 2.1 25.2 1.0
O R:LEU495 2.1 24.0 1.0
NE2 R:HIS549 2.3 23.2 1.0
CE1 R:HIS549 3.1 22.6 1.0
CD R:GLU53 3.1 25.6 1.0
C R:LEU495 3.3 24.2 1.0
OE1 R:GLU53 3.4 25.6 1.0
CD2 R:HIS549 3.4 23.4 1.0
N R:LEU495 3.8 26.1 1.0
OE2 R:GLU334 4.0 22.2 1.0
OE1 R:GLN494 4.0 27.1 1.0
CA R:LEU495 4.0 24.9 1.0
ND1 R:HIS549 4.3 22.2 1.0
O R:HOH2278 4.3 21.6 1.0
O R:HOH2249 4.3 19.4 1.0
NZ R:LYS372 4.3 24.0 1.0
OE1 R:GLU334 4.3 23.9 1.0
CB R:LEU495 4.3 25.1 1.0
N R:VAL496 4.4 23.3 1.0
CD R:LYS372 4.4 22.6 1.0
CG R:HIS549 4.4 22.8 1.0
CG R:GLU53 4.5 26.2 1.0
CD R:GLU334 4.6 23.1 1.0
CA R:VAL496 4.7 22.4 1.0
C R:GLN494 4.7 27.1 1.0
CE R:LYS372 4.7 23.4 1.0
CA R:GLN494 5.0 27.7 1.0

Magnesium binding site 3 out of 3 in 4uew

Go back to Magnesium Binding Sites List in 4uew
Magnesium binding site 3 out of 3 in the Structure of H2-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 H2-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1553

b:34.5
occ:1.00
O S:HOH2021 2.0 35.1 1.0
O S:HOH2166 2.0 35.3 1.0
O S:HOH2022 2.0 36.3 1.0
OE2 S:GLU53 2.1 33.9 1.0
O S:LEU495 2.1 33.8 1.0
NE2 S:HIS549 2.2 33.4 1.0
CE1 S:HIS549 3.1 33.3 1.0
CD S:GLU53 3.1 33.7 1.0
C S:LEU495 3.3 32.7 1.0
CD2 S:HIS549 3.3 32.9 1.0
OE1 S:GLU53 3.4 34.2 1.0
N S:LEU495 3.7 31.9 1.0
OE1 S:GLN494 4.0 34.8 1.0
CA S:LEU495 4.0 31.4 1.0
OE2 S:GLU334 4.2 40.9 1.0
NZ S:LYS372 4.2 39.9 1.0
ND1 S:HIS549 4.2 32.3 1.0
O S:HOH2185 4.2 31.5 1.0
OE1 S:GLU334 4.3 41.6 1.0
CB S:LEU495 4.3 30.1 1.0
O S:HOH2171 4.3 44.8 1.0
CD S:LYS372 4.4 40.0 1.0
N S:VAL496 4.4 32.8 1.0
CG S:HIS549 4.4 32.1 1.0
CG S:GLU53 4.4 32.5 1.0
CE S:LYS372 4.6 40.3 1.0
CD S:GLU334 4.7 42.1 1.0
CA S:VAL496 4.7 33.6 1.0
C S:GLN494 4.7 32.3 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 19:37:06 2020

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