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Magnesium in PDB 4ue2: Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

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

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

Protein crystallography data

The structure of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue2 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) 19.91 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.090, 99.650, 184.170, 90.00, 91.16, 90.00
R / Rfree (%) 16.381 / 19.135

Other elements in 4ue2:

The structure of Structure of Air-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 Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4ue2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ue2

Go back to Magnesium Binding Sites List in 4ue2
Magnesium binding site 1 out of 4 in the Structure of Air-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 Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1553

b:12.2
occ:1.00
 O Q:HOH2289 2.0 11.7 1.0
O Q:HOH2043 2.1 12.4 1.0
O Q:HOH2044 2.1 11.3 1.0
O Q:LEU495 2.1 12.2 1.0
OE2 Q:GLU53 2.1 12.8 1.0
NE2 Q:HIS549 2.2 12.4 1.0
CE1 Q:HIS549 3.1 12.0 1.0
CD Q:GLU53 3.1 13.4 1.0
C Q:LEU495 3.3 12.4 1.0
CD2 Q:HIS549 3.3 11.5 1.0
OE1 Q:GLU53 3.4 13.3 1.0
N Q:LEU495 3.7 12.8 1.0
CA Q:LEU495 3.9 13.1 1.0
OE1 Q:GLN494 4.0 11.9 1.0
OE1 Q:GLU334 4.1 12.6 1.0
OE2 Q:GLU334 4.1 11.6 1.0
CB Q:LEU495 4.2 13.5 1.0
O Q:HOH2323 4.3 14.3 1.0
NZ Q:LYS372 4.3 13.7 1.0
ND1 Q:HIS549 4.3 11.3 1.0
O Q:HOH2295 4.3 11.7 1.0
N Q:VAL496 4.4 11.8 1.0
CG Q:GLU53 4.4 13.0 1.0
CG Q:HIS549 4.4 11.7 1.0
CD Q:LYS372 4.6 13.0 1.0
CD Q:GLU334 4.6 12.5 1.0
CE Q:LYS372 4.7 13.3 1.0
CA Q:VAL496 4.7 11.5 1.0
C Q:GLN494 4.7 12.7 1.0

Magnesium binding site 2 out of 4 in 4ue2

Go back to Magnesium Binding Sites List in 4ue2
Magnesium binding site 2 out of 4 in the Structure of Air-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 Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1553

b:16.6
occ:1.00
 O R:HOH2044 2.0 15.9 1.0
O R:HOH2045 2.0 15.3 1.0
O R:HOH2266 2.0 14.7 1.0
O R:LEU495 2.1 16.1 1.0
OE2 R:GLU53 2.1 16.6 1.0
NE2 R:HIS549 2.2 15.8 1.0
CE1 R:HIS549 3.0 14.9 1.0
CD R:GLU53 3.1 17.1 1.0
C R:LEU495 3.2 15.6 1.0
CD2 R:HIS549 3.3 15.6 1.0
OE1 R:GLU53 3.4 16.2 1.0
N R:LEU495 3.7 16.1 1.0
CA R:LEU495 3.9 15.9 1.0
OE1 R:GLN494 4.1 17.7 1.0
OE2 R:GLU334 4.1 14.1 1.0
CB R:LEU495 4.2 16.3 1.0
OE1 R:GLU334 4.2 15.3 1.0
ND1 R:HIS549 4.2 14.8 1.0
NZ R:LYS372 4.3 15.1 1.0
N R:VAL496 4.3 14.7 1.0
O R:HOH2305 4.3 16.6 1.0
O R:HOH2275 4.3 18.8 1.0
CG R:HIS549 4.4 14.9 1.0
CG R:GLU53 4.4 16.4 1.0
CD R:LYS372 4.5 14.7 1.0
CD R:GLU334 4.6 15.2 1.0
CA R:VAL496 4.7 14.2 1.0
C R:GLN494 4.7 16.6 1.0
CE R:LYS372 4.7 15.2 1.0
CA R:GLN494 5.0 17.0 1.0

Magnesium binding site 3 out of 4 in 4ue2

Go back to Magnesium Binding Sites List in 4ue2
Magnesium binding site 3 out of 4 in the Structure of Air-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 Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1560

b:46.0
occ:1.00
 O R:HOH2158 2.2 15.4 1.0
O B:HOH2075 2.4 26.3 1.0
OD1 R:ASN181 2.5 16.8 1.0
CG R:ASN181 3.6 16.9 1.0
N R:ASN181 3.9 16.5 1.0
O B:HOH2022 4.0 37.9 1.0
CA R:ASN181 4.0 16.8 1.0
CB R:ASN181 4.4 16.4 1.0
CD1 R:LEU185 4.6 16.5 1.0
ND2 R:ASN181 4.6 16.3 1.0
O2 R:GOL1562 4.6 24.4 1.0
OE1 B:GLN62 4.8 41.1 1.0
CG2 R:THR180 4.8 17.6 1.0
NE2 B:GLN62 4.9 37.3 1.0

Magnesium binding site 4 out of 4 in 4ue2

Go back to Magnesium Binding Sites List in 4ue2
Magnesium binding site 4 out of 4 in the Structure of Air-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 4 of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg1553

b:18.8
occ:1.00
 O S:HOH2032 2.0 18.8 1.0
O S:HOH2031 2.0 18.3 1.0
O S:HOH2206 2.0 19.3 1.0
OE2 S:GLU53 2.1 17.1 1.0
O S:LEU495 2.1 19.1 1.0
NE2 S:HIS549 2.1 17.2 1.0
CE1 S:HIS549 3.0 16.7 1.0
CD S:GLU53 3.1 17.2 1.0
CD2 S:HIS549 3.2 16.6 1.0
C S:LEU495 3.3 19.4 1.0
OE1 S:GLU53 3.4 16.6 1.0
N S:LEU495 3.7 19.2 1.0
CA S:LEU495 4.0 18.9 1.0
OE2 S:GLU334 4.1 20.9 1.0
OE1 S:GLN494 4.1 20.3 1.0
OE1 S:GLU334 4.1 20.7 1.0
ND1 S:HIS549 4.2 16.6 1.0
NZ S:LYS372 4.2 21.3 1.0
CB S:LEU495 4.2 19.6 1.0
O S:HOH2213 4.3 22.8 1.0
O S:HOH2239 4.3 19.5 1.0
CG S:HIS549 4.3 16.3 1.0
N S:VAL496 4.4 18.6 1.0
CG S:GLU53 4.4 16.6 1.0
CD S:GLU334 4.5 21.9 1.0
CD S:LYS372 4.6 20.7 1.0
CE S:LYS372 4.7 20.8 1.0
CA S:VAL496 4.7 18.8 1.0
C S:GLN494 4.8 19.8 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: Tue Aug 20 04:38:54 2024

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